class QuteMolPropertyManager(PM_Dialog):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = ["Render axes", "Hide axes"]
_bases_display_choices = ["Render bases", "Hide bases"]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__(self, win):
"""
Construct the QuteMolX Property Manager.
@param win: The main window.
@type win: QMainWindow
"""
self.win = win
self.pw = None
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
msg = "Select a QuteMolX rendering style and click the \
<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
# Hide Preview and Restore defaults button for Alpha9.
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON | PM_PREVIEW_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title="DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title="Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(pmGroupBox,
label='Axes: ',
choices=self._axes_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
self.basesCombobox = PM_ComboBox(pmGroupBox,
label='Bases: ',
choices=self._bases_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text="Launch QuteMolX",
iconPath="ui/actions/Properties Manager/QuteMol.png",
spanWidth=True)
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show)
"""
if self.isVisible(): # Fixes bug 2680. --Mark 2008-03-19
return
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
#First exit temporary modes (e.g. Pan mode) if any.
currentCommand = self.win.commandSequencer.currentCommand
if not currentCommand.command_has_its_own_gui:
currentCommand.Done()
self.connect_or_disconnect_signals(isConnect=False)
PM_Dialog.close(self)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.accept()
self.close() # Close the property manager.
# The following reopens the property manager of the mode after
# when the PM of the reference geometry is closed. -- Ninad 20070603
# Note: the value of self.modePropertyManager can be None
# @see: anyMode.propMgr
#
# (Note: once we have a real command sequencer, it will be
# handling this kind of thing itself, and the situation
# in which the currentCommand does not correspond to
# the current PM (as is true here while this separate PM
# is open, since it's not currentCommand.propMgr)
# will be deprecated or impossible. [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.reject()
self.close()
# The following reopens the property manager of the command after
# the PM of the reference geometry editCommand (i.e. Plane) is closed.
# Note: the value of self.modePropertyManager can be None.
# See anyMode.propMgr
# (See similar code in ok_btn_clicked [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton, SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg=''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault=False,
minLines=5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class DnaDisplayStyle_PropertyManager(Command_PropertyManager):
"""
The DnaDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Dna mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit DNA Display Style"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/EditDnaDisplayStyle.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the DNA display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect(self.applyFavoriteButton, SIGNAL("clicked()"),
self.applyFavorite)
change_connect(self.addFavoriteButton, SIGNAL("clicked()"),
self.addFavorite)
change_connect(self.deleteFavoriteButton, SIGNAL("clicked()"),
self.deleteFavorite)
change_connect(self.saveFavoriteButton, SIGNAL("clicked()"),
self.saveFavorite)
change_connect(self.loadFavoriteButton, SIGNAL("clicked()"),
self.loadFavorite)
# Current display settings groupbox.
change_connect(self.dnaRenditionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaRendition)
# Axis options.
change_connect(self.axisShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisShape)
change_connect(self.axisScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleAxisScale)
change_connect(self.axisColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisColor)
change_connect(self.axisEndingStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisEndingStyle)
# Strands options.
change_connect(self.strandsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsShape)
change_connect(self.strandsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrandsScale)
change_connect(self.strandsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsColor)
change_connect(self.strandsArrowsComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsArrows)
# Structs options.
change_connect(self.strutsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsShape)
change_connect(self.strutsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrutsScale)
change_connect(self.strutsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsColor)
# Nucleotides options.
change_connect(self.nucleotidesShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesShape)
change_connect(self.nucleotidesScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleBasesScale)
change_connect(self.nucleotidesColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesColor)
connect_checkbox_with_boolean_pref(
self.dnaStyleBasesDisplayLettersCheckBox,
dnaStyleBasesDisplayLetters_prefs_key)
# Dna Strand labels option.
change_connect(self.standLabelColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaStrandLabelsDisplay)
def show(self):
"""
Shows the Property Manager. Extends superclass method
"""
_superclass.show(self)
#@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
#-- Ninad 2008-10-02
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
# TODO: rename that public attr of GLPane (widely used)
# from displayMode to displayStyle. [bruce 080910 comment]
self.o.setGlobalDisplayStyle(diDNACYLINDER)
# Update all PM widgets, .
# note: It is important to update the widgets by blocking the
# 'signals'. If done in the reverse order, it will generate signals
#when updating the PM widgets (via updateDnaDisplayStyleWidgets()),
#causing unneccessary repaints of the model view.
self.updateDnaDisplayStyleWidgets(blockSignals=True)
def close(self):
"""
Closes the Property Manager. Extends superclass method.
"""
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Favorites")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Current Display Settings")
self._loadGroupBox2(self._pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/DnaDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/DnaDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join(_dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch(file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file) - 4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis("""<b> List of Favorites </b>
<p>
Creates a list of favorite DNA display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
dnaRenditionChoices = [
'3D (default)', '2D with base letters', '2D ball and stick',
'2D ladder'
]
self.dnaRenditionComboBox = \
PM_ComboBox( pmGroupBox,
label = "Rendition:",
choices = dnaRenditionChoices,
setAsDefault = True)
dnaComponentChoices = ['Axis', 'Strands', 'Struts', 'Nucleotides']
self.dnaComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Component:",
choices = dnaComponentChoices,
setAsDefault = True)
self._loadAxisGroupBox()
self._loadStrandsGroupBox()
self._loadStrutsGroupBox()
self._loadNucleotidesGroupBox()
widgetList = [
self.axisGroupBox, self.strandsGroupBox, self.strutsGroupBox,
self.nucleotidesGroupBox
]
self.dnaComponentStackedWidget = \
PM_StackedWidget( pmGroupBox,
self.dnaComponentComboBox,
widgetList )
standLabelColorChoices = [
'Hide', 'Show (in strand color)', 'Black', 'White',
'Custom color...'
]
self.standLabelColorComboBox = \
PM_ComboBox( pmGroupBox,
label = "Strand labels:",
choices = standLabelColorChoices,
setAsDefault = True)
# This disables "Component" widgets if rendition style is 2D.
self.change_dnaRendition(env.prefs[dnaRendition_prefs_key])
def _loadAxisGroupBox(self):
"""
Load the Axis group box.
"""
axisGroupBox = PM_GroupBox(None)
self.axisGroupBox = axisGroupBox
axisShapeChoices = ['None', 'Wide tube', 'Narrow tube']
self.axisShapeComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Shape:",
choices = axisShapeChoices,
setAsDefault = True)
self.axisScaleDoubleSpinBox = \
PM_DoubleSpinBox( axisGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 2.0,
decimals = 2,
singleStep = 0.1 )
axisColorChoices = [
'Same as chunk', 'Base order', 'Base order (discrete)',
'Base type', 'Strand order'
]
self.axisColorComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Color:",
choices = axisColorChoices,
setAsDefault = True)
endingTypeChoices = [
'Flat', 'Taper start', 'Taper end', 'Taper both', 'Spherical'
]
self.axisEndingStyleComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Ending style:",
choices = endingTypeChoices,
setAsDefault = True)
def _loadStrandsGroupBox(self):
"""
Load the Strands group box.
"""
strandsGroupBox = PM_GroupBox(None)
self.strandsGroupBox = strandsGroupBox
strandsShapeChoices = ['None', 'Cylinders', 'Tube']
self.strandsShapeComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Shape:",
choices = strandsShapeChoices,
setAsDefault = True)
self.strandsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strandsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 5.0,
decimals = 2,
singleStep = 0.1 )
strandsColorChoices = ['Same as chunk', 'Base order', 'Strand order']
self.strandsColorComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Color:",
choices = strandsColorChoices,
setAsDefault = True)
strandsArrowsChoices = ['None', '5\'', '3\'', '5\' and 3\'']
self.strandsArrowsComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Arrows:",
choices = strandsArrowsChoices,
setAsDefault = True)
def _loadStrutsGroupBox(self):
"""
Load the Struts group box.
"""
strutsGroupBox = PM_GroupBox(None)
self.strutsGroupBox = strutsGroupBox
strutsShapeChoices = [
'None', 'Base-axis-base cylinders', 'Straight cylinders'
]
self.strutsShapeComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Shape:",
choices = strutsShapeChoices,
setAsDefault = True)
self.strutsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strutsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
strutsColorChoices = [
'Same as strand', 'Base order', 'Strand order', 'Base type'
]
self.strutsColorComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Color:",
choices = strutsColorChoices,
setAsDefault = True)
def _loadNucleotidesGroupBox(self):
"""
Load the Nucleotides group box.
"""
nucleotidesGroupBox = PM_GroupBox(None)
self.nucleotidesGroupBox = nucleotidesGroupBox
nucleotidesShapeChoices = ['None', 'Sugar spheres', 'Base cartoons']
self.nucleotidesShapeComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Shape:",
choices = nucleotidesShapeChoices,
setAsDefault = True)
self.nucleotidesScaleDoubleSpinBox = \
PM_DoubleSpinBox( nucleotidesGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
nucleotidesColorChoices = [
'Same as strand', 'Base order', 'Strand order', 'Base type'
]
self.nucleotidesColorComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Color:",
choices = nucleotidesColorChoices,
setAsDefault = True)
self.dnaStyleBasesDisplayLettersCheckBox = \
PM_CheckBox(nucleotidesGroupBox ,
text = 'Display base letters',
widgetColumn = 1
)
def updateDnaDisplayStyleWidgets(self, blockSignals=False):
"""
Updates all the DNA Display style widgets based on the current pref keys
values.
@param blockSignals: If its set to True, the set* methods of the
the widgets (currently only PM_ Spinboxes and
ComboBoxes) won't emit a signal.
@type blockSignals: bool
@see: self.show() where this method is called.
@see: PM_Spinbox.setValue()
@see: PM_ComboBox.setCurrentIndex()
@note: This should be called each time the PM is displayed (see show()).
"""
self.dnaRenditionComboBox.setCurrentIndex(
env.prefs[dnaRendition_prefs_key], blockSignals=blockSignals)
self.axisShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisShape_prefs_key], blockSignals=blockSignals)
self.axisScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleAxisScale_prefs_key], blockSignals=blockSignals)
self.axisColorComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisColor_prefs_key], blockSignals=blockSignals)
self.axisEndingStyleComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisEndingStyle_prefs_key],
blockSignals=blockSignals)
self.strandsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsShape_prefs_key],
blockSignals=blockSignals)
self.strandsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrandsScale_prefs_key],
blockSignals=blockSignals)
self.strandsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsColor_prefs_key],
blockSignals=blockSignals)
self.strandsArrowsComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsArrows_prefs_key],
blockSignals=blockSignals)
self.strutsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsShape_prefs_key],
blockSignals=blockSignals)
self.strutsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrutsScale_prefs_key],
blockSignals=blockSignals)
self.strutsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsColor_prefs_key],
blockSignals=blockSignals)
self.nucleotidesShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesShape_prefs_key], blockSignals=blockSignals)
self.nucleotidesScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleBasesScale_prefs_key], blockSignals=blockSignals)
self.nucleotidesColorComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesColor_prefs_key], blockSignals=blockSignals)
# DNA Strand label combobox.
if env.prefs[dnaStrandLabelsEnabled_prefs_key]:
_dnaStrandColorItem = env.prefs[
dnaStrandLabelsColorMode_prefs_key] + 1
else:
_dnaStrandColorItem = 0
self.standLabelColorComboBox.setCurrentIndex(_dnaStrandColorItem,
blockSignals=blockSignals)
def change_dnaStrandLabelsDisplay(self, mode):
"""
Changes DNA Strand labels display (and color) mode.
@param mode: The display mode:
- 0 = hide all labels
- 1 = show (same color as chunk)
- 2 = show (black)
- 3 = show (white)
- 4 = show (custom color...)
@type mode: int
"""
if mode == 4:
self.win.userPrefs.change_dnaStrandLabelsColor()
if mode == 0:
#@ Fix this at the same time I (we) remove the DNA display style
# prefs options from the Preferences dialog. --Mark 2008-05-13
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(False)
else:
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(True)
self.win.userPrefs.change_dnaStrandLabelsColorMode(mode - 1)
def applyFavorite(self):
"""
Apply the DNA display style settings stored in the current favorite
(selected in the combobox) to the current DNA display style settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateDnaDisplayStyleWidgets()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current DNA display style
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The DNA display style settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/DnaDisplayStyle/$FAV_NAME.fav).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename(name)
if os.path.exists(fname):
#favorite file already exists!
_ext = ".txt"
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + _ext +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Cancel",
"",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(
name)
indexOfDuplicateItem = self.favoritesComboBox.findText(
name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message(
"Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text
) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile = getFavoritePathFromBasename(currentText)
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
#Check to see if favfilepath exists first
if not os.path.exists(favfilepath):
msg = "%s does not exist" % favfilepath
env.history.message(cmd + msg)
return
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
saveLocation, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir=None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir=None):
"""
[private method]
Set the working directory in the user preferences database.
@param workdir: The fullpath directory to write to the user pref db.
If I{workdir} is None (default), there is no change.
@type workdir: string
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[
workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message(redmsg(msg))
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory = getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self, "Choose a file to load",
directory, formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile = loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName) - 4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Rename",
"&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(
name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
env.history.message(
"Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateDnaDisplayStyleWidgets()
return
def change_dnaRendition(self, rendition):
"""
Sets the DNA rendition to 3D or one of the optional 2D styles.
@param rendition: The rendition mode, where:
- 0 = 3D (default)
- 1 = 2D with base letters
- 2 = 2D ball and stick
- 3 = 2D ladder
@type rendition: int
"""
if rendition == 0:
_enabled_flag = True
else:
_enabled_flag = False
self.dnaComponentComboBox.setEnabled(_enabled_flag)
self.dnaComponentStackedWidget.setEnabled(_enabled_flag)
self.standLabelColorComboBox.setEnabled(_enabled_flag)
env.prefs[dnaRendition_prefs_key] = rendition
self.o.gl_update() # Force redraw
return
def _addWhatsThisText(self):
"""
What's This text for widgets in the DNA Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditDnaDisplayStyle_PropertyManager
ToolTip_EditDnaDisplayStyle_PropertyManager(self)
class TestGraphics_PropertyManager(Command_PropertyManager):
"""
The TestGraphics_PropertyManager class provides a Property Manager
for the Test Graphics command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Test Graphics"
pmName = title
iconPath = None ###k "ui/actions/View/Stereo_View.png" ### FIX - use some generic or default icon
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON |
PM_WHATS_THIS_BUTTON)
msg = "Test the performance effect of graphics settings below. " \
"(To avoid bugs, choose testCase before bypassing paintGL.)"
self.updateMessage(msg)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Settings") ### fix title
self._loadGroupBox1( self._pmGroupBox1 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
from widgets.prefs_widgets import ObjAttr_StateRef ### toplevel
self._cb2 = \
PM_CheckBox(pmGroupBox,
text = "redraw continuously",
)
self._cb2.connectWithState( ObjAttr_StateRef( self.command, 'redraw_continuously' ))
self._cb3 = \
PM_CheckBox(pmGroupBox,
text = "spin model",
)
self._cb3.connectWithState( ObjAttr_StateRef( self.command, 'spin_model' ))
self._cb4 = \
PM_CheckBox(pmGroupBox,
text = "print fps to console",
)
self._cb4.connectWithState( ObjAttr_StateRef( self.command, 'print_fps' ))
self._cb1 = \
PM_CheckBox(pmGroupBox,
text = "replace paintGL with testCase",
)
self._cb1.connectWithState( ObjAttr_StateRef( self.command, 'bypass_paintgl' ))
# note: this state (unlike the highest-quality staterefs)
# is not change-tracked [as of 081003], so nothing aside from
# user clicks on this checkbox should modify it after this runs,
# or our UI state will become out of sync with the state.
self.testCase_ComboBox = PM_ComboBox(pmGroupBox,
label = "testCase:", labelColumn = 0,
choices = self.command.testCaseChoicesText,
setAsDefault = False )
self.testCase_ComboBox.setCurrentIndex(self.command.testCaseIndex)
self.nSpheres_ComboBox = PM_ComboBox(pmGroupBox,
label = "n x n spheres:", labelColumn = 0,
choices = self.command._NSPHERES_CHOICES,
setAsDefault = False )
nSpheres_index = self.command._NSPHERES_CHOICES.index( str( self.command.nSpheres) )
self.nSpheres_ComboBox.setCurrentIndex( nSpheres_index)
self._set_nSpheresIndex( nSpheres_index)
self.detail_level_ComboBox = PM_ComboBox(pmGroupBox,
label = "Level of detail:", labelColumn = 0,
choices = ["Low", "Medium", "High", "Variable"],
setAsDefault = False )
lod = env.prefs[levelOfDetail_prefs_key]
if lod > 2:
lod = 2
if lod < 0: # only lod == -1 is legal here
lod = 3
self.detail_level_ComboBox.setCurrentIndex(lod)
self.set_level_of_detail_index(lod)
self._updateWidgets()
## def updateUI(self): # BUG: this is not being called -- I guess the bypassed paintGL doesn't call it.
## self._updateWidgets() ### will this be too slow?
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.testCase_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self.command._set_testCaseIndex )
change_connect(self.nSpheres_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self._set_nSpheresIndex )
change_connect(self.detail_level_ComboBox,
SIGNAL("currentIndexChanged(int)"),
# in current code, SIGNAL("activated(int)")
self.set_level_of_detail_index )
return
# ==
def _set_nSpheresIndex(self, index):
self.command.nSpheres = int( self.command._NSPHERES_CHOICES[index] )
def set_level_of_detail_index(self, level_of_detail_index): # copied from other code, renamed, revised
"""
Change the level of detail, where <level_of_detail_index> is a value
between 0 and 3 where:
- 0 = low
- 1 = medium
- 2 = high
- 3 = variable (based on number of atoms in the part)
@note: the prefs db value for 'variable' is -1, to allow for higher LOD
levels in the future.
"""
lod = level_of_detail_index
if lod == 3:
lod = -1
self.command.detailLevel = lod
def _updateWidgets(self):
"""
Update widget configuration based on state of prior widgets.
"""
## # presently, the LOD is not noticed by the test cases... oops, not true!
## self.detail_level_ComboBox.setEnabled( not self.command.bypass_paintgl )
return
pass
class DnaGeneratorPropertyManager(PM_Dialog, DebugMenuMixin):
"""
The DnaGeneratorPropertyManager class provides a Property Manager
for the "Build > Atoms" command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
@ivar validSymbols: Miscellaneous symbols that may appear in the sequence
(but are ignored). The hyphen '-' is a special case
that must be dealt with individually; it is not
included because it can confuse regular expressions.
@type validSymbols: QString
"""
title = "DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?')
# The following class variables guarantee the UI's menu items
# are synchronized with their action code. The arrays should
# not be changed, unless an item is removed or inserted.
# Changes should be made via only the _action... variables.
# e.g., Change _action_Complement from "Complement"
# to "Complement Sequences". The menu item will
# change and its related code will need no update.
_action_Complement = "Complement"
_action_Reverse = "Reverse"
_action_RemoveUnrecognized = 'Remove unrecognized letters'
_action_ConvertUnrecognized = 'Convert unrecognized letters to "N"'
_actionChoices = [
"Action", "---", _action_Complement, _action_Reverse,
_action_RemoveUnrecognized, _action_ConvertUnrecognized
]
_modeltype_PAM3 = "PAM3"
_modeltype_PAM5 = "PAM5"
_modeltype_Atomistic = "Atomistic" # deprecated
_modelChoices = [_modeltype_PAM3, _modeltype_PAM5]
def __init__(self):
"""
Constructor for the DNA Generator property manager.
"""
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
msg = "Edit the DNA parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into \
the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PM is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True)
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Strand Sequence")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="DNA Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox3(self._pmGroupBox3)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
# Duplex Length
self.duplexLengthSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Duplex Length: ",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 34000,
singleStep = self.getDuplexRise("B-DNA"),
decimals = 3,
suffix = ' Angstroms')
self.connect(self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Strand Length
self.strandLengthSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Strand Length :",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000,
suffix = ' bases' )
self.connect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
# New Base choices
newBaseChoices = []
for theBase in basesDict.keys():
newBaseChoices = newBaseChoices \
+ [ theBase + ' (' \
+ basesDict[theBase]['Name'] + ')' ]
try:
defaultBaseChoice = basesDict.keys().index('N')
except:
defaultBaseChoice = 0
# Strand Sequence
self.sequenceTextEdit = \
PM_TextEdit( pmGroupBox,
label = "",
spanWidth = True )
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.connect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
self.connect(self.sequenceTextEdit, SIGNAL("cursorPositionChanged()"),
self.cursorPosChanged)
# Actions
self.actionsComboBox = \
PM_ComboBox( pmGroupBox,
label = '',
choices = self._actionChoices,
index = 0,
setAsDefault = True,
spanWidth = True )
# If SIGNAL("activate(const QString&)") is used, we get a TypeError.
# This is a bug that needs Bruce. Using currentIndexChanged(int) as
# a workaround, but there is still a bug when the "Reverse" action
# is selected. Mark 2007-08-15
self.connect(self.actionsComboBox, SIGNAL("currentIndexChanged(int)"),
self.actionsComboBoxChanged)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
self.modelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model :",
choices = self._modelChoices,
setAsDefault = True)
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation :",
choices = ["B-DNA"],
setAsDefault = True)
self.connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
self.basesPerTurnComboBox= \
PM_ComboBox( pmGroupBox,
label = "Bases Per Turn :",
choices = ["10.0", "10.5", "10.67"],
setAsDefault = True)
# I may decide to reintroduce "base-pair chunks" at a later time.
# Please talk to me if you have a strong feeling about including
# this. Mark 2007-08-19.
createChoices = ["Strand chunks", \
"Single chunk" ]
#@ "Base-pair chunks"]
self.createComboBox = \
PM_ComboBox( pmGroupBox,
label = "Create :",
choices = createChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
self._endPoint1GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint1")
self._endPoint2GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint2")
# Point 1
self.x1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
# Point 2
self.x2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 10.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in the
DNA Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
self.conformationComboBox.setWhatsThis("""<b>Conformation</b>
<p>There are three DNA geometries, A-DNA, B-DNA,
and Z-DNA. Only B-DNA and Z-DNA are currently supported.</p>""")
self.sequenceTextEdit.setWhatsThis("""<b>Strand Sequence</b>
<p>Type in the strand sequence you want to generate here (5' => 3')<br>
<br>
Recognized base letters:<br>
<br>
A = Adenosine<br>
C = Cytosine<br>
G = Guanosine<br>
T = Thymidine<br>
N = aNy base<br>
X = Unassigned<br>
<br>
Other base letters currently recognized:<br>
<br>
B = C,G, or T<br>
D = A,G, or T<br>
H = A,C, or T<br>
V = A,C, or G<br>
R = A or G (puRine)<br>
Y = C or T (pYrimidine)<br>
K = G or T (Keto)<br>
M = A or C (aMino)<br>
S = G or C (Strong -3H bonds)<br>
W = A or T (Weak - 2H bonds)<br>
</p>""")
self.actionsComboBox.setWhatsThis("""<b>Action</b>
<p>Select an action to perform on the sequence.</p>""")
def conformationComboBoxChanged(self, inIndex):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.basesPerTurnComboBox.clear()
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnComboBox.insertItem(0, "10.0")
self.basesPerTurnComboBox.insertItem(1, "10.5")
self.basesPerTurnComboBox.insertItem(2, "10.67")
#10.5 is the default value for Bases per turn.
#So set the current index to 1
self.basesPerTurnComboBox.setCurrentIndex(1)
elif conformation == "Z-DNA":
self.basesPerTurnComboBox.insertItem(0, "12.0")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
conformation = "B-DNA" # Workaround for "Restore Defaults".
pass
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = " + inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(
self.getDuplexRise(conformation))
def modelComboBoxChanged(self, inIndex):
"""
Slot for the Model combobox. It is called whenever the
Model choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self._modelChoices[inIndex]
self.disconnect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
self.conformationComboBox.clear() # Generates signal!
if conformation == self._modeltype_PAM3:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_PAM5:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_Atomistic:
self.conformationComboBox.addItem("B-DNA")
self.conformationComboBox.addItem("Z-DNA")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
pass
else:
msg = "Error - unknown model representation. Index = " + inIndex
env.history.message(redmsg(msg))
self.connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
# GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox.
def getDuplexRise(self, inConformation):
"""
Return the 'rise' between base pairs of the
specified DNA type (conformation).
@param inConformation: The current conformation.
@type inConformation: int
"""
return dnaDict[str(inConformation)]['DuplexRise']
def synchronizeLengths(self):
"""
Guarantees the values of the duplex length and strand length
spinboxes agree with the strand sequence (textedit).
"""
self.updateStrandLength()
self.updateDuplexLength()
return
# Added :jbirac 20070613:
def duplexLengthChanged(self, inDuplexLength):
"""
Slot for the duplex length spinbox, called whenever the value of the
Duplex Length spinbox changes.
@param inDuplexLength: The duplex length.
@type inDuplexLength: float
"""
conformation = self.conformationComboBox.currentText()
duplexRise = self.getDuplexRise(conformation)
newStrandLength = inDuplexLength / duplexRise + 0.5
newStrandLength = int(newStrandLength)
self.strandLengthChanged(newStrandLength)
def updateDuplexLength(self): # Added :jbirac 20070615:
"""
Update the Duplex Length spinbox; always the length of the
strand sequence multiplied by the 'rise' of the duplex. This
method is called by slots of other controls (i.e., this itself
is not a slot.)
"""
conformation = self.conformationComboBox.currentText()
newDuplexLength = self.getDuplexRise( conformation ) \
* self.getSequenceLength()
self.disconnect(self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
self.duplexLengthSpinBox.setValue(newDuplexLength)
self.connect(self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Renamed from length_changed :jbirac 20070613:
def strandLengthChanged(self, inStrandLength):
"""
Slot for the Strand Length spin box, called whenever the value of the
Strand Length spin box changes.
@param inStrandLength: The number of bases in the strand sequence.
@type inStrandLength: int
"""
theSequence = self.getPlainSequence()
sequenceLen = len(theSequence)
lengthChange = inStrandLength - self.getSequenceLength()
# Preserve the cursor's position/selection
cursor = self.sequenceTextEdit.textCursor()
#cursorPosition = cursor.position()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStrandLength < 0:
return # Should never happen.
if lengthChange < 0:
# If length is less than the previous length,
# simply truncate the current sequence.
theSequence.chop(-lengthChange)
elif lengthChange > 0:
# If length has increased, add the correct number of base
# letters to the current strand sequence.
numNewBases = lengthChange
# Get current base selected in combobox.
chosenBase = 'X' # Unassigned.
basesToAdd = chosenBase * numNewBases
theSequence.append(basesToAdd)
else:
env.history.message(
orangemsg("strandLengthChanged(): Length has not changed."))
self.setSequence(theSequence)
return
# Renamed from updateLength :jbirac 20070613:
def updateStrandLength(self):
"""
Update the Strand Length spinbox; always the length of the strand
sequence.
"""
self.disconnect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
self.strandLengthSpinBox.setValue(self.getSequenceLength())
self.connect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
return
def sequenceChanged(self):
"""
Slot for the Strand Sequence textedit widget.
Assumes the sequence changed directly by user's keystroke in the
textedit. Other methods...
"""
cursorPosition = self.getCursorPosition()
theSequence = self.getPlainSequence()
# Disconnect while we edit the sequence.
self.disconnect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
# How has the text changed?
if theSequence.length() == 0: # There is no sequence.
self.updateStrandLength()
self.updateDuplexLength()
else:
# Insert the sequence; it will be "stylized" by setSequence().
self.setSequence(theSequence)
# Reconnect to respond when the sequence is changed.
self.connect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
self.synchronizeLengths()
return
def getPlainSequence(self, inOmitSymbols=False):
"""
Returns a plain text QString (without HTML stylization)
of the current sequence. All characters are preserved (unless
specified explicitly), including valid base letters, punctuation
symbols, whitespace and invalid letters.
@param inOmitSymbols: Omits characters listed in self.validSymbols.
@type inOmitSymbols: bool
@return: The current DNA sequence in the PM.
@rtype: QString
"""
outSequence = self.sequenceTextEdit.toPlainText()
if inOmitSymbols:
# This may look like a sloppy piece of code, but Qt's QRegExp
# class makes it pretty tricky to remove all punctuation.
theString = '[<>' \
+ str( QRegExp.escape(self.validSymbols) ) \
+ ']|-'
outSequence.remove(QRegExp(theString))
return outSequence
def stylizeSequence(self, inSequence):
"""
Converts a plain text string of a sequence (including optional
symbols) to an HTML rich text string.
@param inSequence: A DNA sequence.
@type inSequence: QString
@return: The sequence.
@rtype: QString
"""
outSequence = str(inSequence)
# Verify that all characters (bases) in the sequence are "valid".
invalidSequence = False
basePosition = 0
sequencePosition = 0
invalidStartTag = "<b><font color=black>"
invalidEndTag = "</b>"
previousChar = chr(1) # Null character; may be revised.
# Some characters must be substituted to preserve
# whitespace and tags in HTML code.
substituteDict = {' ': ' ', '<': '<', '>': '>'}
while basePosition < len(outSequence):
theSeqChar = outSequence[basePosition]
if (theSeqChar in basesDict or theSeqChar in self.validSymbols):
# Close any preceding invalid sequence segment.
if invalidSequence == True:
outSequence = outSequence[:basePosition] \
+ invalidEndTag \
+ outSequence[basePosition:]
basePosition += len(invalidEndTag)
invalidSequence = False
# Color the valid characters.
if theSeqChar != previousChar:
# We only need to insert 'color' tags in places where
# the adjacent characters are different.
if theSeqChar in basesDict:
theTag = '<font color=' \
+ basesDict[ theSeqChar ]['Color'] \
+ '>'
elif not previousChar in self.validSymbols:
# The character is a 'valid' symbol to be greyed
# out. Only one 'color' tag is needed for a
# group of adjacent symbols.
theTag = '<font color=dimgrey>'
else:
theTag = ''
outSequence = outSequence[:basePosition] \
+ theTag + outSequence[basePosition:]
basePosition += len(theTag)
# Any <space> character must be substituted with an
# ASCII code tag because the HTML engine will collapse
# whitespace to a single <space> character; whitespace
# is truncated from the end of HTML by default.
# Also, many symbol characters must be substituted
# because they confuse the HTML syntax.
#if str( outSequence[basePosition] ) in substituteDict:
if outSequence[basePosition] in substituteDict:
#theTag = substituteDict[theSeqChar]
theTag = substituteDict[outSequence[basePosition]]
outSequence = outSequence[:basePosition] \
+ theTag \
+ outSequence[basePosition + 1:]
basePosition += len(theTag) - 1
else:
# The sequence character is invalid (but permissible).
# Tags (e.g., <b> and </b>) must be inserted at both the
# beginning and end of a segment of invalid characters.
if invalidSequence == False:
outSequence = outSequence[:basePosition] \
+ invalidStartTag \
+ outSequence[basePosition:]
basePosition += len(invalidStartTag)
invalidSequence = True
basePosition += 1
previousChar = theSeqChar
#basePosition += 1
# Specify that theSequence is definitely HTML format, because
# Qt can get confused between HTML and Plain Text.
outSequence = "<html>" + outSequence
outSequence += "</html>"
return outSequence
def setSequence(self, inSequence, inStylize=True, inRestoreCursor=True):
"""
Replace the current strand sequence with the new sequence text.
@param inSequence: The new sequence.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
text string (including optional symbols) to an HTML
rich text string.
@type inStylize: bool
@param inRestoreCursor: Not implemented yet.
@type inRestoreCursor: bool
@attention: Signals/slots must be managed before calling this method.
The textChanged() signal will be sent to any connected widgets.
"""
cursor = self.sequenceTextEdit.textCursor()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStylize:
inSequence = self.stylizeSequence(inSequence)
self.sequenceTextEdit.insertHtml(inSequence)
if inRestoreCursor:
cursor.setPosition(min(selectionStart, self.getSequenceLength()),
QTextCursor.MoveAnchor)
cursor.setPosition(min(selectionEnd, self.getSequenceLength()),
QTextCursor.KeepAnchor)
self.sequenceTextEdit.setTextCursor(cursor)
return
def getSequenceLength(self):
"""
Returns the number of characters in
the strand sequence textedit widget.
"""
theSequence = self.getPlainSequence(inOmitSymbols=True)
outLength = theSequence.length()
return outLength
def getCursorPosition(self):
"""
Returns the cursor position in the
strand sequence textedit widget.
"""
cursor = self.sequenceTextEdit.textCursor()
return cursor.position()
def cursorPosChanged(self):
"""
Slot called when the cursor position changes.
"""
cursor = self.sequenceTextEdit.textCursor()
if 0:
env.history.message(
greenmsg("cursorPosChanged: Selection (" +
str(cursor.selectionStart()) + " thru " +
str(cursor.selectionEnd()) + ')'))
return
def actionsComboBoxChanged(self, inIndex):
"""
Slot for the Actions combobox. It is called whenever the
Action choice is changed.
@param inIndex: The index of the selected action choice.
@type inIndex: int
"""
if inIndex == 0: # Very important.
return
actionName = str(self.actionsComboBox.currentText())
self.actionsComboBox.setCurrentIndex(0) # Generates signal!
self.invokeAction(actionName)
return
def invokeAction(self, inActionName):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='N')
self.setSequence(outResult)
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='')
self.setSequence(outResult)
return
class EditRotamers_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit Rotamers"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__(self, parentCommand):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit protein rotamers."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nextAAPushButton, SIGNAL("clicked()"),
self._expandNextRotamer)
change_connect(self.previousAAPushButton, SIGNAL("clicked()"),
self._expandPreviousRotamer)
change_connect(self.expandAllPushButton, SIGNAL("clicked()"),
self._expandAllRotamers)
change_connect(self.collapseAllPushButton, SIGNAL("clicked()"),
self._collapseAllRotamers)
self.connect(self.aminoAcidsComboBox,
SIGNAL("currentIndexChanged(int)"),
self._aminoAcidChanged)
#Protein Display methods
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Position")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Rotamer")
self._loadGroupBox2(self._pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
aa_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
aa_list = mol.protein.get_amino_acid_id_list()
break
self.aminoAcidsComboBox = PM_ComboBox(pmGroupBox,
label="Residue:",
choices=aa_list,
setAsDefault=False)
self.previousAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Previous AA",
setAsDefault = True)
self.nextAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Next AA",
setAsDefault = True)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.expandAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Expand All",
setAsDefault = True)
self.collapseAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Collapse All",
setAsDefault = True)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi1 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi2SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi2 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi3SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi3 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
def _addWhatsThisText(self):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditRotamers_PropertyManager
#WhatsThis_EditRotamers_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def _expandNextRotamer(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.traverse_forward()
self._display_and_recenter()
self._updateAminoAcidInfo(
chunk.protein.get_current_amino_acid_index())
return
def _expandPreviousRotamer(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.traverse_backward()
self._display_and_recenter()
self._updateAminoAcidInfo(
chunk.protein.get_current_amino_acid_index())
return
def _collapseAllRotamers(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.collapse_all_rotamers()
self.win.glpane.gl_update()
return
def _expandAllRotamers(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.expand_all_rotamers()
self.win.glpane.gl_update()
return
def _display_and_recenter(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.collapse_all_rotamers()
current_aa = chunk.protein.get_current_amino_acid()
if current_aa:
chunk.protein.expand_rotamer(current_aa)
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
#self.win.glpane.gl_update()
self.win.glpane.gl_update()
def _updateAminoAcidInfo(self, index):
"""
"""
self.aminoAcidsComboBox.setCurrentIndex(index)
def _aminoAcidChanged(self, index):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.set_current_amino_acid_index(index)
self._display_and_recenter()
class ColorScheme_PropertyManager(Command_PropertyManager):
"""
The ColorScheme_PropertyManager class provides a Property Manager
for choosing background and other colors for the Choose Color toolbar command
as well as the View/Color Scheme command
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Color Scheme"
pmName = title
iconPath = "ui/actions/View/ColorScheme.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit the color scheme for NE1, including the background color, "\
"hover highlighting and selection colors, etc."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
# background color setting combo box.
change_connect( self.backgroundColorComboBox,
SIGNAL("activated(int)"),
self.changeBackgroundColor )
#hover highlighting style combo box
change_connect(self.hoverHighlightingStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeHoverHighlightingStyle)
change_connect(self.hoverHighlightingColorComboBox,
SIGNAL("editingFinished()"),
self.changeHoverHighlightingColor)
#selection style combo box
change_connect(self.selectionStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeSelectionStyle)
change_connect(self.selectionColorComboBox,
SIGNAL("editingFinished()"),
self.changeSelectionColor)
def changeHoverHighlightingColor(self):
"""
Slot method for Hover Highlighting color chooser.
Change the (3D) hover highlighting color.
"""
color = self.hoverHighlightingColorComboBox.getColor()
env.prefs[hoverHighlightingColor_prefs_key] = color
return
def changeHoverHighlightingStyle(self, idx):
"""
Slot method for Hover Highlighting combobox.
Change the (3D) hover highlighting style.
"""
env.prefs[hoverHighlightingColorStyle_prefs_key] = HHS_INDEXES[idx]
def changeSelectionStyle(self, idx):
"""
Slot method for Selection color style combobox.
Change the (3D) Selection color style.
"""
env.prefs[selectionColorStyle_prefs_key] = SS_INDEXES[idx]
def changeSelectionColor(self):
"""
Slot method for Selection color chooser.
Change the (3D) Selection color.
"""
color = self.selectionColorComboBox.getColor()
env.prefs[selectionColor_prefs_key] = color
return
def show(self):
"""
Shows the Property Manager. Extends superclass method.
"""
self._updateAllWidgets()
_superclass.show(self)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Background")
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self,
title = "Highlighting and Selection")
self._loadGroupBox3( self._pmGroupBox3 )
self._updateAllWidgets()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/DnaDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/ColorScheme')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyColorSchemeFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
#background color combo box
self.backgroundColorComboBox = \
PM_ComboBox( pmGroupBox,
label = "Color:",
spanWidth = False)
self._loadBackgroundColorItems()
self.enableFogCheckBox = \
PM_CheckBox( pmGroupBox, text = "Enable fog" )
connect_checkbox_with_boolean_pref( self.enableFogCheckBox, fogEnabled_prefs_key )
return
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
# hover highlighting style and color
self.hoverHighlightingStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Highlighting:",
)
self._loadHoverHighlightingStyleItems()
hhColorList = [yellow, orange, red, magenta,
cyan, blue, white, black, gray]
hhColorNames = ["Yellow (default)", "Orange", "Red", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."]
self.hoverHighlightingColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = env.prefs[hoverHighlightingColor_prefs_key]
)
# selection style and color
self.selectionStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Selection:",
)
self._loadSelectionStyleItems()
selColorList = [darkgreen, green, orange, red,
magenta, cyan, blue, white, black,
gray]
selColorNames = ["Dark green (default)", "Green", "Orange", "Red",
"Magenta", "Cyan", "Blue", "White", "Black",
"Other color..."]
self.selectionColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = selColorList,
colorNames = selColorNames,
color = env.prefs[selectionColor_prefs_key]
)
return
def _updateAllWidgets(self):
"""
Update all the PM widgets. This is typically called after applying
a favorite.
"""
self._updateBackgroundColorComboBoxIndex()
self.updateCustomColorItemIcon(RGBf_to_QColor(env.prefs[backgroundColor_prefs_key]))
self.hoverHighlightingStyleComboBox.setCurrentIndex(HHS_INDEXES.index(env.prefs[hoverHighlightingColorStyle_prefs_key]))
self.hoverHighlightingColorComboBox.setColor(env.prefs[hoverHighlightingColor_prefs_key])
self.selectionStyleComboBox.setCurrentIndex(SS_INDEXES.index(env.prefs[selectionColorStyle_prefs_key]))
self.selectionColorComboBox.setColor(env.prefs[selectionColor_prefs_key])
return
def _loadSelectionStyleItems(self):
"""
Load the selection color style combobox with items.
"""
for selectionStyle in SS_OPTIONS:
self.selectionStyleComboBox.addItem(selectionStyle)
return
def _loadHoverHighlightingStyleItems(self):
"""
Load the hover highlighting style combobox with items.
"""
for hoverHighlightingStyle in HHS_OPTIONS:
self.hoverHighlightingStyleComboBox.addItem(hoverHighlightingStyle)
return
def _loadBackgroundColorItems(self):
"""
Load the background color combobox with all the color options and sets
the current background color
"""
backgroundIndexes = [bg_BLUE_SKY, bg_EVENING_SKY, bg_SEAGREEN,
bg_BLACK, bg_WHITE, bg_GRAY, bg_CUSTOM]
backgroundNames = ["Blue Sky (default)", "Evening Sky", "Sea Green",
"Black", "White", "Gray", "Custom..."]
backgroundIcons = ["Background_BlueSky", "Background_EveningSky",
"Background_SeaGreen",
"Background_Black", "Background_White",
"Background_Gray", "Background_Custom"]
backgroundIconsDict = dict(zip(backgroundNames, backgroundIcons))
backgroundNamesDict = dict(zip(backgroundIndexes, backgroundNames))
for backgroundName in backgroundNames:
basename = backgroundIconsDict[backgroundName] + ".png"
iconPath = os.path.join("ui/dialogs/Preferences/",
basename)
self.backgroundColorComboBox.addItem(geticon(iconPath),
backgroundName)
self._updateBackgroundColorComboBoxIndex() # Not needed, but OK.
return
def _updateBackgroundColorComboBoxIndex(self):
"""
Set current index in the background color combobox.
"""
if self.win.glpane.backgroundGradient:
self.backgroundColorComboBox.setCurrentIndex(self.win.glpane.backgroundGradient - 1)
else:
if (env.prefs[ backgroundColor_prefs_key ] == black):
self.backgroundColorComboBox.setCurrentIndex(bg_BLACK)
elif (env.prefs[ backgroundColor_prefs_key ] == white):
self.backgroundColorComboBox.setCurrentIndex(bg_WHITE)
elif (env.prefs[ backgroundColor_prefs_key ] == gray):
self.backgroundColorComboBox.setCurrentIndex(bg_GRAY)
else:
self.backgroundColorComboBox.setCurrentIndex(bg_CUSTOM)
return
def changeBackgroundColor(self, idx):
"""
Slot method for the background color combobox.
"""
#print "changeBackgroundColor(): Slot method called. Idx =", idx
if idx == bg_BLUE_SKY:
self.win.glpane.setBackgroundGradient(idx + 1)
elif idx == bg_EVENING_SKY:
self.win.glpane.setBackgroundGradient(idx + 1)
elif idx == bg_SEAGREEN:
self.win.glpane.setBackgroundGradient(idx + 1)
elif idx == bg_BLACK:
self.win.glpane.setBackgroundColor(black)
elif idx == bg_WHITE:
self.win.glpane.setBackgroundColor(white)
elif idx == bg_GRAY:
self.win.glpane.setBackgroundColor(gray)
elif idx == bg_CUSTOM:
#change background color to Custom Color
self.chooseCustomBackgroundColor()
else:
msg = "Unknown color idx=", idx
print_compact_traceback(msg)
self.win.glpane.gl_update() # Needed!
return
def chooseCustomBackgroundColor(self):
"""
Choose a custom background color.
"""
c = QColorDialog.getColor(RGBf_to_QColor(self.win.glpane.getBackgroundColor()), self)
if c.isValid():
self.win.glpane.setBackgroundColor(QColor_to_RGBf(c))
self.updateCustomColorItemIcon(c)
else:
# User cancelled. Need to reset combobox to correct index.
self._updateBackgroundColorComboBoxIndex()
return
def updateCustomColorItemIcon(self, qcolor):
"""
Update the custom color item icon in the background color combobox
with I{qcolor}.
"""
pixmap = QPixmap(16, 16)
pixmap.fill(qcolor)
self.backgroundColorComboBox.setItemIcon(bg_CUSTOM, QIcon(pixmap))
return
def applyFavorite(self):
"""
Apply the color scheme settings stored in the current favorite
(selected in the combobox) to the current color scheme settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(colorSchemePrefsList)
# set it back to blue sky
self.win.glpane.setBackgroundGradient(1)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
if env.prefs[backgroundGradient_prefs_key]:
self.win.glpane.setBackgroundGradient(env.prefs[backgroundGradient_prefs_key])
else:
self.win.glpane.setBackgroundColor(env.prefs[backgroundColor_prefs_key])
#self.hoverHighlightingColorComboBox.setColor(env.prefs[hoverHighlightingColor_prefs_key])
#self.selectionColorComboBox.setColor(env.prefs[selectionColor_prefs_key])
self._updateAllWidgets()
self.win.glpane.gl_update()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current color scheme
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The color scheme settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/ColorScheme/$FAV_NAME.txt).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/ColorScheme/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeColorSchemeToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeColorSchemeToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
#Check to see if favfilepath exists first
if not os.path.exists(favfilepath):
msg = "%s does not exist" % favfilepath
env.history.message(cmd + msg)
return
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
saveLocation, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
#remember this directory
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir = None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir = None):
"""
[private method]
Set the working directory in the user preferences database.
@param workdir: The fullpath directory to write to the user pref db.
If I{workdir} is None (default), there is no change.
@type workdir: string
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message( redmsg(msg))
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile = loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeColorSchemeToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(colorSchemePrefsList)
# set it back to blue sky
self.win.glpane.setBackgroundGradient(1)
self.win.glpane.gl_update()
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
if env.prefs[backgroundGradient_prefs_key]:
self.win.glpane.setBackgroundGradient(env.prefs[backgroundGradient_prefs_key])
else:
self.win.glpane.setBackgroundColor(env.prefs[backgroundColor_prefs_key])
self.win.glpane.gl_update()
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Color Scheme Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_ColorScheme_PropertyManager
WhatsThis_ColorScheme_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Color Scheme Property Manager.
"""
#modify this for color schemes
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_ColorScheme_PropertyManager
ToolTip_ColorScheme_PropertyManager(self)
class ProteinDisplayStyle_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit Protein Display Style"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the protein display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect = True):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
#Display group box signal slot connections
change_connect(self.proteinStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayStyle)
change_connect(self.smoothingCheckBox,
SIGNAL("stateChanged(int)"),
self.smoothProteinDisplay)
change_connect(self.scaleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayScale)
change_connect(self.splineDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinSplineValue)
change_connect(self.scaleFactorDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinScaleFactor)
#color groupbox
change_connect(self.proteinComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseProteinComponent)
change_connect(self.proteinAuxComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseAuxilliaryProteinComponent)
change_connect(self.customColorComboBox,
SIGNAL("editingFinished()"),
self.chooseCustomColor)
change_connect(self.auxColorComboBox,
SIGNAL("editingFinished()"),
self.chooseAuxilliaryColor)
#change_connect(self.discColorCheckBox,
# SIGNAL("stateChanged(int)"),
# self.setDiscreteColors)
change_connect(self.helixColorComboBox,
SIGNAL("editingFinished()"),
self.chooseHelixColor)
change_connect(self.strandColorComboBox,
SIGNAL("editingFinished()"),
self.chooseStrandColor)
change_connect(self.coilColorComboBox,
SIGNAL("editingFinished()"),
self.chooseCoilColor)
#Protein Display methods
def changeProteinDisplayStyle(self, idx):
"""
Change protein display style
@param idx: index of the protein display style combo box
@type idx: int
"""
env.prefs[proteinStyle_prefs_key] = idx
return
def changeProteinDisplayQuality(self, idx):
env.prefs[proteinStyleQuality_prefs_key] = idx
return
def smoothProteinDisplay(self, state):
"""
Smoooth protein display.
@param state: state of the smooth protein display check box.
@type state: int
"""
if state == Qt.Checked:
env.prefs[proteinStyleSmooth_prefs_key] = True
else:
env.prefs[proteinStyleSmooth_prefs_key] = False
return
def changeProteinDisplayScale(self, idx):
"""
Change protein display scale
@param idx: index of the protein display scaling choices combo box
@type idx: int
"""
env.prefs[proteinStyleScaling_prefs_key] = idx
return
def changeProteinSplineValue(self, val):
"""
Change protein display resolution
@param val: value in the protein display resolution double spinbox
@type val: double
"""
env.prefs[proteinStyleQuality_prefs_key] = val
return
def changeProteinScaleFactor(self, val):
"""
Change protein display scale factor
@param val: value in the protein display scale factor double spinbox
@type val: double
"""
env.prefs[proteinStyleScaleFactor_prefs_key] = val
return
def chooseProteinComponent(self, idx):
"""
Choose protein component to set the color of
@param idx: index of the protein component choices combo box
@type idx: int
"""
env.prefs[proteinStyleColors_prefs_key] = idx
return
def chooseAuxilliaryProteinComponent(self, idx):
"""
Choose auxilliary protein component to set the color of
@param idx: index of the auxilliary protein component choices combo box
@type idx: int
"""
env.prefs[proteinStyleAuxColors_prefs_key] = idx - 1
return
def chooseCustomColor(self):
"""
Choose custom color of the chosen protein component
"""
color = self.customColorComboBox.getColor()
env.prefs[proteinStyleCustomColor_prefs_key] = color
return
def chooseAuxilliaryColor(self):
"""
Choose custom color of the chosen auxilliary protein component
"""
color = self.auxColorComboBox.getColor()
env.prefs[proteinStyleAuxCustomColor_prefs_key] = color
return
def chooseHelixColor(self):
"""
Choose helix color
"""
color = self.helixColorComboBox.getColor()
env.prefs[proteinStyleHelixColor_prefs_key] = color
return
def chooseStrandColor(self):
"""
Choose strand color
"""
color = self.strandColorComboBox.getColor()
env.prefs[proteinStyleStrandColor_prefs_key] = color
return
def chooseCoilColor(self):
"""
Choose coil color
"""
color = self.coilColorComboBox.getColor()
env.prefs[proteinStyleCoilColor_prefs_key] = color
return
def setDiscreteColors(self, state):
"""
Set discrete colors.
@param state: state of the set discrete colors check box.
@type state: int
"""
if state == Qt.Checked:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = True
else:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = False
return
def show_OLD(self):
"""
Shows the Property Manager.Extends superclass method.
"""
#@REVIEW: See comment in CompareProteins_PropertyManager
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
self.updateProteinDisplayStyleWidgets()
_superclass.show(self)
def show(self):
"""
Shows the Property Manager. Extends superclass method
"""
_superclass.show(self)
#@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
#-- Ninad 2008-10-02
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
# TODO: rename that public attr of GLPane (widely used)
# from displayMode to displayStyle. [bruce 080910 comment]
self.o.setGlobalDisplayStyle(diPROTEIN)
# Update all PM widgets, .
# note: It is important to update the widgets by blocking the
# 'signals'. If done in the reverse order, it will generate signals
#when updating the PM widgets (via updateDnaDisplayStyleWidgets()),
#causing unneccessary repaints of the model view.
self.updateProteinDisplayStyleWidgets()#@@@ blockSignals = True)
return
def close(self):
"""
Closes the Property Manager. Extends superclass method.
"""
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Display")
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self,
title = "Color")
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
@param pmGroupBox: group box that contains various favorite buttons
@see: L{PM_GroupBox}
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/ProteinDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/ProteinDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis(
"""<b> List of Favorites </b>
<p>
Creates a list of favorite Protein display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE","ui/actions/Properties Manager/ApplyPeptideDisplayStyleFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png","Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE", "ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
@param pmGroupBox: group box that contains protein display choices
@see: L{PM_GroupBox}
"""
proteinStyleChoices = ['CA trace (wire)',
'CA trace (cylinders)',
'CA trace (ball and stick)',
'Tube',
'Ladder',
'Zigzag',
'Flat ribbon',
'Solid ribbon',
'Cartoons',
'Fancy cartoons',
'Peptide tiles'
]
self.proteinStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Style:",
choices = proteinStyleChoices,
setAsDefault = True)
scaleChoices = ['Constant', 'Secondary structure', 'B-factor']
self.scaleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Scaling:",
choices = scaleChoices,
setAsDefault = True)
self.scaleFactorDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Scaling factor:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 1,
singleStep = 0.1 )
self.splineDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Resolution:",
value = 3,
setAsDefault = True,
minimum = 2,
maximum = 8,
decimals = 0,
singleStep = 1 )
self.smoothingCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Smoothing",
setAsDefault = True)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
@param pmGroupBox: group box that contains various color choices
@see: L{PM_GroupBox}
"""
colorChoices = ['Chunk', 'Chain', 'Order', 'Hydropathy', 'Polarity',
'Acidity', 'Size', 'Character', 'Number of contacts',
'Secondary structure type', 'Secondary structure order',
'B-factor', 'Occupancy', 'Custom']
self.proteinComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Color by:",
choices = colorChoices,
setAsDefault = True)
colorList = [orange, yellow, red, magenta,
cyan, blue, white, black, gray]
colorNames = ["Orange(default)", "Yellow", "Red", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."]
self.customColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorList,
colorNames = colorNames,
label = "Custom:",
color = orange,
setAsDefault = True)
colorChoices1 = [ 'Same as main color', 'Lighter', 'Darker',
'Gray', 'Custom']
self.proteinAuxComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Aux:",
choices = colorChoices1,
setAsDefault = True)
colorListAux = [orange, yellow, red, magenta,cyan, blue, white, black, gray]
colorNamesAux = ["Orange(default)", "Yellow", "Red", "Magenta", "Cyan",
"Blue", "White", "Black", "Other color..."]
self.auxColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Custom aux:",
color = gray,
setAsDefault = True)
#self.discColorCheckBox = \
# PM_CheckBox( pmGroupBox,
# text = "Discretize colors",
# setAsDefault = True
# )
#
colorListHelix = [red, yellow, gray, magenta,
cyan, blue, white, black, orange]
colorNamesHelix = ["Red(default)", "Yellow", "Gray", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."]
self.helixColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListHelix,
colorNames = colorNamesHelix,
label = "Helix:",
color = red,
setAsDefault = True)
colorListStrand = [cyan, yellow, gray, magenta,
red, blue, white, black, orange]
colorNamesStrand = ["Cyan(default)", "Yellow", "Gray", "Magenta",
"Red", "Blue", "White", "Black", "Other color..."]
self.strandColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListStrand,
colorNames = colorNamesStrand,
label = "Strand:",
color = cyan,
setAsDefault = True)
self.coilColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Coil:",
color = orange,
setAsDefault = True)
def updateProteinDisplayStyleWidgets( self ):
"""
Updates all the Protein Display style widgets based on the current pref keys
values
"""
self.proteinStyleComboBox.setCurrentIndex(env.prefs[proteinStyle_prefs_key])
self.splineDoubleSpinBox.setValue(env.prefs[proteinStyleQuality_prefs_key])
if env.prefs[proteinStyleSmooth_prefs_key] == True:
self.smoothingCheckBox.setCheckState(Qt.Checked)
else:
self.smoothingCheckBox.setCheckState(Qt.Unchecked)
self.scaleComboBox.setCurrentIndex(env.prefs[proteinStyleScaling_prefs_key])
self.scaleFactorDoubleSpinBox.setValue(env.prefs[proteinStyleScaleFactor_prefs_key])
self.proteinComponentComboBox.setCurrentIndex(env.prefs[proteinStyleColors_prefs_key])
self.customColorComboBox.setColor(env.prefs[proteinStyleCustomColor_prefs_key])
self.proteinAuxComponentComboBox.setCurrentIndex(env.prefs[proteinStyleAuxColors_prefs_key])
self.auxColorComboBox.setColor(env.prefs[proteinStyleAuxCustomColor_prefs_key])
#if env.prefs[proteinStyleColorsDiscrete_prefs_key] == True:
# self.discColorCheckBox.setCheckState(Qt.Checked)
#else:
# self.discColorCheckBox.setCheckState(Qt.Unchecked)
self.helixColorComboBox.setColor(env.prefs[proteinStyleHelixColor_prefs_key])
self.strandColorComboBox.setColor(env.prefs[proteinStyleStrandColor_prefs_key])
self.coilColorComboBox.setColor(env.prefs[proteinStyleCoilColor_prefs_key])
return
def applyFavorite(self):
"""
Apply a favorite to the current display chosen in the favorites combo box
"""
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateProteinDisplayStyleWidgets()
return
def addFavorite(self):
"""
create and add favorite to favorites directory and favorites combo box
in PM
@note: Rules and other info:
- The new favorite is defined by the current Protein display style
settings.
- The user is prompted to type in a name for the new
favorite.
- The Protein display style settings are written to a file in a special
directory on the disk
(i.e. $HOME/Nanorex/Favorites/ProteinDisplayStyle/$FAV_NAME.txt).
- The name of the new favorite is added to the list of favorites in
the combobox, which becomes the current option.
Existence of a favorite with the same name is checked in the above
mentioned location and if a duplicate exists, then the user can either
overwrite and provide a new name.
"""
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Delete favorite file from the favorites directory
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Save favorite file in a user chosen location
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir = None):
"""
Set dir as current working diretcory
@param dir: dirname
@type dir: str
"""
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
return
def _setWorkingDirectoryInPrefsDB(self, workdir = None):
"""
Set workdir as current working diretcory in prefDB
@param workdir: dirname
@type workdir: str
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message( redmsg(msg))
return
def loadFavorite(self):
"""
Load a favorite file
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile=loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateProteinDisplayStyleWidgets()
return
def _addWhatsThisText( self ):
"""
Add what's this text for this PM
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
"""
Add tool tip text to all widgets.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
ToolTip_EditProteinDisplayStyle_PropertyManager(self)
class StereoProperties_PropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The StereoProperties_PropertyManager class provides a Property Manager
for the Stereo View command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Stereo View"
pmName = title
iconPath = "ui/actions/View/Stereo_View.png"
def __init__( self, parentCommand ):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the Stereo View settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.stereoEnabledCheckBox,
SIGNAL("toggled(bool)"),
self._enableStereo )
change_connect( self.stereoModeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._stereoModeComboBoxChanged )
change_connect(self.stereoSeparationSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeSeparationSliderChanged )
change_connect(self.stereoAngleSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeAngleSliderChanged )
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
PM_Dialog.show(self)
# self.updateDnaDisplayStyleWidgets()
self.connect_or_disconnect_signals(isConnect = True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Settings")
self._loadGroupBox1( self._pmGroupBox1 )
#@ self._pmGroupBox1.hide()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = ['Relaxed view',
'Cross-eyed view',
'Red/blue anaglyphs',
'Red/cyan anaglyphs',
'Red/green anaglyphs']
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(env.prefs[stereoViewMode_prefs_key]-1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def _enableStereo(self, enabled):
"""
Enable stereo view.
"""
if self.o:
self.o.stereo_enabled = enabled
# switch to perspective mode
if enabled:
# store current projection mode
self.o.last_ortho = self.o.ortho
if self.o.ortho is not 0:
# dont use glpane.setViewProjection
# because we don't want to modify
# default projection setting
self.o.ortho = 0
else:
# restore default mode
if hasattr(self.o, "last_ortho"):
projection = self.o.last_ortho
if self.o.ortho != projection:
self.o.ortho = projection
self._updateWidgets()
self.o.gl_update()
def _stereoModeComboBoxChanged(self, mode):
"""
Change stereo mode.
"""
env.prefs[stereoViewMode_prefs_key] = mode + 1
self._updateSeparationSlider()
if self.o:
self.o.gl_update()
def _stereoModeSeparationSliderChanged(self, value):
"""
Change stereo view separation.
"""
env.prefs[stereoViewSeparation_prefs_key] = value
if self.o:
self.o.gl_update()
def _stereoModeAngleSliderChanged(self, value):
"""
Change stereo view angle.
"""
env.prefs[stereoViewAngle_prefs_key] = value
if self.o:
self.o.gl_update()
def _updateSeparationSlider(self):
if self.stereoModeComboBox.currentIndex() >= 2:
# for anaglyphs disable the separation slider
self.stereoSeparationSlider.setEnabled(False)
else:
# otherwise, enable the separation slider
self.stereoSeparationSlider.setEnabled(True)
def _updateWidgets(self):
if self.stereoEnabledCheckBox.isChecked():
self.stereoModeComboBox.setEnabled(True)
self.stereoSeparationSlider.setEnabled(True)
self.stereoAngleSlider.setEnabled(True)
self._updateSeparationSlider()
else:
self.stereoModeComboBox.setEnabled(False)
self.stereoSeparationSlider.setEnabled(False)
self.stereoAngleSlider.setEnabled(False)
class StereoProperties_PropertyManager(Command_PropertyManager):
"""
The StereoProperties_PropertyManager class provides a Property Manager
for the Stereo View command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Stereo View"
pmName = title
iconPath = "ui/actions/View/Stereo_View.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the Stereo View settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.stereoEnabledCheckBox, SIGNAL("toggled(bool)"),
self._enableStereo)
change_connect(self.stereoModeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._stereoModeComboBoxChanged)
change_connect(self.stereoSeparationSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeSeparationSliderChanged)
change_connect(self.stereoAngleSlider, SIGNAL("valueChanged(int)"),
self._stereoModeAngleSliderChanged)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Settings")
self._loadGroupBox1(self._pmGroupBox1)
#@ self._pmGroupBox1.hide()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = [
'Relaxed view', 'Cross-eyed view', 'Red/blue anaglyphs',
'Red/cyan anaglyphs', 'Red/green anaglyphs'
]
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(
env.prefs[stereoViewMode_prefs_key] - 1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(
env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _addWhatsThisText(self):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def _enableStereo(self, enabled):
"""
Enable stereo view.
"""
glpane = self.o
if glpane:
glpane.set_stereo_enabled(enabled)
# switch to perspective mode
if enabled:
# store current projection mode
glpane.__StereoProperties_last_ortho = glpane.ortho
if glpane.ortho:
# dont use glpane.setViewProjection
# because we don't want to modify
# default projection setting
glpane.ortho = 0
else:
# restore default mode
if hasattr(glpane, "__StereoProperties_last_ortho"):
projection = glpane.__StereoProperties_last_ortho
if glpane.ortho != projection:
glpane.ortho = projection
self._updateWidgets()
glpane.gl_update()
def _stereoModeComboBoxChanged(self, mode):
"""
Change stereo mode.
@param mode: stereo mode (0=relaxed, 1=cross-eyed, 2=red/blue,
3=red/cyan, 4=red/green)
@type value: int
"""
env.prefs[stereoViewMode_prefs_key] = mode + 1
self._updateSeparationSlider()
def _stereoModeSeparationSliderChanged(self, value):
"""
Change stereo view separation.
@param value: separation (0..300)
@type value: int
"""
env.prefs[stereoViewSeparation_prefs_key] = value
def _stereoModeAngleSliderChanged(self, value):
"""
Change stereo view angle.
@param value: stereo angle (0..100)
@type value: int
"""
env.prefs[stereoViewAngle_prefs_key] = value
def _updateSeparationSlider(self):
"""
Update the separation slider widget.
"""
if self.stereoModeComboBox.currentIndex() >= 2:
# for anaglyphs disable the separation slider
self.stereoSeparationSlider.setEnabled(False)
else:
# otherwise, enable the separation slider
self.stereoSeparationSlider.setEnabled(True)
def _updateWidgets(self):
"""
Update stereo PM widgets.
"""
if self.stereoEnabledCheckBox.isChecked():
self.stereoModeComboBox.setEnabled(True)
self.stereoSeparationSlider.setEnabled(True)
self.stereoAngleSlider.setEnabled(True)
self._updateSeparationSlider()
else:
self.stereoModeComboBox.setEnabled(False)
self.stereoSeparationSlider.setEnabled(False)
self.stereoAngleSlider.setEnabled(False)
class EditProtein_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Edit Protein} command on the Build Protein command toolbar.
The selected peptide/protein is displayed in the protein reduced display
style. The user can select individual rotamers and edit their chi angles.
This is useful for certain types of protein design protocols using a
3rd party program like Rosetta.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Protein Properties"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/EditProtein.png"
current_protein = None # The currently selected peptide.
previous_protein = None # The last peptide selected.
current_aa = None # The current amino acid.
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect = True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nameLineEdit,
SIGNAL("editingFinished()"),
self._nameChanged)
change_connect(self.currentResidueComboBox,
SIGNAL("activated(int)"),
self.setCurrentAminoAcid)
change_connect(self.prevButton,
SIGNAL("clicked()"),
self._expandPreviousRotamer)
change_connect(self.nextButton,
SIGNAL("clicked()"),
self._expandNextRotamer)
change_connect(self.recenterViewCheckBox,
SIGNAL("toggled(bool)"),
self._centerViewToggled)
change_connect(self.showAllResiduesCheckBox,
SIGNAL("toggled(bool)"),
self._showAllResidues)
# Rotamer control widgets.
change_connect(self.chi1Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi1)
change_connect(self.chi2Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi2)
change_connect(self.chi3Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi3)
# Chi4 dial is hidden.
change_connect(self.chi4Dial,
SIGNAL("valueChanged(double)"),
self._rotateChi4)
return
#==
def _nameChanged(self):
"""
Slot for "Name" field.
@TODO: Include a validator for the name field.
"""
if not self.current_protein:
return
_name = str(self.nameLineEdit.text())
if not _name: # Minimal test. Need to implement a validator.
if self.current_protein:
self.nameLineEdit.setText(self.current_protein.name)
return
self.current_protein.name = _name
msg = "Editing structure <b>%s</b>." % _name
self.updateMessage(msg)
return
def update_name_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.nameLineEdit.setText("")
else:
self.nameLineEdit.setText(self.current_protein.name)
return
def update_length_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.lengthLineEdit.setText("")
else:
length_str = "%d residues" % self.current_protein.protein.count_amino_acids()
self.lengthLineEdit.setText(length_str)
return
def update_residue_combobox(self):
"""
Update the residue combobox with the amino acid sequence of the
currently selected protein. If there is no currently selected protein,
clear the combobox list.
"""
self.currentResidueComboBox.clear()
if not self.current_protein:
return
aa_list = self.current_protein.protein.get_amino_acid_id_list()
for j in range(len(aa_list)):
aa_id, residue_id = aa_list[j].strip().split(":")
self.currentResidueComboBox.addItem(residue_id)
pass
self.setCurrentAminoAcid()
return
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
self.sequenceEditor.hide()
env.history.statusbar_msg("")
if self.current_protein:
self.current_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = None
# Update name in case the it was changed by the user.
self.current_protein.name = str(self.nameLineEdit.text())
_superclass.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
_superclass.show(self)
env.history.statusbar_msg("")
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Parameters")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Rotamer Controls")
self._loadGroupBox2( self._pmGroupBox2 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Name:")
self.lengthLineEdit = PM_LineEdit( pmGroupBox,
label = "Length:")
self.lengthLineEdit.setEnabled(False)
self.currentResidueComboBox = PM_ComboBox( pmGroupBox,
label = "Current residue:",
setAsDefault = False)
BUTTON_LIST = [
("QToolButton", 1, "Previous residue",
"ui/actions/Properties Manager/Previous.png",
"", "Previous residue", 0 ),
( "QToolButton", 2, "Next residue",
"ui/actions/Properties Manager/Next.png",
"", "Next residue", 1 )
]
self.prevNextButtonRow = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
label = 'Previous / Next:',
isAutoRaise = True,
isCheckable = False
)
self.prevButton = self.prevNextButtonRow.getButtonById(1)
self.nextButton = self.prevNextButtonRow.getButtonById(2)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Center view on current residue",
setAsDefault = True,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
self.lockEditedCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Lock edited rotamers",
setAsDefault = True,
state = Qt.Checked,
widgetColumn = 0,
spanWidth = True)
self.showAllResiduesCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show all residues",
setAsDefault = False,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1Dial = \
PM_Dial( pmGroupBox,
label = "Chi1:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
wrapping = True,
suffix = "deg",
spanWidth = False)
self.chi1Dial.setEnabled(False)
self.chi2Dial = \
PM_Dial( pmGroupBox,
label = "Chi2:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi2Dial.setEnabled(False)
self.chi3Dial = \
PM_Dial( pmGroupBox,
label = "Chi3:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi3Dial.setEnabled(False)
self.chi4Dial = \
PM_Dial( pmGroupBox,
label = "Chi4:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi4Dial.setEnabled(False)
self.chi4Dial.hide()
return
def _addWhatsThisText( self ):
pass
def _addToolTipText(self):
pass
def _expandNextRotamer(self):
"""
Displays the next rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_forward()
self.setCurrentAminoAcid()
return
def _expandPreviousRotamer(self):
"""
Displays the previous rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_backward()
self.setCurrentAminoAcid()
return
def _centerViewToggled(self, checked):
"""
Slot for "Center view on current residue" checkbox.
"""
if checked:
self.display_and_recenter()
return
def _showAllResidues(self, show):
"""
Slot for "Show all residues" checkbox.
"""
if not self.current_protein:
return
print "Show =",show
if show:
self._expandAllRotamers()
else:
self._collapseAllRotamers()
return
def _collapseAllRotamers(self):
"""
Hides all the rotamers (except the current rotamer).
"""
self.display_and_recenter()
return
def _expandAllRotamers(self):
"""
Displays all the rotamers.
"""
if not self.current_protein:
return
self.current_protein.protein.expand_all_rotamers()
self.win.glpane.gl_update()
return
def display_and_recenter(self):
"""
Recenter the view on the current amino acid selected in the
residue combobox (or the sequence editor). All rotamers
except the current rotamer are collapsed (hidden).
"""
if not self.current_protein:
return
# Uncheck the "Show all residues" checkbox since they are being collapsed.
# Disconnect signals so that showAllResiduesCheckBox won't general a signal.
self.connect_or_disconnect_signals(isConnect = False)
self.showAllResiduesCheckBox.setChecked(False)
self.connect_or_disconnect_signals(isConnect = True)
self.current_protein.protein.collapse_all_rotamers()
# Display the current amino acid and center it in the view if the
# "Center view on current residue" is checked.
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self._update_chi_angles(self.current_aa)
if self.recenterViewCheckBox.isChecked():
ca_atom = self.current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
return
def _update_chi_angles(self, aa):
"""
"""
angle = aa.get_chi_angle(0)
if angle:
self.chi1Dial.setEnabled(True)
self.chi1Dial.setValue(angle)
else:
self.chi1Dial.setEnabled(False)
self.chi1Dial.setValue(0.0)
angle = aa.get_chi_angle(1)
if angle:
self.chi2Dial.setEnabled(True)
self.chi2Dial.setValue(angle)
else:
self.chi2Dial.setEnabled(False)
self.chi2Dial.setValue(0.0)
angle = aa.get_chi_angle(2)
if angle:
self.chi3Dial.setEnabled(True)
self.chi3Dial.setValue(angle)
else:
self.chi3Dial.setEnabled(False)
self.chi3Dial.setValue(0.0)
angle = aa.get_chi_angle(3)
if angle:
self.chi4Dial.setEnabled(True)
self.chi4Dial.setValue(angle)
else:
self.chi4Dial.setEnabled(False)
self.chi4Dial.setValue(0.0)
return
def setCurrentAminoAcid(self, aa_index = -1):
"""
Set the current amino acid to I{aa_index} and update the
"Current residue" combobox and the sequence editor.
@param aa_index: the amino acid index. If negative, update the PM and
sequence editor based on the current aa_index.
@type aa_index: int
@note: This is the slot for the "Current residue" combobox.
"""
if not self.current_protein:
return
if aa_index < 0:
aa_index = self.current_protein.protein.get_current_amino_acid_index()
if 0: # Debugging statement
print"setCurrentAminoAcid(): aa_index=", aa_index
self.currentResidueComboBox.setCurrentIndex(aa_index)
self.current_protein.protein.set_current_amino_acid_index(aa_index)
self.current_aa = self.current_protein.protein.get_current_amino_acid()
self.display_and_recenter()
self.sequenceEditor.setCursorPosition(aa_index)
return
def _rotateChiAngle(self, chi, angle):
"""
Rotate around chi1 angle.
"""
if not self.current_protein:
return
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self.current_aa.set_chi_angle(chi, angle)
self.win.glpane.gl_update()
return
def _rotateChi1(self, angle):
"""
Slot for Chi1 dial.
"""
self._rotateChiAngle(0, angle)
self.chi1Dial.updateValueLabel()
return
def _rotateChi2(self, angle):
"""
Slot for Chi2 dial.
"""
self._rotateChiAngle(1, angle)
self.chi2Dial.updateValueLabel()
return
def _rotateChi3(self, angle):
"""
Slot for Chi3 dial.
"""
self._rotateChiAngle(2, angle)
self.chi3Dial.updateValueLabel()
return
def _rotateChi4(self, angle):
"""
Slot for Chi4 dial.
@note: this dial is currently hidden and unused.
"""
self._rotateChiAngle(3, angle)
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
if self.current_protein is self.previous_protein:
if 0:
print "Edit Protein: _update_UI_do_updates() - DO NOTHING."
return
# It is common that the user will unselect the current protein.
# If so, set current_protein to previous_protein so that it
# (the previously selected protein) remains the current protein
# in the PM and sequence editor.
if not self.current_protein:
self.current_protein = self.previous_protein
return
# Update all PM widgets that need to be since something has changed.
if 0:
print "Edit Protein: _update_UI_do_updates() - UPDATING THE PMGR."
self.update_name_field()
self.update_length_field()
self.sequenceEditor.updateSequence(proteinChunk = self.current_protein)
self.update_residue_combobox()
# NOTE: Changing the display style of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor and restore
# before returning.
if self.previous_protein:
self.previous_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = self.current_protein
if self.current_protein:
self.previous_protein_display_style = self.current_protein.getDisplayStyle()
self.current_protein.setDisplayStyle(diPROTEIN)
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
else:
msg = "Select a single structure to edit."
self.updateMessage(msg)
return
class LightingScheme_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The LightingScheme_PropertyManager class provides a Property Manager
for changing light properties as well as material properties.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Lighting Scheme"
pmName = title
iconPath = "ui/actions/View/LightingScheme.png"
def __init__(self, parentCommand):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit the lighting scheme for NE1. Includes turning lights on and off, "\
"changing light colors, changing the position of lights as well as,"\
"changing the ambient, diffuse, and specular properites."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect(self.applyFavoriteButton, SIGNAL("clicked()"),
self.applyFavorite)
change_connect(self.addFavoriteButton, SIGNAL("clicked()"),
self.addFavorite)
change_connect(self.deleteFavoriteButton, SIGNAL("clicked()"),
self.deleteFavorite)
change_connect(self.saveFavoriteButton, SIGNAL("clicked()"),
self.saveFavorite)
change_connect(self.loadFavoriteButton, SIGNAL("clicked()"),
self.loadFavorite)
# Directional Lighting Properties
change_connect(self.ambientDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.lightColorComboBox, SIGNAL("editingFinished()"),
self.changeLightColor)
change_connect(self.enableLightCheckBox, SIGNAL("toggled(bool)"),
self.toggle_light)
change_connect(self.lightComboBox, SIGNAL("activated(int)"),
self.change_active_light)
change_connect(self.diffuseDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.specularDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.xDoubleSpinBox, SIGNAL("editingFinished()"),
self.save_lighting)
change_connect(self.yDoubleSpinBox, SIGNAL("editingFinished()"),
self.save_lighting)
change_connect(self.zDoubleSpinBox, SIGNAL("editingFinished()"),
self.save_lighting)
# Material Specular Properties
change_connect(self.brightnessDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.change_material_brightness)
change_connect(self.finishDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.change_material_finish)
change_connect(self.enableMaterialPropertiesComboBox,
SIGNAL("toggled(bool)"),
self.toggle_material_specularity)
change_connect(self.shininessDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.change_material_shininess)
self._setup_material_group()
return
def _updatePage_Lighting(self, lights=None): #mark 051124
"""
Setup widgets to initial (default or defined) values on the Lighting page.
"""
if not lights:
self.lights = self.original_lights = self.win.glpane.getLighting()
else:
self.lights = lights
light_num = self.lightComboBox.currentIndex()
# Move lc_prefs_keys upstairs. Mark.
lc_prefs_keys = [
light1Color_prefs_key, light2Color_prefs_key, light3Color_prefs_key
]
self.current_light_key = lc_prefs_keys[
light_num] # Get prefs key for current light color.
self.lightColorComboBox.setColor(env.prefs[self.current_light_key])
self.light_color = env.prefs[self.current_light_key]
# These sliders generate signals whenever their 'setValue()' slot is called (below).
# This creates problems (bugs) for us, so we disconnect them temporarily.
self.disconnect(self.ambientDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
self.disconnect(self.diffuseDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
self.disconnect(self.specularDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
# self.lights[light_num][0] contains 'color' attribute.
# We already have it (self.light_color) from the prefs key (above).
a = self.lights[light_num][1] # ambient intensity
d = self.lights[light_num][2] # diffuse intensity
s = self.lights[light_num][3] # specular intensity
g = self.lights[light_num][4] # xpos
h = self.lights[light_num][5] # ypos
k = self.lights[light_num][6] # zpos
self.ambientDoubleSpinBox.setValue(a) # generates signal
self.diffuseDoubleSpinBox.setValue(d) # generates signal
self.specularDoubleSpinBox.setValue(s) # generates signal
self.xDoubleSpinBox.setValue(g) # generates signal
self.yDoubleSpinBox.setValue(h) # generates signal
self.zDoubleSpinBox.setValue(k) # generates signal
self.enableLightCheckBox.setChecked(self.lights[light_num][7])
# Reconnect the slots to the light sliders.
self.connect(self.ambientDoubleSpinBox, SIGNAL("valueChanged(double)"),
self.change_lighting)
self.connect(self.diffuseDoubleSpinBox, SIGNAL("valueChanged(double)"),
self.change_lighting)
self.connect(self.specularDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.change_lighting)
self.update_light_combobox_items()
self.save_lighting()
self._setup_material_group()
return
def _setup_material_group(self, reset=False):
"""
Setup Material Specularity widgets to initial (default or defined) values on the Lighting page.
If reset = False, widgets are reset from the prefs db.
If reset = True, widgets are reset from their previous values.
"""
if reset:
self.material_specularity = self.original_material_specularity
self.whiteness = self.original_whiteness
self.shininess = self.original_shininess
self.brightness = self.original_brightness
else:
self.material_specularity = self.original_material_specularity = \
env.prefs[material_specular_highlights_prefs_key]
self.whiteness = self.original_whiteness = \
env.prefs[material_specular_finish_prefs_key]
self.shininess = self.original_shininess = \
env.prefs[material_specular_shininess_prefs_key]
self.brightness = self.original_brightness= \
env.prefs[material_specular_brightness_prefs_key]
# Enable/disable material specularity properites.
self.enableMaterialPropertiesComboBox.setChecked(
self.material_specularity)
# For whiteness, the stored range is 0.0 (Plastic) to 1.0 (Metal).
self.finishDoubleSpinBox.setValue(self.whiteness) # generates signal
# For shininess, the range is 15 (low) to 60 (high). Mark. 051129.
self.shininessDoubleSpinBox.setValue(
self.shininess) # generates signal
# For brightness, the range is 0.0 (low) to 1.0 (high). Mark. 051203.
self.brightnessDoubleSpinBox.setValue(
self.brightness) # generates signal
return
def toggle_material_specularity(self, val):
"""
This is the slot for the Material Specularity Enabled checkbox.
"""
env.prefs[material_specular_highlights_prefs_key] = val
def change_material_finish(self, finish):
"""
This is the slot for the Material Finish spin box.
'finish' is between 0.0 and 1.0.
Saves finish parameter to pref db.
"""
# For whiteness, the stored range is 0.0 (Metal) to 1.0 (Plastic).
env.prefs[material_specular_finish_prefs_key] = finish
def change_material_shininess(self, shininess):
"""
This is the slot for the Material Shininess spin box.
'shininess' is between 15 (low) and 60 (high).
"""
env.prefs[material_specular_shininess_prefs_key] = shininess
def change_material_brightness(self, brightness):
"""
This is the slot for the Material Brightness sping box.
'brightness' is between 0.0 (low) and 1.0 (high).
"""
env.prefs[material_specular_brightness_prefs_key] = brightness
def toggle_light(self, on):
"""
Slot for light 'On' checkbox.
It updates the current item in the light combobox with '(On)' or
'(Off)' label.
"""
if on:
txt = "%d (On)" % (self.lightComboBox.currentIndex() + 1)
else:
txt = "%d (Off)" % (self.lightComboBox.currentIndex() + 1)
self.lightComboBox.setItemText(self.lightComboBox.currentIndex(), txt)
self.save_lighting()
def change_lighting(self, specularityValueJunk=None):
"""
Updates win.glpane lighting using the current lighting parameters from
the light checkboxes and sliders. This is also the slot for the light
spin boxes.
@param specularityValueJunk: This value from the spin box is not used
We are interested in valueChanged signal
only
@type specularityValueJunk = int or None
"""
light_num = self.lightComboBox.currentIndex()
light1, light2, light3 = self.win.glpane.getLighting()
a = self.ambientDoubleSpinBox.value()
d = self.diffuseDoubleSpinBox.value()
s = self.specularDoubleSpinBox.value()
g = self.xDoubleSpinBox.value()
h = self.yDoubleSpinBox.value()
k = self.zDoubleSpinBox.value()
new_light = [ self.light_color, a, d, s, g, h, k,\
self.enableLightCheckBox.isChecked()]
# This is a kludge. I'm certain there is a more elegant way. Mark 051204.
if light_num == 0:
self.win.glpane.setLighting([new_light, light2, light3])
elif light_num == 1:
self.win.glpane.setLighting([light1, new_light, light3])
elif light_num == 2:
self.win.glpane.setLighting([light1, light2, new_light])
else:
print "Unsupported light # ", light_num, ". No lighting change made."
def change_active_light(self, currentIndexJunk=None):
"""
Slot for the Light number combobox. This changes the current light.
@param currentIndexJunk: This index value from the combobox is not used
We are interested in 'activated' signal only
@type currentIndexJunk = int or None
"""
self._updatePage_Lighting()
def reset_lighting(self):
"""
Slot for Reset button.
"""
# This has issues.
# I intend to remove the Reset button for A7. Confirm with Bruce. Mark 051204.
self._setup_material_group(reset=True)
self._updatePage_Lighting(self.original_lights)
self.win.glpane.saveLighting()
def save_lighting(self):
"""
Saves lighting parameters (but not material specularity parameters)
to pref db. This is also the slot for light sliders (only when
released).
"""
self.change_lighting()
self.win.glpane.saveLighting()
def restore_default_lighting(self):
"""
Slot for Restore Defaults button.
"""
self.win.glpane.restoreDefaultLighting()
# Restore defaults for the Material Specularity properties
env.prefs.restore_defaults([
material_specular_highlights_prefs_key,
material_specular_shininess_prefs_key,
material_specular_finish_prefs_key,
material_specular_brightness_prefs_key, #bruce 051203 bugfix
])
self._updatePage_Lighting()
self.save_lighting()
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect=True)
self._updateAllWidgets()
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Favorites")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Directional Lights")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Material Properties")
self._loadGroupBox3(self._pmGroupBox3)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/LightingScheme')
for file in os.listdir(_dir):
fullname = os.path.join(_dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch(file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file) - 4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyLightingSchemeFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.lightComboBox = \
PM_ComboBox( pmGroupBox,
choices = ["1", "2", "3"],
label = "Light:")
self.enableLightCheckBox = \
PM_CheckBox( pmGroupBox, text = "On" )
self.lightColorComboBox = \
PM_ColorComboBox(pmGroupBox)
self.ambientDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Ambient:")
self.diffuseDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Diffuse:")
self.specularDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Specular:")
self.positionGroupBox = \
PM_GroupBox( pmGroupBox,
title = "Position:")
self.xDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "X:")
self.yDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "Y:")
self.zDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "Z:")
return
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.enableMaterialPropertiesComboBox = \
PM_CheckBox( pmGroupBox, text = "On")
self.finishDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Finish:")
self.shininessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 60,
minimum = 15,
decimals = 2,
label = "Shininess:")
self.brightnessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Brightness:")
return
def _updateAllWidgets(self):
"""
Update all the PM widgets. This is typically called after applying
a favorite.
"""
self._updatePage_Lighting()
return
def update_light_combobox_items(self):
"""
Updates all light combobox items with '(On)' or '(Off)' label.
"""
for i in range(3):
if self.lights[i][7]:
txt = "%d (On)" % (i + 1)
else:
txt = "%d (Off)" % (i + 1)
self.lightComboBox.setItemText(i, txt)
return
def changeLightColor(self):
"""
Slot method for the ColorComboBox
"""
color = self.lightColorComboBox.getColor()
env.prefs[self.current_light_key] = color
self.light_color = env.prefs[self.current_light_key]
self.save_lighting()
return
def applyFavorite(self):
"""
Apply the lighting scheme settings stored in the current favorite
(selected in the combobox) to the current lighting scheme settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
#env.prefs.restore_defaults(lightingSchemePrefsList)
self.restore_default_lighting()
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self._updateAllWidgets()
self.win.glpane.gl_update()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current lighting scheme
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The lighting scheme settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/LightingScheme/$FAV_NAME.txt).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/LightingScheme/ directory
fname = getFavoritePathFromBasename(name)
if os.path.exists(fname):
#favorite file already exists!
_ext = ".txt"
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + _ext +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Cancel",
"",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeLightingSchemeToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(
name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message(
"Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeLightingSchemeToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text
) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile = getFavoritePathFromBasename(currentText)
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
saveFavoriteFile(str(fn), favfilepath)
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self, "Choose a file to load",
directory, formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
canLoadFile = loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName) - 4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Rename",
"&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeLightingSchemeToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(lightingSchemePrefsList)
self.win.glpane.gl_update()
env.history.message(
"Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.win.glpane.gl_update()
return
#def _addWhatsThisText( self ):
#"""
#What's This text for widgets in the Lighting Scheme Property Manager.
#"""
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_LightingScheme_PropertyManager
#WhatsThis_LightingScheme_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Lighting Scheme Property Manager.
"""
#modify this for lighting schemes
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_LightingScheme_PropertyManager
ToolTip_LightingScheme_PropertyManager(self)
class StereoProperties_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The StereoProperties_PropertyManager class provides a Property Manager
for the Stereo View command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Stereo View"
pmName = title
iconPath = "ui/actions/View/Stereo_View.png"
def __init__(self, parentCommand):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the Stereo View settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.stereoEnabledCheckBox, SIGNAL("toggled(bool)"),
self._enableStereo)
change_connect(self.stereoModeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._stereoModeComboBoxChanged)
change_connect(self.stereoSeparationSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeSeparationSliderChanged)
change_connect(self.stereoAngleSlider, SIGNAL("valueChanged(int)"),
self._stereoModeAngleSliderChanged)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
PM_Dialog.show(self)
# self.updateDnaDisplayStyleWidgets()
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Settings")
self._loadGroupBox1(self._pmGroupBox1)
#@ self._pmGroupBox1.hide()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = [
'Relaxed view', 'Cross-eyed view', 'Red/blue anaglyphs',
'Red/cyan anaglyphs', 'Red/green anaglyphs'
]
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(
env.prefs[stereoViewMode_prefs_key] - 1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(
env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _addWhatsThisText(self):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def _enableStereo(self, enabled):
"""
Enable stereo view.
"""
if self.o:
self.o.stereo_enabled = enabled
# switch to perspective mode
if enabled:
# store current projection mode
self.o.last_ortho = self.o.ortho
if self.o.ortho is not 0:
# dont use glpane.setViewProjection
# because we don't want to modify
# default projection setting
self.o.ortho = 0
else:
# restore default mode
if hasattr(self.o, "last_ortho"):
projection = self.o.last_ortho
if self.o.ortho != projection:
self.o.ortho = projection
self._updateWidgets()
self.o.gl_update()
def _stereoModeComboBoxChanged(self, mode):
"""
Change stereo mode.
"""
env.prefs[stereoViewMode_prefs_key] = mode + 1
self._updateSeparationSlider()
if self.o:
self.o.gl_update()
def _stereoModeSeparationSliderChanged(self, value):
"""
Change stereo view separation.
"""
env.prefs[stereoViewSeparation_prefs_key] = value
if self.o:
self.o.gl_update()
def _stereoModeAngleSliderChanged(self, value):
"""
Change stereo view angle.
"""
env.prefs[stereoViewAngle_prefs_key] = value
if self.o:
self.o.gl_update()
def _updateSeparationSlider(self):
if self.stereoModeComboBox.currentIndex() >= 2:
# for anaglyphs disable the separation slider
self.stereoSeparationSlider.setEnabled(False)
else:
# otherwise, enable the separation slider
self.stereoSeparationSlider.setEnabled(True)
def _updateWidgets(self):
if self.stereoEnabledCheckBox.isChecked():
self.stereoModeComboBox.setEnabled(True)
self.stereoSeparationSlider.setEnabled(True)
self.stereoAngleSlider.setEnabled(True)
self._updateSeparationSlider()
else:
self.stereoModeComboBox.setEnabled(False)
self.stereoSeparationSlider.setEnabled(False)
self.stereoAngleSlider.setEnabled(False)
class EditRotamers_PropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit Rotamers"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__( self, parentCommand ):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit protein rotamers."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect = True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nextAAPushButton,
SIGNAL("clicked()"),
self._expandNextRotamer)
change_connect(self.previousAAPushButton,
SIGNAL("clicked()"),
self._expandPreviousRotamer)
change_connect(self.expandAllPushButton,
SIGNAL("clicked()"),
self._expandAllRotamers)
change_connect(self.collapseAllPushButton,
SIGNAL("clicked()"),
self._collapseAllRotamers)
self.connect( self.aminoAcidsComboBox,
SIGNAL("currentIndexChanged(int)"),
self._aminoAcidChanged)
#Protein Display methods
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self.connect_or_disconnect_signals(isConnect = True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Position")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Rotamer")
self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
aa_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
aa_list = mol.protein.get_amino_acid_id_list()
break
self.aminoAcidsComboBox = PM_ComboBox( pmGroupBox,
label = "Residue:",
choices = aa_list,
setAsDefault = False)
self.previousAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Previous AA",
setAsDefault = True)
self.nextAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Next AA",
setAsDefault = True)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.expandAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Expand All",
setAsDefault = True)
self.collapseAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Collapse All",
setAsDefault = True)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi1 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi2SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi2 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi3SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi3 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
def _addWhatsThisText( self ):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditRotamers_PropertyManager
#WhatsThis_EditRotamers_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def _expandNextRotamer(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.traverse_forward()
self._display_and_recenter()
self._updateAminoAcidInfo(
chunk.protein.get_current_amino_acid_index())
return
def _expandPreviousRotamer(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.traverse_backward()
self._display_and_recenter()
self._updateAminoAcidInfo(
chunk.protein.get_current_amino_acid_index())
return
def _collapseAllRotamers(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.collapse_all_rotamers()
self.win.glpane.gl_update()
return
def _expandAllRotamers(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.expand_all_rotamers()
self.win.glpane.gl_update()
return
def _display_and_recenter(self):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.collapse_all_rotamers()
current_aa = chunk.protein.get_current_amino_acid()
if current_aa:
chunk.protein.expand_rotamer(current_aa)
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
#self.win.glpane.gl_update()
self.win.glpane.gl_update()
def _updateAminoAcidInfo(self, index):
"""
"""
self.aminoAcidsComboBox.setCurrentIndex(index)
def _aminoAcidChanged(self, index):
"""
"""
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.set_current_amino_acid_index(index)
self._display_and_recenter()
class LightingScheme_PropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The LightingScheme_PropertyManager class provides a Property Manager
for changing light properties as well as material properties.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Lighting Scheme"
pmName = title
iconPath = "ui/actions/View/LightingScheme.png"
def __init__( self, parentCommand ):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit the lighting scheme for NE1. Includes turning lights on and off, "\
"changing light colors, changing the position of lights as well as,"\
"changing the ambient, diffuse, and specular properites."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
# Directional Lighting Properties
change_connect(self.ambientDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.lightColorComboBox, SIGNAL("editingFinished()"), self.changeLightColor)
change_connect(self.enableLightCheckBox, SIGNAL("toggled(bool)"), self.toggle_light)
change_connect(self.lightComboBox, SIGNAL("activated(int)"), self.change_active_light)
change_connect(self.diffuseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.specularDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
change_connect(self.xDoubleSpinBox, SIGNAL("editingFinished()"), self.save_lighting)
change_connect(self.yDoubleSpinBox, SIGNAL("editingFinished()"), self.save_lighting)
change_connect(self.zDoubleSpinBox, SIGNAL("editingFinished()"), self.save_lighting)
# Material Specular Properties
change_connect(self.brightnessDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_material_brightness)
change_connect(self.finishDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_material_finish)
change_connect(self.enableMaterialPropertiesComboBox, SIGNAL("toggled(bool)"), self.toggle_material_specularity)
change_connect(self.shininessDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_material_shininess)
self._setup_material_group()
return
def _updatePage_Lighting(self, lights = None): #mark 051124
"""
Setup widgets to initial (default or defined) values on the Lighting page.
"""
if not lights:
self.lights = self.original_lights = self.win.glpane.getLighting()
else:
self.lights = lights
light_num = self.lightComboBox.currentIndex()
# Move lc_prefs_keys upstairs. Mark.
lc_prefs_keys = [light1Color_prefs_key, light2Color_prefs_key, light3Color_prefs_key]
self.current_light_key = lc_prefs_keys[light_num] # Get prefs key for current light color.
self.lightColorComboBox.setColor(env.prefs[self.current_light_key])
self.light_color = env.prefs[self.current_light_key]
# These sliders generate signals whenever their 'setValue()' slot is called (below).
# This creates problems (bugs) for us, so we disconnect them temporarily.
self.disconnect(self.ambientDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
self.disconnect(self.diffuseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
self.disconnect(self.specularDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
# self.lights[light_num][0] contains 'color' attribute.
# We already have it (self.light_color) from the prefs key (above).
a = self.lights[light_num][1] # ambient intensity
d = self.lights[light_num][2] # diffuse intensity
s = self.lights[light_num][3] # specular intensity
g = self.lights[light_num][4] # xpos
h = self.lights[light_num][5] # ypos
k = self.lights[light_num][6] # zpos
self.ambientDoubleSpinBox.setValue(a)# generates signal
self.diffuseDoubleSpinBox.setValue(d) # generates signal
self.specularDoubleSpinBox.setValue(s) # generates signal
self.xDoubleSpinBox.setValue(g) # generates signal
self.yDoubleSpinBox.setValue(h) # generates signal
self.zDoubleSpinBox.setValue(k) # generates signal
self.enableLightCheckBox.setChecked(self.lights[light_num][7])
# Reconnect the slots to the light sliders.
self.connect(self.ambientDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
self.connect(self.diffuseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
self.connect(self.specularDoubleSpinBox, SIGNAL("valueChanged(double)"), self.change_lighting)
self.update_light_combobox_items()
self.save_lighting()
self._setup_material_group()
return
def _setup_material_group(self, reset = False):
"""
Setup Material Specularity widgets to initial (default or defined) values on the Lighting page.
If reset = False, widgets are reset from the prefs db.
If reset = True, widgets are reset from their previous values.
"""
if reset:
self.material_specularity = self.original_material_specularity
self.whiteness = self.original_whiteness
self.shininess = self.original_shininess
self.brightness = self.original_brightness
else:
self.material_specularity = self.original_material_specularity = \
env.prefs[material_specular_highlights_prefs_key]
self.whiteness = self.original_whiteness = \
env.prefs[material_specular_finish_prefs_key]
self.shininess = self.original_shininess = \
env.prefs[material_specular_shininess_prefs_key]
self.brightness = self.original_brightness= \
env.prefs[material_specular_brightness_prefs_key]
# Enable/disable material specularity properites.
self.enableMaterialPropertiesComboBox.setChecked(self.material_specularity)
# For whiteness, the stored range is 0.0 (Plastic) to 1.0 (Metal).
self.finishDoubleSpinBox.setValue(self.whiteness) # generates signal
# For shininess, the range is 15 (low) to 60 (high). Mark. 051129.
self.shininessDoubleSpinBox.setValue(self.shininess) # generates signal
# For brightness, the range is 0.0 (low) to 1.0 (high). Mark. 051203.
self.brightnessDoubleSpinBox.setValue(self.brightness) # generates signal
return
def toggle_material_specularity(self, val):
"""
This is the slot for the Material Specularity Enabled checkbox.
"""
env.prefs[material_specular_highlights_prefs_key] = val
def change_material_finish(self, finish):
"""
This is the slot for the Material Finish spin box.
'finish' is between 0.0 and 1.0.
Saves finish parameter to pref db.
"""
# For whiteness, the stored range is 0.0 (Metal) to 1.0 (Plastic).
env.prefs[material_specular_finish_prefs_key] = finish
def change_material_shininess(self, shininess):
"""
This is the slot for the Material Shininess spin box.
'shininess' is between 15 (low) and 60 (high).
"""
env.prefs[material_specular_shininess_prefs_key] = shininess
def change_material_brightness(self, brightness):
"""
This is the slot for the Material Brightness sping box.
'brightness' is between 0.0 (low) and 1.0 (high).
"""
env.prefs[material_specular_brightness_prefs_key] = brightness
def toggle_light(self, on):
"""
Slot for light 'On' checkbox.
It updates the current item in the light combobox with '(On)' or
'(Off)' label.
"""
if on:
txt = "%d (On)" % (self.lightComboBox.currentIndex()+1)
else:
txt = "%d (Off)" % (self.lightComboBox.currentIndex()+1)
self.lightComboBox.setItemText(self.lightComboBox.currentIndex(),txt)
self.save_lighting()
def change_lighting(self, specularityValueJunk = None):
"""
Updates win.glpane lighting using the current lighting parameters from
the light checkboxes and sliders. This is also the slot for the light
spin boxes.
@param specularityValueJunk: This value from the spin box is not used
We are interested in valueChanged signal
only
@type specularityValueJunk = int or None
"""
light_num = self.lightComboBox.currentIndex()
light1, light2, light3 = self.win.glpane.getLighting()
a = self.ambientDoubleSpinBox.value()
d = self.diffuseDoubleSpinBox.value()
s = self.specularDoubleSpinBox.value()
g = self.xDoubleSpinBox.value()
h = self.yDoubleSpinBox.value()
k = self.zDoubleSpinBox.value()
new_light = [ self.light_color, a, d, s, g, h, k,\
self.enableLightCheckBox.isChecked()]
# This is a kludge. I'm certain there is a more elegant way. Mark 051204.
if light_num == 0:
self.win.glpane.setLighting([new_light, light2, light3])
elif light_num == 1:
self.win.glpane.setLighting([light1, new_light, light3])
elif light_num == 2:
self.win.glpane.setLighting([light1, light2, new_light])
else:
print "Unsupported light # ", light_num,". No lighting change made."
def change_active_light(self, currentIndexJunk = None):
"""
Slot for the Light number combobox. This changes the current light.
@param currentIndexJunk: This index value from the combobox is not used
We are interested in 'activated' signal only
@type currentIndexJunk = int or None
"""
self._updatePage_Lighting()
def reset_lighting(self):
"""
Slot for Reset button.
"""
# This has issues.
# I intend to remove the Reset button for A7. Confirm with Bruce. Mark 051204.
self._setup_material_group(reset = True)
self._updatePage_Lighting(self.original_lights)
self.win.glpane.saveLighting()
def save_lighting(self):
"""
Saves lighting parameters (but not material specularity parameters)
to pref db. This is also the slot for light sliders (only when
released).
"""
self.change_lighting()
self.win.glpane.saveLighting()
def restore_default_lighting(self):
"""
Slot for Restore Defaults button.
"""
self.win.glpane.restoreDefaultLighting()
# Restore defaults for the Material Specularity properties
env.prefs.restore_defaults([
material_specular_highlights_prefs_key,
material_specular_shininess_prefs_key,
material_specular_finish_prefs_key,
material_specular_brightness_prefs_key, #bruce 051203 bugfix
])
self._updatePage_Lighting()
self.save_lighting()
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect = True)
self._updateAllWidgets()
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Directional Lights")
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self,
title = "Material Properties")
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/LightingScheme')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyLightingSchemeFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.lightComboBox = \
PM_ComboBox( pmGroupBox,
choices = ["1", "2", "3"],
label = "Light:")
self.enableLightCheckBox = \
PM_CheckBox( pmGroupBox, text = "On" )
self.lightColorComboBox = \
PM_ColorComboBox(pmGroupBox)
self.ambientDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Ambient:")
self.diffuseDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Diffuse:")
self.specularDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Specular:")
self.positionGroupBox = \
PM_GroupBox( pmGroupBox,
title = "Position:")
self.xDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "X:")
self.yDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "Y:")
self.zDoubleSpinBox = \
PM_DoubleSpinBox(self.positionGroupBox,
maximum = 1000,
minimum = -1000,
decimals = 1,
singleStep = 10,
label = "Z:")
return
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.enableMaterialPropertiesComboBox = \
PM_CheckBox( pmGroupBox, text = "On")
self.finishDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Finish:")
self.shininessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 60,
minimum = 15,
decimals = 2,
label = "Shininess:")
self.brightnessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Brightness:")
return
def _updateAllWidgets(self):
"""
Update all the PM widgets. This is typically called after applying
a favorite.
"""
self._updatePage_Lighting()
return
def update_light_combobox_items(self):
"""
Updates all light combobox items with '(On)' or '(Off)' label.
"""
for i in range(3):
if self.lights[i][7]:
txt = "%d (On)" % (i+1)
else:
txt = "%d (Off)" % (i+1)
self.lightComboBox.setItemText(i, txt)
return
def changeLightColor(self):
"""
Slot method for the ColorComboBox
"""
color = self.lightColorComboBox.getColor()
env.prefs[self.current_light_key] = color
self.light_color = env.prefs[self.current_light_key]
self.save_lighting()
return
def applyFavorite(self):
"""
Apply the lighting scheme settings stored in the current favorite
(selected in the combobox) to the current lighting scheme settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
#env.prefs.restore_defaults(lightingSchemePrefsList)
self.restore_default_lighting()
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self._updateAllWidgets()
self.win.glpane.gl_update()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current lighting scheme
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The lighting scheme settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/LightingScheme/$FAV_NAME.txt).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/LightingScheme/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeLightingSchemeToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeLightingSchemeToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
saveFavoriteFile(str(fn), favfilepath)
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
canLoadFile=loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeLightingSchemeToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(lightingSchemePrefsList)
self.win.glpane.gl_update()
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.win.glpane.gl_update()
return
#def _addWhatsThisText( self ):
#"""
#What's This text for widgets in the Lighting Scheme Property Manager.
#"""
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_LightingScheme_PropertyManager
#WhatsThis_LightingScheme_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Lighting Scheme Property Manager.
"""
#modify this for lighting schemes
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_LightingScheme_PropertyManager
ToolTip_LightingScheme_PropertyManager(self)
class QuteMolPropertyManager(PM_Dialog):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = [ "Render axes",
"Hide axes" ]
_bases_display_choices = [ "Render bases",
"Hide bases" ]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__(self, win):
"""
Construct the QuteMolX Property Manager.
@param win: The main window.
@type win: QMainWindow
"""
self.win = win
self.pw = None
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
msg = "Select a QuteMolX rendering style and click the \
<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
# Hide Preview and Restore defaults button for Alpha9.
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON | PM_PREVIEW_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title = "DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title = "Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Axes: ',
choices = self._axes_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.basesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Bases: ',
choices = self._bases_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text = "Launch QuteMolX",
iconPath = "ui/actions/Properties Manager/QuteMol.png",
spanWidth = True )
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show)
"""
if self.isVisible(): # Fixes bug 2680. --Mark 2008-03-19
return
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect = True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
#First exit temporary modes (e.g. Pan mode) if any.
currentCommand = self.win.commandSequencer.currentCommand
if not currentCommand.command_has_its_own_gui:
currentCommand.Done()
self.connect_or_disconnect_signals(isConnect = False)
PM_Dialog.close(self)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.accept()
self.close() # Close the property manager.
# The following reopens the property manager of the mode after
# when the PM of the reference geometry is closed. -- Ninad 20070603
# Note: the value of self.modePropertyManager can be None
# @see: anyMode.propMgr
#
# (Note: once we have a real command sequencer, it will be
# handling this kind of thing itself, and the situation
# in which the currentCommand does not correspond to
# the current PM (as is true here while this separate PM
# is open, since it's not currentCommand.propMgr)
# will be deprecated or impossible. [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.reject()
self.close()
# The following reopens the property manager of the command after
# the PM of the reference geometry editCommand (i.e. Plane) is closed.
# Note: the value of self.modePropertyManager can be None.
# See anyMode.propMgr
# (See similar code in ok_btn_clicked [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton,
SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class ProteinDisplayStyle_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit Protein Display Style"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__(self, parentCommand):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the protein display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect(self.applyFavoriteButton, SIGNAL("clicked()"),
self.applyFavorite)
change_connect(self.addFavoriteButton, SIGNAL("clicked()"),
self.addFavorite)
change_connect(self.deleteFavoriteButton, SIGNAL("clicked()"),
self.deleteFavorite)
change_connect(self.saveFavoriteButton, SIGNAL("clicked()"),
self.saveFavorite)
change_connect(self.loadFavoriteButton, SIGNAL("clicked()"),
self.loadFavorite)
#Display group box signal slot connections
change_connect(self.proteinStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayStyle)
change_connect(self.smoothingCheckBox, SIGNAL("stateChanged(int)"),
self.smoothProteinDisplay)
change_connect(self.scaleComboBox, SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayScale)
change_connect(self.splineDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinSplineValue)
change_connect(self.scaleFactorDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinScaleFactor)
#color groupbox
change_connect(self.proteinComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseProteinComponent)
change_connect(self.proteinAuxComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseAuxilliaryProteinComponent)
change_connect(self.customColorComboBox, SIGNAL("editingFinished()"),
self.chooseCustomColor)
change_connect(self.auxColorComboBox, SIGNAL("editingFinished()"),
self.chooseAuxilliaryColor)
change_connect(self.discColorCheckBox, SIGNAL("stateChanged(int)"),
self.setDiscreteColors)
change_connect(self.helixColorComboBox, SIGNAL("editingFinished()"),
self.chooseHelixColor)
change_connect(self.strandColorComboBox, SIGNAL("editingFinished()"),
self.chooseStrandColor)
change_connect(self.coilColorComboBox, SIGNAL("editingFinished()"),
self.chooseCoilColor)
#Protein Display methods
def changeProteinDisplayStyle(self, idx):
env.prefs[proteinStyle_prefs_key] = idx
return
def changeProteinDisplayQuality(self, idx):
env.prefs[proteinStyleQuality_prefs_key] = idx
return
def smoothProteinDisplay(self, state):
if state == Qt.Checked:
env.prefs[proteinStyleSmooth_prefs_key] = True
else:
env.prefs[proteinStyleSmooth_prefs_key] = False
return
def changeProteinDisplayScale(self, idx):
env.prefs[proteinStyleScaling_prefs_key] = idx
return
def changeProteinSplineValue(self, val):
env.prefs[proteinStyleQuality_prefs_key] = val
return
def changeProteinScaleFactor(self, val):
env.prefs[proteinStyleScaleFactor_prefs_key] = val
return
def chooseProteinComponent(self, idx):
env.prefs[proteinStyleColors_prefs_key] = idx
return
def chooseAuxilliaryProteinComponent(self, idx):
env.prefs[proteinStyleAuxColors_prefs_key] = idx - 1
return
def chooseCustomColor(self):
color = self.customColorComboBox.getColor()
env.prefs[proteinStyleCustomColor_prefs_key] = color
return
def chooseAuxilliaryColor(self):
color = self.auxColorComboBox.getColor()
env.prefs[proteinStyleAuxCustomColor_prefs_key] = color
return
def chooseHelixColor(self):
color = self.helixColorComboBox.getColor()
env.prefs[proteinStyleHelixColor_prefs_key] = color
return
def chooseStrandColor(self):
color = self.strandColorComboBox.getColor()
env.prefs[proteinStyleStrandColor_prefs_key] = color
return
def chooseCoilColor(self):
color = self.coilColorComboBox.getColor()
env.prefs[proteinStyleCoilColor_prefs_key] = color
return
def setDiscreteColors(self, state):
if state == Qt.Checked:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = True
else:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = False
return
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
#Not required for Proteins
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
#self.originalDisplayStyle = self.o.getGlobalDisplayStyle()
#self.o.setGlobalDisplayStyle(diDNACYLINDER)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self.updateProteinDisplayStyleWidgets()
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
#Not required for proteins
# Restore the original global display style.
#self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Favorites")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Display")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Color")
self._loadGroupBox3(self._pmGroupBox3)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/ProteinDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/ProteinDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join(_dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch(file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file) - 4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis("""<b> List of Favorites </b>
<p>
Creates a list of favorite Protein display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE","ui/actions/Properties Manager/ApplyPeptideDisplayStyleFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png","Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE", "ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
proteinStyleChoices = [
'CA trace (wire)', 'CA trace (cylinders)',
'CA trace (ball and stick)', 'Tube', 'Ladder', 'Zigzag',
'Flat ribbon', 'Solid ribbon', 'Cartoons', 'Fancy cartoons',
'Peptide tiles'
]
self.proteinStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Style:",
choices = proteinStyleChoices,
setAsDefault = True)
scaleChoices = ['Constant', 'Secondary structure', 'B-factor']
self.scaleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Scaling:",
choices = scaleChoices,
setAsDefault = True)
self.scaleFactorDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Scaling factor:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 1,
singleStep = 0.1 )
self.splineDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Resolution:",
value = 4,
setAsDefault = True,
minimum = 2,
maximum = 8,
decimals = 0,
singleStep = 1 )
self.smoothingCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Smoothing",
setAsDefault = True)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
colorChoices = [
'Chunk', 'Chain', 'Order', 'Hydropathy', 'Polarity', 'Acidity',
'Size', 'Character', 'Number of contacts',
'Secondary structure type', 'Secondary structure order',
'B-factor', 'Occupancy', 'Custom'
]
self.proteinComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Color by:",
choices = colorChoices,
setAsDefault = True)
colorList = [
orange, yellow, red, magenta, cyan, blue, white, black, gray
]
colorNames = [
"Orange(default)", "Yellow", "Red", "Magenta", "Cyan", "Blue",
"White", "Black", "Other color..."
]
self.customColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorList,
colorNames = colorNames,
label = "Custom:",
color = orange,
setAsDefault = True)
colorChoices1 = [
'Same as main color', 'Chunk', 'Chain', 'Order', 'Hydropathy',
'Polarity', 'Acidity', 'Size', 'Character', 'Number of contacts',
'Secondary structure type', 'Secondary structure order',
'B-factor', 'Occupancy', 'Custom'
]
self.proteinAuxComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Aux:",
choices = colorChoices1,
setAsDefault = True)
colorListAux = [
orange, yellow, red, magenta, cyan, blue, white, black, gray
]
colorNamesAux = [
"Orange(default)", "Yellow", "Red", "Magenta", "Cyan", "Blue",
"White", "Black", "Other color..."
]
self.auxColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Custom aux:",
color = gray,
setAsDefault = True)
self.discColorCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Discretize colors",
setAsDefault = True
)
colorListHelix = [
red, yellow, gray, magenta, cyan, blue, white, black, orange
]
colorNamesHelix = [
"Red(default)", "Yellow", "Gray", "Magenta", "Cyan", "Blue",
"White", "Black", "Other color..."
]
self.helixColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListHelix,
colorNames = colorNamesHelix,
label = "Helix:",
color = red,
setAsDefault = True)
colorListStrand = [
cyan, yellow, gray, magenta, red, blue, white, black, orange
]
colorNamesStrand = [
"Cyan(default)", "Yellow", "Gray", "Magenta", "Red", "Blue",
"White", "Black", "Other color..."
]
self.strandColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListStrand,
colorNames = colorNamesStrand,
label = "Strand:",
color = cyan,
setAsDefault = True)
self.coilColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Coil:",
color = orange,
setAsDefault = True)
def updateProteinDisplayStyleWidgets(self):
"""
Updates all the Protein Display style widgets based on the current pref keys
values
"""
self.proteinStyleComboBox.setCurrentIndex(
env.prefs[proteinStyle_prefs_key])
self.splineDoubleSpinBox.setValue(
env.prefs[proteinStyleQuality_prefs_key])
if env.prefs[proteinStyleSmooth_prefs_key] == True:
self.smoothingCheckBox.setCheckState(Qt.Checked)
else:
self.smoothingCheckBox.setCheckState(Qt.Unchecked)
self.scaleComboBox.setCurrentIndex(
env.prefs[proteinStyleScaling_prefs_key])
self.scaleFactorDoubleSpinBox.setValue(
env.prefs[proteinStyleScaleFactor_prefs_key])
self.proteinComponentComboBox.setCurrentIndex(
env.prefs[proteinStyleColors_prefs_key])
self.customColorComboBox.setColor(
env.prefs[proteinStyleCustomColor_prefs_key])
self.proteinAuxComponentComboBox.setCurrentIndex(
env.prefs[proteinStyleAuxColors_prefs_key])
self.auxColorComboBox.setColor(
env.prefs[proteinStyleAuxCustomColor_prefs_key])
if env.prefs[proteinStyleColorsDiscrete_prefs_key] == True:
self.discColorCheckBox.setCheckState(Qt.Checked)
else:
self.discColorCheckBox.setCheckState(Qt.Unchecked)
self.helixColorComboBox.setColor(
env.prefs[proteinStyleHelixColor_prefs_key])
self.strandColorComboBox.setColor(
env.prefs[proteinStyleStrandColor_prefs_key])
self.coilColorComboBox.setColor(
env.prefs[proteinStyleCoilColor_prefs_key])
return
def applyFavorite(self):
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateProteinDisplayStyleWidgets()
return
def addFavorite(self):
# Rules and other info:
# - The new favorite is defined by the current Protein display style
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The DNA display style settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/ProteinDisplayStyle/$FAV_NAME.txt).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename(name)
if os.path.exists(fname):
#favorite file already exists!
_ext = ".txt"
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + _ext +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Cancel",
"",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(
name)
indexOfDuplicateItem = self.favoritesComboBox.findText(
name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message(
"Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(
name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text
) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile = getFavoritePathFromBasename(currentText)
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir=None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir=None):
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[
workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message(redmsg(msg))
return
def loadFavorite(self):
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory = getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self, "Choose a file to load",
directory, formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile = loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName) - 4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning(
self,
"Warning!",
"The favorite file \"" + name + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Rename",
"&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(
name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(
proteinDisplayStylePrefsList)
env.history.message(
"Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateProteinDisplayStyleWidgets()
return
def _addWhatsThisText(self):
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
ToolTip_EditProteinDisplayStyle_PropertyManager(self)
class PlanePropertyManager(EditCommand_PM):
"""
The PlanePropertyManager class provides a Property Manager for a
(reference) Plane.
"""
# The title that appears in the Property Manager header.
title = "Plane"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Insert/Reference Geometry/Plane.png"
def __init__(self, command):
"""
Construct the Plane Property Manager.
@param plane: The plane.
@type plane: L{Plane}
"""
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self.gridColor = black
self.gridXSpacing = 4.0
self.gridYSpacing = 4.0
self.gridLineType = 3
self.displayLabels = False
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
EditCommand_PM.__init__(self, command)
# Hide Preview and Restore defaults buttons
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen", "Parallel to screen" ),
( 1, "Through selected atoms", "Through selected atoms" ),
( 2, "Offset to a plane", "Offset to a plane" ),
( 3, "Custom", "Custom" )
]
self.pmPlacementOptions = \
PM_RadioButtonList( self,
title = "Placement Options",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 3 )
self.pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self.pmGroupBox1)
#image groupbox
self.pmGroupBox2 = PM_GroupBox(self, title="Image")
self._loadGroupBox2(self.pmGroupBox2)
#grid plane groupbox
self.pmGroupBox3 = PM_GroupBox(self, title="Grid")
self._loadGroupBox3(self.pmGroupBox3)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in the grid plane group box.
@param pmGroupBox: The grid group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.gridPlaneCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show grid",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
connect_checkbox_with_boolean_pref(self.gridPlaneCheckBox,
PlanePM_showGrid_prefs_key)
self.gpXSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "X Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
self.gpYSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Y Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
lineTypeChoices = ['Dotted (default)', 'Dashed', 'Solid']
self.gpLineTypeComboBox = \
PM_ComboBox( pmGroupBox ,
label = "Line type:",
choices = lineTypeChoices,
setAsDefault = True)
hhColorList = [
black, orange, red, magenta, cyan, blue, white, yellow, gray
]
hhColorNames = [
"Black (default)", "Orange", "Red", "Magenta", "Cyan", "Blue",
"White", "Yellow", "Other color..."
]
self.gpColorTypeComboBox = \
PM_ColorComboBox( pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = black )
self.pmGroupBox5 = PM_GroupBox(pmGroupBox)
self.gpDisplayLabels =\
PM_CheckBox( self.pmGroupBox5,
text = "Display labels",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True )
originChoices = [
'Lower left (default)', 'Upper left', 'Lower right', 'Upper right'
]
self.gpOriginComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Origin:",
choices = originChoices,
setAsDefault = True )
positionChoices = ['Origin axes (default)', 'Plane perimeter']
self.gpPositionComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Position:",
choices = positionChoices,
setAsDefault = True)
self._showHideGPWidgets()
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.displayLabels = True
self.gpOriginComboBox.setEnabled(True)
self.gpPositionComboBox.setEnabled(True)
else:
self.displayLabels = False
self.gpOriginComboBox.setEnabled(False)
self.gpPositionComboBox.setEnabled(False)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
#TODO: Fix for bug: When you invoke a temporary mode
# entering such a temporary mode keeps the signals of
#PM from the previous mode connected (
#but while exiting that temporary mode and reentering the
#previous mode, it actually reconnects the signal! This gives rise to
#lots of bugs. This needs more general fix in Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
#UPDATE: (comment copied and modifief from BuildNanotube_PropertyManager.
#The general problem still remains -- Ninad 2008-06-25
if isConnect and self.isAlreadyConnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to connect widgets"\
"in this PM that are already connected." )
return
if not isConnect and self.isAlreadyDisconnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to disconnect widgets"\
"in this PM that are already disconnected.")
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.pmPlacementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"), self.changePlanePlacement)
change_connect(self.widthDblSpinBox, SIGNAL("valueChanged(double)"),
self.change_plane_width)
change_connect(self.heightDblSpinBox, SIGNAL("valueChanged(double)"),
self.change_plane_height)
change_connect(self.aspectRatioCheckBox, SIGNAL("stateChanged(int)"),
self._enableAspectRatioSpinBox)
#signal slot connection for imageDisplayCheckBox
change_connect(self.imageDisplayCheckBox, SIGNAL("stateChanged(int)"),
self.toggleFileChooserBehavior)
#signal slot connection for imageDisplayFileChooser
change_connect(self.imageDisplayFileChooser.lineEdit,
SIGNAL("editingFinished()"), self.update_imageFile)
#signal slot connection for heightfieldDisplayCheckBox
change_connect(self.heightfieldDisplayCheckBox,
SIGNAL("stateChanged(int)"), self.toggleHeightfield)
#signal slot connection for heightfieldHQDisplayCheckBox
change_connect(self.heightfieldHQDisplayCheckBox,
SIGNAL("stateChanged(int)"), self.toggleHeightfieldHQ)
#signal slot connection for heightfieldTextureCheckBox
change_connect(self.heightfieldTextureCheckBox,
SIGNAL("stateChanged(int)"), self.toggleTexture)
#signal slot connection for vScaleSpinBox
change_connect(self.vScaleSpinBox, SIGNAL("valueChanged(double)"),
self.change_vertical_scale)
change_connect(self.plusNinetyButton, SIGNAL("clicked()"),
self.rotate_90)
change_connect(self.minusNinetyButton, SIGNAL("clicked()"),
self.rotate_neg_90)
change_connect(self.flipButton, SIGNAL("clicked()"), self.flip_image)
change_connect(self.mirrorButton, SIGNAL("clicked()"),
self.mirror_image)
change_connect(self.gridPlaneCheckBox, SIGNAL("stateChanged(int)"),
self.displayGridPlane)
change_connect(self.gpXSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.changeXSpacingInGP)
change_connect(self.gpYSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.changeYSpacingInGP)
change_connect(self.gpLineTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeLineTypeInGP)
change_connect(self.gpColorTypeComboBox, SIGNAL("editingFinished()"),
self.changeColorTypeInGP)
change_connect(self.gpDisplayLabels, SIGNAL("stateChanged(int)"),
self.displayLabelsInGP)
change_connect(self.gpOriginComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeOriginInGP)
change_connect(self.gpPositionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changePositionInGP)
self._connect_checkboxes_to_global_prefs_keys()
return
def _connect_checkboxes_to_global_prefs_keys(self):
"""
"""
connect_checkbox_with_boolean_pref(self.gridPlaneCheckBox,
PlanePM_showGrid_prefs_key)
connect_checkbox_with_boolean_pref(self.gpDisplayLabels,
PlanePM_showGridLabels_prefs_key)
def changePositionInGP(self, idx):
"""
Change Display of origin Labels (choices are along origin edges or along
the plane perimeter.
@param idx: Current index of the change grid label position combo box
@type idx: int
"""
if idx == 0:
self.displayLabelStyle = LABELS_ALONG_ORIGIN
elif idx == 1:
self.displayLabelStyle = LABELS_ALONG_PLANE_EDGES
else:
print "Invalid index", idx
return
def changeOriginInGP(self, idx):
"""
Change Display of origin Labels based on the location of the origin
@param idx: Current index of the change origin position combo box
@type idx: int
"""
if idx == 0:
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
elif idx == 1:
self.originLocation = PLANE_ORIGIN_UPPER_LEFT
elif idx == 2:
self.originLocation = PLANE_ORIGIN_LOWER_RIGHT
elif idx == 3:
self.originLocation = PLANE_ORIGIN_UPPER_RIGHT
else:
print "Invalid index", idx
return
def displayLabelsInGP(self, state):
"""
Choose to show or hide grid labels
@param state: State of the Display Label Checkbox
@type state: boolean
"""
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.gpOriginComboBox.setEnabled(True)
self.gpPositionComboBox.setEnabled(True)
self.displayLabels = True
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
else:
self.gpOriginComboBox.setEnabled(False)
self.gpPositionComboBox.setEnabled(False)
self.displayLabels = False
return
def changeColorTypeInGP(self):
"""
Change Color of grid
"""
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def changeLineTypeInGP(self, idx):
"""
Change line type in grid
@param idx: Current index of the Line type combo box
@type idx: int
"""
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
if idx == 0:
self.gridLineType = 3
if idx == 1:
self.gridLineType = 2
if idx == 2:
self.gridLineType = 1
return
def changeYSpacingInGP(self, val):
"""
Change Y spacing on the grid
@param val:value of Y spacing
@type val: double
"""
self.gridYSpacing = float(val)
return
def changeXSpacingInGP(self, val):
"""
Change X spacing on the grid
@param val:value of X spacing
@type val: double
"""
self.gridXSpacing = float(val)
return
def displayGridPlane(self, state):
"""
Display or hide grid based on the state of the checkbox
@param state: State of the Display Label Checkbox
@type state: boolean
"""
self._showHideGPWidgets()
if self.gridPlaneCheckBox.isChecked():
env.prefs[PlanePM_showGrid_prefs_key] = True
self._makeGridPlane()
else:
env.prefs[PlanePM_showGrid_prefs_key] = False
return
def _makeGridPlane(self):
"""
Show grid on the plane
"""
#get all the grid related values in here
self.gridXSpacing = float(self.gpXSpacingDoubleSpinBox.value())
self.gridYSpacing = float(self.gpYSpacingDoubleSpinBox.value())
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
idx = self.gpLineTypeComboBox.currentIndex()
self.changeLineTypeInGP(idx)
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def _showHideGPWidgets(self):
"""
Enable Disable grid related widgets based on the state of the show grid
checkbox.
"""
if self.gridPlaneCheckBox.isChecked():
self.gpXSpacingDoubleSpinBox.setEnabled(True)
self.gpYSpacingDoubleSpinBox.setEnabled(True)
self.gpLineTypeComboBox.setEnabled(True)
self.gpColorTypeComboBox.setEnabled(True)
self.gpDisplayLabels.setEnabled(True)
else:
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpYSpacingDoubleSpinBox.setEnabled(False)
self.gpLineTypeComboBox.setEnabled(False)
self.gpColorTypeComboBox.setEnabled(False)
self.gpDisplayLabels.setEnabled(False)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the image group box.
@param pmGroupBox: The image group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.imageDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Display image",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.imageDisplayFileChooser = \
PM_FileChooser(pmGroupBox,
label = 'Image file:',
text = '' ,
spanWidth = True,
filter = "PNG (*.png);;"\
"All Files (*.*)"
)
self.imageDisplayFileChooser.setEnabled(False)
# add change image properties button
BUTTON_LIST = [
("QToolButton", 1, "+90",
"ui/actions/Properties Manager/RotateImage+90.png", "+90", "", 0),
("QToolButton", 2, "-90",
"ui/actions/Properties Manager/RotateImage-90.png", "-90", "", 1),
("QToolButton", 3, "FLIP",
"ui/actions/Properties Manager/FlipImageVertical.png", "Flip", "",
2),
("QToolButton", 4, "MIRROR",
"ui/actions/Properties Manager/FlipImageHorizontal.png", "Mirror",
"", 3)
]
#image change button groupbox
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title="Modify Image")
self.imageChangeButtonGroup = \
PM_ToolButtonRow( self.pmGroupBox2,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.imageChangeButtonGroup.buttonGroup.setExclusive(False)
self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1)
self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2)
self.flipButton = self.imageChangeButtonGroup.getButtonById(3)
self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4)
# buttons enabled when a valid image is loaded
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Create 3D relief",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldHQDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "High quality",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldTextureCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use texture",
widgetColumn = 0,
state = Qt.Checked,
setAsDefault = True,
spanWidth = True
)
self.vScaleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = " Vertical scale:",
value = 1.0,
setAsDefault = True,
minimum = -1000.0, # -1000 A
maximum = 1000.0, # 1000 A
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.widthDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Width:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.heightDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label =" Height:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.aspectRatioCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Maintain Aspect Ratio of:' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.aspectRatioSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "",
value = 1.0,
setAsDefault = True,
minimum = 0.1,
maximum = 10.0,
singleStep = 0.1,
decimals = 2,
suffix = " to 1.00")
if self.aspectRatioCheckBox.isChecked():
self.aspectRatioSpinBox.setEnabled(True)
else:
self.aspectRatioSpinBox.setEnabled(False)
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager
whatsThis_PlanePropertyManager(self)
def toggleFileChooserBehavior(self, checked):
"""
Enables FileChooser and displays image when checkbox is checked otherwise
not
"""
self.imageDisplayFileChooser.lineEdit.emit(SIGNAL("editingFinished()"))
if checked == Qt.Checked:
self.imageDisplayFileChooser.setEnabled(True)
elif checked == Qt.Unchecked:
self.imageDisplayFileChooser.setEnabled(False)
# if an image is already displayed, that's need to be hidden as well
else:
pass
self.command.struct.glpane.gl_update()
def toggleHeightfield(self, checked):
"""
Enables 3D relief drawing mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.display_heightfield = checked
if checked:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
plane.computeHeightfield()
else:
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane.heightfield = None
plane.glpane.gl_update()
def toggleHeightfieldHQ(self, checked):
"""
Enables high quality rendering in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_hq = checked
plane.computeHeightfield()
plane.glpane.gl_update()
def toggleTexture(self, checked):
"""
Enables texturing in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_use_texture = checked
# It is not necessary to re-compute the heightfield coordinates
# at this point, they are re-computed whenever the "3D relief image"
# checkbox is set.
plane.glpane.gl_update()
def update_spinboxes(self):
"""
Update the width and height spinboxes.
@see: Plane.resizeGeometry()
This typically gets called when the plane is resized from the
3D workspace (which marks assy as modified) .So, update the spinboxes
that represent the Plane's width and height, but do no emit 'valueChanged'
signal when the spinbox value changes.
@see: Plane.resizeGeometry()
@see: self._update_UI_do_updates()
@see: Plane_EditCommand.command_update_internal_state()
"""
# blockSignals = True make sure that spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue(). This is done
#because the spinbox valu changes as a result of resizing the plane
#from the 3D workspace.
if self.command.hasValidStructure():
self.heightDblSpinBox.setValue(self.command.struct.height,
blockSignals=True)
self.widthDblSpinBox.setValue(self.command.struct.width,
blockSignals=True)
def update_imageFile(self):
"""
Loads image file if path is valid
"""
# Update buttons and checkboxes.
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane = self.command.struct
# Delete current image and heightfield
plane.deleteImage()
plane.heightfield = None
plane.display_image = self.imageDisplayCheckBox.isChecked()
if plane.display_image:
imageFile = str(self.imageDisplayFileChooser.lineEdit.text())
from model.Plane import checkIfValidImagePath
validPath = checkIfValidImagePath(imageFile)
if validPath:
from PIL import Image
# Load image from file
plane.image = Image.open(imageFile)
plane.loadImage(imageFile)
# Compute the relief image
plane.computeHeightfield()
if plane.image:
self.mirrorButton.setEnabled(True)
self.plusNinetyButton.setEnabled(True)
self.minusNinetyButton.setEnabled(True)
self.flipButton.setEnabled(True)
self.heightfieldDisplayCheckBox.setEnabled(True)
if plane.display_heightfield:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
def show(self):
"""
Show the Plane Property Manager.
"""
EditCommand_PM.show(self)
#It turns out that if updateCosmeticProps is called before
#EditCommand_PM.show, the 'preview' properties are not updated
#when you are editing an existing plane. Don't know the cause at this
#time, issue is trivial. So calling it in the end -- Ninad 2007-10-03
if self.command.struct:
plane = self.command.struct
plane.updateCosmeticProps(previewing=True)
if plane.imagePath:
self.imageDisplayFileChooser.setText(plane.imagePath)
self.imageDisplayCheckBox.setChecked(plane.display_image)
#Make sure that the plane placement option is always set to
#'Custom' when the Plane PM is shown. This makes sure that bugs like
#2949 won't occur. Let the user change the plane placement option
#explicitely
button = self.pmPlacementOptions.getButtonById(3)
button.setChecked(True)
def setParameters(self, params):
"""
"""
width, height, gridColor, gridLineType, \
gridXSpacing, gridYSpacing, originLocation, \
displayLabelStyle = params
# blockSignals = True flag makes sure that the
# spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue().
self.widthDblSpinBox.setValue(width, blockSignals=True)
self.heightDblSpinBox.setValue(height, blockSignals=True)
self.win.glpane.gl_update()
self.gpColorTypeComboBox.setColor(gridColor)
self.gridLineType = gridLineType
self.gpXSpacingDoubleSpinBox.setValue(gridXSpacing)
self.gpYSpacingDoubleSpinBox.setValue(gridYSpacing)
self.gpOriginComboBox.setCurrentIndex(originLocation)
self.gpPositionComboBox.setCurrentIndex(displayLabelStyle)
def getCurrrentDisplayParams(self):
"""
Returns a tuple containing current display parameters such as current
image path and grid display params.
@see: Plane_EditCommand.command_update_internal_state() which uses this
to decide whether to modify the structure (e.g. because of change in the
image path or display parameters.)
"""
imagePath = self.imageDisplayFileChooser.text
gridColor = self.gpColorTypeComboBox.getColor()
return (imagePath, gridColor, self.gridLineType, self.gridXSpacing,
self.gridYSpacing, self.originLocation, self.displayLabelStyle)
def getParameters(self):
"""
"""
width = self.widthDblSpinBox.value()
height = self.heightDblSpinBox.value()
gridColor = self.gpColorTypeComboBox.getColor()
params = (width, height, gridColor, self.gridLineType,
self.gridXSpacing, self.gridYSpacing, self.originLocation,
self.displayLabelStyle)
return params
def change_plane_width(self, newWidth):
"""
Slot for width spinbox in the Property Manager.
@param newWidth: width in Angstroms.
@type newWidth: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.width = newWidth
self.command.struct.height = self.command.struct.width / \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_height(self, newHeight):
"""
Slot for height spinbox in the Property Manager.
@param newHeight: height in Angstroms.
@type newHeight: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.height = newHeight
self.command.struct.width = self.command.struct.height * \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_size(self, gl_update=True):
"""
Slot to change the Plane's width and height.
@param gl_update: Forces an update of the glpane.
@type gl_update: bool
"""
self.command.struct.width = self.widthDblSpinBox.value()
self.command.struct.height = self.heightDblSpinBox.value()
if gl_update:
self.command.struct.glpane.gl_update()
def change_vertical_scale(self, scale):
"""
Changes vertical scaling of the heightfield.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_scale = scale
plane.computeHeightfield()
plane.glpane.gl_update()
def changePlanePlacement(self, buttonId):
"""
Slot to change the placement of the plane depending upon the
option checked in the "Placement Options" group box of the PM.
@param buttonId: The button id of the selected radio button (option).
@type buttonId: int
"""
if buttonId == 0:
msg = "Create a Plane parallel to the screen. "\
"With <b>Parallel to Screen</b> plane placement option, the "\
"center of the plane is always (0,0,0)"
self.updateMessage(msg)
self.command.placePlaneParallelToScreen()
elif buttonId == 1:
msg = "Create a Plane with center coinciding with the common center "\
"of <b> 3 or more selected atoms </b>. If exactly 3 atoms are "\
"selected, the Plane will pass through those atoms."
self.updateMessage(msg)
self.command.placePlaneThroughAtoms()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 2:
msg = "Create a Plane at an <b>offset</b> to the selected plane "\
"indicated by the direction arrow. "\
"you can click on the direction arrow to reverse its direction."
self.updateMessage(msg)
self.command.placePlaneOffsetToAnother()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 3:
#'Custom' plane placement. Do nothing (only update message box)
# Fixes bug 2439
msg = "Create a plane with a <b>Custom</b> plane placement. "\
"The plane is placed parallel to the screen, with "\
"center at (0, 0, 0). User can then modify the plane placement."
self.updateMessage(msg)
def _enableAspectRatioSpinBox(self, enable):
"""
Slot for "Maintain Aspect Ratio" checkbox which enables or disables
the Aspect Ratio spin box.
@param enable: True = enable, False = disable.
@type enable: bool
"""
self.aspectRatioSpinBox.setEnabled(enable)
def _updateAspectRatio(self):
"""
Updates the Aspect Ratio spin box based on the current width and height.
"""
aspectRatio = self.command.struct.width / self.command.struct.height
self.aspectRatioSpinBox.setValue(aspectRatio)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates() for documentation.
@see: Plane.resizeGeometry()
@see: self.update_spinboxes()
@see: Plane_EditCommand.command_update_internal_state()
"""
#This typically gets called when the plane is resized from the
#3D workspace (which marks assy as modified) . So, update the spinboxes
#that represent the Plane's width and height.
self.update_spinboxes()
def update_props_if_needed_before_closing(self):
"""
This updates some cosmetic properties of the Plane (e.g. fill color,
border color, etc.) before closing the Property Manager.
"""
# Example: The Plane Property Manager is open and the user is
# 'previewing' the plane. Now the user clicks on "Build > Atoms"
# to invoke the next command (without clicking "Done").
# This calls openPropertyManager() which replaces the current PM
# with the Build Atoms PM. Thus, it creates and inserts the Plane
# that was being previewed. Before the plane is permanently inserted
# into the part, it needs to change some of its cosmetic properties
# (e.g. fill color, border color, etc.) which distinguishes it as
# a new plane in the part. This function changes those properties.
# ninad 2007-06-13
#called in updatePropertyManager in MWsemeantics.py --(Partwindow class)
EditCommand_PM.update_props_if_needed_before_closing(self)
#Don't draw the direction arrow when the object is finalized.
if self.command.struct and \
self.command.struct.offsetParentGeometry:
dirArrow = self.command.struct.offsetParentGeometry.directionArrow
dirArrow.setDrawRequested(False)
def updateMessage(self, msg=''):
"""
Updates the message box with an informative message
@param message: Message to be displayed in the Message groupbox of
the property manager
@type message: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault=False,
minLines=5)
def rotate_90(self):
"""
Rotate the image clockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(0)
return
def rotate_neg_90(self):
"""
Rotate the image counterclockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(1)
return
def flip_image(self):
"""
Flip the image horizontally.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(1)
return
def mirror_image(self):
"""
Flip the image vertically.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(0)
return
class PlanePropertyManager(EditCommand_PM):
"""
The PlanePropertyManager class provides a Property Manager for a
(reference) Plane.
"""
# The title that appears in the Property Manager header.
title = "Plane"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Insert/Reference Geometry/Plane.png"
def __init__(self, command):
"""
Construct the Plane Property Manager.
@param plane: The plane.
@type plane: L{Plane}
"""
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self.gridColor = black
self.gridXSpacing = 4.0
self.gridYSpacing = 4.0
self.gridLineType = 3
self.displayLabels = False
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
EditCommand_PM.__init__( self, command)
# Hide Preview and Restore defaults buttons
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen", "Parallel to screen" ),
( 1, "Through selected atoms", "Through selected atoms" ),
( 2, "Offset to a plane", "Offset to a plane" ),
( 3, "Custom", "Custom" )
]
self.pmPlacementOptions = \
PM_RadioButtonList( self,
title = "Placement Options",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 3 )
self.pmGroupBox1 = PM_GroupBox(self, title = "Parameters")
self._loadGroupBox1(self.pmGroupBox1)
#image groupbox
self.pmGroupBox2 = PM_GroupBox(self, title = "Image")
self._loadGroupBox2(self.pmGroupBox2)
#grid plane groupbox
self.pmGroupBox3 = PM_GroupBox(self, title = "Grid")
self._loadGroupBox3(self.pmGroupBox3)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in the grid plane group box.
@param pmGroupBox: The grid group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.gridPlaneCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show grid",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
connect_checkbox_with_boolean_pref(
self.gridPlaneCheckBox ,
PlanePM_showGrid_prefs_key)
self.gpXSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "X Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
self.gpYSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Y Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
lineTypeChoices = [ 'Dotted (default)',
'Dashed',
'Solid' ]
self.gpLineTypeComboBox = \
PM_ComboBox( pmGroupBox ,
label = "Line type:",
choices = lineTypeChoices,
setAsDefault = True)
hhColorList = [ black, orange, red, magenta,
cyan, blue, white, yellow, gray ]
hhColorNames = [ "Black (default)", "Orange", "Red", "Magenta",
"Cyan", "Blue", "White", "Yellow", "Other color..." ]
self.gpColorTypeComboBox = \
PM_ColorComboBox( pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = black )
self.pmGroupBox5 = PM_GroupBox( pmGroupBox )
self.gpDisplayLabels =\
PM_CheckBox( self.pmGroupBox5,
text = "Display labels",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True )
originChoices = [ 'Lower left (default)',
'Upper left',
'Lower right',
'Upper right' ]
self.gpOriginComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Origin:",
choices = originChoices,
setAsDefault = True )
positionChoices = [ 'Origin axes (default)',
'Plane perimeter' ]
self.gpPositionComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Position:",
choices = positionChoices,
setAsDefault = True)
self._showHideGPWidgets()
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.displayLabels = True
self.gpOriginComboBox.setEnabled( True )
self.gpPositionComboBox.setEnabled( True )
else:
self.displayLabels = False
self.gpOriginComboBox.setEnabled( False )
self.gpPositionComboBox.setEnabled( False )
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
#TODO: Fix for bug: When you invoke a temporary mode
# entering such a temporary mode keeps the signals of
#PM from the previous mode connected (
#but while exiting that temporary mode and reentering the
#previous mode, it actually reconnects the signal! This gives rise to
#lots of bugs. This needs more general fix in Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
#UPDATE: (comment copied and modifief from BuildNanotube_PropertyManager.
#The general problem still remains -- Ninad 2008-06-25
if isConnect and self.isAlreadyConnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to connect widgets"\
"in this PM that are already connected." )
return
if not isConnect and self.isAlreadyDisconnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to disconnect widgets"\
"in this PM that are already disconnected.")
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.pmPlacementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.changePlanePlacement)
change_connect(self.widthDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_plane_width)
change_connect(self.heightDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_plane_height)
change_connect(self.aspectRatioCheckBox,
SIGNAL("stateChanged(int)"),
self._enableAspectRatioSpinBox)
#signal slot connection for imageDisplayCheckBox
change_connect(self.imageDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleFileChooserBehavior)
#signal slot connection for imageDisplayFileChooser
change_connect(self.imageDisplayFileChooser.lineEdit,
SIGNAL("editingFinished()"),
self.update_imageFile)
#signal slot connection for heightfieldDisplayCheckBox
change_connect(self.heightfieldDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleHeightfield)
#signal slot connection for heightfieldHQDisplayCheckBox
change_connect(self.heightfieldHQDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleHeightfieldHQ)
#signal slot connection for heightfieldTextureCheckBox
change_connect(self.heightfieldTextureCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleTexture)
#signal slot connection for vScaleSpinBox
change_connect(self.vScaleSpinBox,
SIGNAL("valueChanged(double)"),
self.change_vertical_scale)
change_connect(self.plusNinetyButton,
SIGNAL("clicked()"),
self.rotate_90)
change_connect(self.minusNinetyButton,
SIGNAL("clicked()"),
self.rotate_neg_90)
change_connect(self.flipButton,
SIGNAL("clicked()"),
self.flip_image)
change_connect(self.mirrorButton,
SIGNAL("clicked()"),
self.mirror_image)
change_connect(self.gridPlaneCheckBox,
SIGNAL("stateChanged(int)"),
self.displayGridPlane)
change_connect(self.gpXSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeXSpacingInGP)
change_connect(self.gpYSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeYSpacingInGP)
change_connect( self.gpLineTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeLineTypeInGP )
change_connect( self.gpColorTypeComboBox,
SIGNAL("editingFinished()"),
self.changeColorTypeInGP )
change_connect( self.gpDisplayLabels,
SIGNAL("stateChanged(int)"),
self.displayLabelsInGP )
change_connect( self.gpOriginComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeOriginInGP )
change_connect( self.gpPositionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changePositionInGP )
self._connect_checkboxes_to_global_prefs_keys()
return
def _connect_checkboxes_to_global_prefs_keys(self):
"""
"""
connect_checkbox_with_boolean_pref(
self.gridPlaneCheckBox ,
PlanePM_showGrid_prefs_key)
connect_checkbox_with_boolean_pref(
self.gpDisplayLabels,
PlanePM_showGridLabels_prefs_key)
def changePositionInGP(self, idx):
"""
Change Display of origin Labels (choices are along origin edges or along
the plane perimeter.
@param idx: Current index of the change grid label position combo box
@type idx: int
"""
if idx == 0:
self.displayLabelStyle = LABELS_ALONG_ORIGIN
elif idx == 1:
self.displayLabelStyle = LABELS_ALONG_PLANE_EDGES
else:
print "Invalid index", idx
return
def changeOriginInGP(self, idx):
"""
Change Display of origin Labels based on the location of the origin
@param idx: Current index of the change origin position combo box
@type idx: int
"""
if idx == 0:
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
elif idx ==1:
self.originLocation = PLANE_ORIGIN_UPPER_LEFT
elif idx == 2:
self.originLocation = PLANE_ORIGIN_LOWER_RIGHT
elif idx == 3:
self.originLocation = PLANE_ORIGIN_UPPER_RIGHT
else:
print "Invalid index", idx
return
def displayLabelsInGP(self, state):
"""
Choose to show or hide grid labels
@param state: State of the Display Label Checkbox
@type state: boolean
"""
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.gpOriginComboBox.setEnabled(True)
self.gpPositionComboBox.setEnabled(True)
self.displayLabels = True
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
else:
self.gpOriginComboBox.setEnabled(False)
self.gpPositionComboBox.setEnabled(False)
self.displayLabels = False
return
def changeColorTypeInGP(self):
"""
Change Color of grid
"""
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def changeLineTypeInGP(self, idx):
"""
Change line type in grid
@param idx: Current index of the Line type combo box
@type idx: int
"""
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
if idx == 0:
self.gridLineType = 3
if idx == 1:
self.gridLineType = 2
if idx == 2:
self.gridLineType = 1
return
def changeYSpacingInGP(self, val):
"""
Change Y spacing on the grid
@param val:value of Y spacing
@type val: double
"""
self.gridYSpacing = float(val)
return
def changeXSpacingInGP(self, val):
"""
Change X spacing on the grid
@param val:value of X spacing
@type val: double
"""
self.gridXSpacing = float(val)
return
def displayGridPlane(self, state):
"""
Display or hide grid based on the state of the checkbox
@param state: State of the Display Label Checkbox
@type state: boolean
"""
self._showHideGPWidgets()
if self.gridPlaneCheckBox.isChecked():
env.prefs[PlanePM_showGrid_prefs_key] = True
self._makeGridPlane()
else:
env.prefs[PlanePM_showGrid_prefs_key] = False
return
def _makeGridPlane(self):
"""
Show grid on the plane
"""
#get all the grid related values in here
self.gridXSpacing = float(self.gpXSpacingDoubleSpinBox.value())
self.gridYSpacing = float(self.gpYSpacingDoubleSpinBox.value())
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
idx = self.gpLineTypeComboBox.currentIndex()
self.changeLineTypeInGP(idx)
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def _showHideGPWidgets(self):
"""
Enable Disable grid related widgets based on the state of the show grid
checkbox.
"""
if self.gridPlaneCheckBox.isChecked():
self.gpXSpacingDoubleSpinBox.setEnabled(True)
self.gpYSpacingDoubleSpinBox.setEnabled(True)
self.gpLineTypeComboBox.setEnabled(True)
self.gpColorTypeComboBox.setEnabled(True)
self.gpDisplayLabels.setEnabled(True)
else:
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpYSpacingDoubleSpinBox.setEnabled(False)
self.gpLineTypeComboBox.setEnabled(False)
self.gpColorTypeComboBox.setEnabled(False)
self.gpDisplayLabels.setEnabled(False)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the image group box.
@param pmGroupBox: The image group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.imageDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Display image",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.imageDisplayFileChooser = \
PM_FileChooser(pmGroupBox,
label = 'Image file:',
text = '' ,
spanWidth = True,
filter = "PNG (*.png);;"\
"All Files (*.*)"
)
self.imageDisplayFileChooser.setEnabled(False)
# add change image properties button
BUTTON_LIST = [
( "QToolButton", 1, "+90",
"ui/actions/Properties Manager/RotateImage+90.png",
"+90", "", 0),
( "QToolButton", 2, "-90",
"ui/actions/Properties Manager/RotateImage-90.png",
"-90", "", 1),
( "QToolButton", 3, "FLIP",
"ui/actions/Properties Manager/FlipImageVertical.png",
"Flip", "", 2),
( "QToolButton", 4, "MIRROR",
"ui/actions/Properties Manager/FlipImageHorizontal.png",
"Mirror", "", 3)
]
#image change button groupbox
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title = "Modify Image")
self.imageChangeButtonGroup = \
PM_ToolButtonRow( self.pmGroupBox2,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.imageChangeButtonGroup.buttonGroup.setExclusive(False)
self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1)
self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2)
self.flipButton = self.imageChangeButtonGroup.getButtonById(3)
self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4)
# buttons enabled when a valid image is loaded
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Create 3D relief",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldHQDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "High quality",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldTextureCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use texture",
widgetColumn = 0,
state = Qt.Checked,
setAsDefault = True,
spanWidth = True
)
self.vScaleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = " Vertical scale:",
value = 1.0,
setAsDefault = True,
minimum = -1000.0, # -1000 A
maximum = 1000.0, # 1000 A
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.widthDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Width:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.heightDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label =" Height:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.aspectRatioCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Maintain Aspect Ratio of:' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.aspectRatioSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "",
value = 1.0,
setAsDefault = True,
minimum = 0.1,
maximum = 10.0,
singleStep = 0.1,
decimals = 2,
suffix = " to 1.00")
if self.aspectRatioCheckBox.isChecked():
self.aspectRatioSpinBox.setEnabled(True)
else:
self.aspectRatioSpinBox.setEnabled(False)
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager
whatsThis_PlanePropertyManager(self)
def toggleFileChooserBehavior(self, checked):
"""
Enables FileChooser and displays image when checkbox is checked otherwise
not
"""
self.imageDisplayFileChooser.lineEdit.emit(SIGNAL("editingFinished()"))
if checked == Qt.Checked:
self.imageDisplayFileChooser.setEnabled(True)
elif checked == Qt.Unchecked:
self.imageDisplayFileChooser.setEnabled(False)
# if an image is already displayed, that's need to be hidden as well
else:
pass
self.command.struct.glpane.gl_update()
def toggleHeightfield(self, checked):
"""
Enables 3D relief drawing mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.display_heightfield = checked
if checked:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
plane.computeHeightfield()
else:
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane.heightfield = None
plane.glpane.gl_update()
def toggleHeightfieldHQ(self, checked):
"""
Enables high quality rendering in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_hq = checked
plane.computeHeightfield()
plane.glpane.gl_update()
def toggleTexture(self, checked):
"""
Enables texturing in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_use_texture = checked
# It is not necessary to re-compute the heightfield coordinates
# at this point, they are re-computed whenever the "3D relief image"
# checkbox is set.
plane.glpane.gl_update()
def update_spinboxes(self):
"""
Update the width and height spinboxes.
@see: Plane.resizeGeometry()
This typically gets called when the plane is resized from the
3D workspace (which marks assy as modified) .So, update the spinboxes
that represent the Plane's width and height, but do no emit 'valueChanged'
signal when the spinbox value changes.
@see: Plane.resizeGeometry()
@see: self._update_UI_do_updates()
@see: Plane_EditCommand.command_update_internal_state()
"""
# blockSignals = True make sure that spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue(). This is done
#because the spinbox valu changes as a result of resizing the plane
#from the 3D workspace.
if self.command.hasValidStructure():
self.heightDblSpinBox.setValue(self.command.struct.height,
blockSignals = True)
self.widthDblSpinBox.setValue(self.command.struct.width,
blockSignals = True)
def update_imageFile(self):
"""
Loads image file if path is valid
"""
# Update buttons and checkboxes.
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane = self.command.struct
# Delete current image and heightfield
plane.deleteImage()
plane.heightfield = None
plane.display_image = self.imageDisplayCheckBox.isChecked()
if plane.display_image:
imageFile = str(self.imageDisplayFileChooser.lineEdit.text())
from model.Plane import checkIfValidImagePath
validPath = checkIfValidImagePath(imageFile)
if validPath:
from PIL import Image
# Load image from file
plane.image = Image.open(imageFile)
plane.loadImage(imageFile)
# Compute the relief image
plane.computeHeightfield()
if plane.image:
self.mirrorButton.setEnabled(True)
self.plusNinetyButton.setEnabled(True)
self.minusNinetyButton.setEnabled(True)
self.flipButton.setEnabled(True)
self.heightfieldDisplayCheckBox.setEnabled(True)
if plane.display_heightfield:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
def show(self):
"""
Show the Plane Property Manager.
"""
EditCommand_PM.show(self)
#It turns out that if updateCosmeticProps is called before
#EditCommand_PM.show, the 'preview' properties are not updated
#when you are editing an existing plane. Don't know the cause at this
#time, issue is trivial. So calling it in the end -- Ninad 2007-10-03
if self.command.struct:
plane = self.command.struct
plane.updateCosmeticProps(previewing = True)
if plane.imagePath:
self.imageDisplayFileChooser.setText(plane.imagePath)
self.imageDisplayCheckBox.setChecked(plane.display_image)
#Make sure that the plane placement option is always set to
#'Custom' when the Plane PM is shown. This makes sure that bugs like
#2949 won't occur. Let the user change the plane placement option
#explicitely
button = self.pmPlacementOptions.getButtonById(3)
button.setChecked(True)
def setParameters(self, params):
"""
"""
width, height, gridColor, gridLineType, \
gridXSpacing, gridYSpacing, originLocation, \
displayLabelStyle = params
# blockSignals = True flag makes sure that the
# spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue().
self.widthDblSpinBox.setValue(width, blockSignals = True)
self.heightDblSpinBox.setValue(height, blockSignals = True)
self.win.glpane.gl_update()
self.gpColorTypeComboBox.setColor(gridColor)
self.gridLineType = gridLineType
self.gpXSpacingDoubleSpinBox.setValue(gridXSpacing)
self.gpYSpacingDoubleSpinBox.setValue(gridYSpacing)
self.gpOriginComboBox.setCurrentIndex(originLocation)
self.gpPositionComboBox.setCurrentIndex(displayLabelStyle)
def getCurrrentDisplayParams(self):
"""
Returns a tuple containing current display parameters such as current
image path and grid display params.
@see: Plane_EditCommand.command_update_internal_state() which uses this
to decide whether to modify the structure (e.g. because of change in the
image path or display parameters.)
"""
imagePath = self.imageDisplayFileChooser.text
gridColor = self.gpColorTypeComboBox.getColor()
return (imagePath, gridColor, self.gridLineType,
self.gridXSpacing, self.gridYSpacing,
self.originLocation, self.displayLabelStyle)
def getParameters(self):
"""
"""
width = self.widthDblSpinBox.value()
height = self.heightDblSpinBox.value()
gridColor = self.gpColorTypeComboBox.getColor()
params = (width, height, gridColor, self.gridLineType,
self.gridXSpacing, self.gridYSpacing, self.originLocation,
self.displayLabelStyle)
return params
def change_plane_width(self, newWidth):
"""
Slot for width spinbox in the Property Manager.
@param newWidth: width in Angstroms.
@type newWidth: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.width = newWidth
self.command.struct.height = self.command.struct.width / \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_height(self, newHeight):
"""
Slot for height spinbox in the Property Manager.
@param newHeight: height in Angstroms.
@type newHeight: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.height = newHeight
self.command.struct.width = self.command.struct.height * \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_size(self, gl_update = True):
"""
Slot to change the Plane's width and height.
@param gl_update: Forces an update of the glpane.
@type gl_update: bool
"""
self.command.struct.width = self.widthDblSpinBox.value()
self.command.struct.height = self.heightDblSpinBox.value()
if gl_update:
self.command.struct.glpane.gl_update()
def change_vertical_scale(self, scale):
"""
Changes vertical scaling of the heightfield.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_scale = scale
plane.computeHeightfield()
plane.glpane.gl_update()
def changePlanePlacement(self, buttonId):
"""
Slot to change the placement of the plane depending upon the
option checked in the "Placement Options" group box of the PM.
@param buttonId: The button id of the selected radio button (option).
@type buttonId: int
"""
if buttonId == 0:
msg = "Create a Plane parallel to the screen. "\
"With <b>Parallel to Screen</b> plane placement option, the "\
"center of the plane is always (0,0,0)"
self.updateMessage(msg)
self.command.placePlaneParallelToScreen()
elif buttonId == 1:
msg = "Create a Plane with center coinciding with the common center "\
"of <b> 3 or more selected atoms </b>. If exactly 3 atoms are "\
"selected, the Plane will pass through those atoms."
self.updateMessage(msg)
self.command.placePlaneThroughAtoms()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 2:
msg = "Create a Plane at an <b>offset</b> to the selected plane "\
"indicated by the direction arrow. "\
"you can click on the direction arrow to reverse its direction."
self.updateMessage(msg)
self.command.placePlaneOffsetToAnother()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 3:
#'Custom' plane placement. Do nothing (only update message box)
# Fixes bug 2439
msg = "Create a plane with a <b>Custom</b> plane placement. "\
"The plane is placed parallel to the screen, with "\
"center at (0, 0, 0). User can then modify the plane placement."
self.updateMessage(msg)
def _enableAspectRatioSpinBox(self, enable):
"""
Slot for "Maintain Aspect Ratio" checkbox which enables or disables
the Aspect Ratio spin box.
@param enable: True = enable, False = disable.
@type enable: bool
"""
self.aspectRatioSpinBox.setEnabled(enable)
def _updateAspectRatio(self):
"""
Updates the Aspect Ratio spin box based on the current width and height.
"""
aspectRatio = self.command.struct.width / self.command.struct.height
self.aspectRatioSpinBox.setValue(aspectRatio)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates() for documentation.
@see: Plane.resizeGeometry()
@see: self.update_spinboxes()
@see: Plane_EditCommand.command_update_internal_state()
"""
#This typically gets called when the plane is resized from the
#3D workspace (which marks assy as modified) . So, update the spinboxes
#that represent the Plane's width and height.
self.update_spinboxes()
def update_props_if_needed_before_closing(self):
"""
This updates some cosmetic properties of the Plane (e.g. fill color,
border color, etc.) before closing the Property Manager.
"""
# Example: The Plane Property Manager is open and the user is
# 'previewing' the plane. Now the user clicks on "Build > Atoms"
# to invoke the next command (without clicking "Done").
# This calls openPropertyManager() which replaces the current PM
# with the Build Atoms PM. Thus, it creates and inserts the Plane
# that was being previewed. Before the plane is permanently inserted
# into the part, it needs to change some of its cosmetic properties
# (e.g. fill color, border color, etc.) which distinguishes it as
# a new plane in the part. This function changes those properties.
# ninad 2007-06-13
#called in updatePropertyManager in MWsemeantics.py --(Partwindow class)
EditCommand_PM.update_props_if_needed_before_closing(self)
#Don't draw the direction arrow when the object is finalized.
if self.command.struct and \
self.command.struct.offsetParentGeometry:
dirArrow = self.command.struct.offsetParentGeometry.directionArrow
dirArrow.setDrawRequested(False)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param message: Message to be displayed in the Message groupbox of
the property manager
@type message: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def rotate_90(self):
"""
Rotate the image clockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(0)
return
def rotate_neg_90(self):
"""
Rotate the image counterclockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(1)
return
def flip_image(self):
"""
Flip the image horizontally.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(1)
return
def mirror_image(self):
"""
Flip the image vertically.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(0)
return
class QuteMolPropertyManager(Command_PropertyManager):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = [ "Render axes",
"Hide axes" ]
_bases_display_choices = [ "Render bases",
"Hide bases" ]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Select a QuteMolX rendering style and click the "\
"<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title = "DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title = "Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Axes: ',
choices = self._axes_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.basesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Bases: ',
choices = self._bases_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text = "Launch QuteMolX",
iconPath = "ui/actions/Properties Manager/QuteMol.png",
spanWidth = True )
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton,
SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class DnaDisplayStyle_PropertyManager( Command_PropertyManager):
"""
The DnaDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Dna mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit DNA Display Style"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/EditDnaDisplayStyle.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the DNA display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
# Current display settings groupbox.
change_connect( self.dnaRenditionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaRendition )
# Axis options.
change_connect( self.axisShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisShape )
change_connect( self.axisScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleAxisScale )
change_connect( self.axisColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisColor )
change_connect( self.axisEndingStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisEndingStyle )
# Strands options.
change_connect( self.strandsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsShape )
change_connect( self.strandsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrandsScale )
change_connect( self.strandsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsColor )
change_connect( self.strandsArrowsComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsArrows )
# Structs options.
change_connect( self.strutsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsShape )
change_connect( self.strutsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrutsScale )
change_connect( self.strutsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsColor )
# Nucleotides options.
change_connect( self.nucleotidesShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesShape )
change_connect( self.nucleotidesScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleBasesScale )
change_connect( self.nucleotidesColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesColor )
connect_checkbox_with_boolean_pref(
self.dnaStyleBasesDisplayLettersCheckBox,
dnaStyleBasesDisplayLetters_prefs_key)
# Dna Strand labels option.
change_connect( self.standLabelColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaStrandLabelsDisplay )
def show(self):
"""
Shows the Property Manager. Extends superclass method
"""
_superclass.show(self)
#@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
#-- Ninad 2008-10-02
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
# TODO: rename that public attr of GLPane (widely used)
# from displayMode to displayStyle. [bruce 080910 comment]
self.o.setGlobalDisplayStyle(diDNACYLINDER)
# Update all PM widgets, .
# note: It is important to update the widgets by blocking the
# 'signals'. If done in the reverse order, it will generate signals
#when updating the PM widgets (via updateDnaDisplayStyleWidgets()),
#causing unneccessary repaints of the model view.
self.updateDnaDisplayStyleWidgets(blockSignals = True)
def close(self):
"""
Closes the Property Manager. Extends superclass method.
"""
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Current Display Settings")
self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/DnaDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/DnaDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis(
"""<b> List of Favorites </b>
<p>
Creates a list of favorite DNA display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
dnaRenditionChoices = ['3D (default)',
'2D with base letters',
'2D ball and stick',
'2D ladder']
self.dnaRenditionComboBox = \
PM_ComboBox( pmGroupBox,
label = "Rendition:",
choices = dnaRenditionChoices,
setAsDefault = True)
dnaComponentChoices = ['Axis',
'Strands',
'Struts',
'Nucleotides']
self.dnaComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Component:",
choices = dnaComponentChoices,
setAsDefault = True)
self._loadAxisGroupBox()
self._loadStrandsGroupBox()
self._loadStrutsGroupBox()
self._loadNucleotidesGroupBox()
widgetList = [self.axisGroupBox,
self.strandsGroupBox,
self.strutsGroupBox,
self.nucleotidesGroupBox]
self.dnaComponentStackedWidget = \
PM_StackedWidget( pmGroupBox,
self.dnaComponentComboBox,
widgetList )
standLabelColorChoices = ['Hide',
'Show (in strand color)',
'Black',
'White',
'Custom color...']
self.standLabelColorComboBox = \
PM_ComboBox( pmGroupBox,
label = "Strand labels:",
choices = standLabelColorChoices,
setAsDefault = True)
# This disables "Component" widgets if rendition style is 2D.
self.change_dnaRendition(env.prefs[dnaRendition_prefs_key])
def _loadAxisGroupBox(self):
"""
Load the Axis group box.
"""
axisGroupBox = PM_GroupBox( None )
self.axisGroupBox = axisGroupBox
axisShapeChoices = ['None', 'Wide tube', 'Narrow tube']
self.axisShapeComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Shape:",
choices = axisShapeChoices,
setAsDefault = True)
self.axisScaleDoubleSpinBox = \
PM_DoubleSpinBox( axisGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 2.0,
decimals = 2,
singleStep = 0.1 )
axisColorChoices = ['Same as chunk',
'Base order',
'Base order (discrete)',
'Base type',
'Strand order']
self.axisColorComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Color:",
choices = axisColorChoices,
setAsDefault = True)
endingTypeChoices = ['Flat',
'Taper start',
'Taper end',
'Taper both',
'Spherical']
self.axisEndingStyleComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Ending style:",
choices = endingTypeChoices,
setAsDefault = True)
def _loadStrandsGroupBox(self):
"""
Load the Strands group box.
"""
strandsGroupBox = PM_GroupBox( None )
self.strandsGroupBox = strandsGroupBox
strandsShapeChoices = ['None', 'Cylinders', 'Tube']
self.strandsShapeComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Shape:",
choices = strandsShapeChoices,
setAsDefault = True)
self.strandsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strandsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 5.0,
decimals = 2,
singleStep = 0.1 )
strandsColorChoices = ['Same as chunk',
'Base order',
'Strand order']
self.strandsColorComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Color:",
choices = strandsColorChoices,
setAsDefault = True)
strandsArrowsChoices = ['None',
'5\'',
'3\'',
'5\' and 3\'']
self.strandsArrowsComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Arrows:",
choices = strandsArrowsChoices,
setAsDefault = True)
def _loadStrutsGroupBox(self):
"""
Load the Struts group box.
"""
strutsGroupBox = PM_GroupBox( None )
self.strutsGroupBox = strutsGroupBox
strutsShapeChoices = ['None',
'Base-axis-base cylinders',
'Straight cylinders']
self.strutsShapeComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Shape:",
choices = strutsShapeChoices,
setAsDefault = True)
self.strutsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strutsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
strutsColorChoices = ['Same as strand',
'Base order',
'Strand order',
'Base type']
self.strutsColorComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Color:",
choices = strutsColorChoices,
setAsDefault = True)
def _loadNucleotidesGroupBox(self):
"""
Load the Nucleotides group box.
"""
nucleotidesGroupBox = PM_GroupBox( None )
self.nucleotidesGroupBox = nucleotidesGroupBox
nucleotidesShapeChoices = ['None',
'Sugar spheres',
'Base cartoons']
self.nucleotidesShapeComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Shape:",
choices = nucleotidesShapeChoices,
setAsDefault = True)
self.nucleotidesScaleDoubleSpinBox = \
PM_DoubleSpinBox( nucleotidesGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
nucleotidesColorChoices = ['Same as strand',
'Base order',
'Strand order',
'Base type']
self.nucleotidesColorComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Color:",
choices = nucleotidesColorChoices,
setAsDefault = True)
self.dnaStyleBasesDisplayLettersCheckBox = \
PM_CheckBox(nucleotidesGroupBox ,
text = 'Display base letters',
widgetColumn = 1
)
def updateDnaDisplayStyleWidgets( self , blockSignals = False):
"""
Updates all the DNA Display style widgets based on the current pref keys
values.
@param blockSignals: If its set to True, the set* methods of the
the widgets (currently only PM_ Spinboxes and
ComboBoxes) won't emit a signal.
@type blockSignals: bool
@see: self.show() where this method is called.
@see: PM_Spinbox.setValue()
@see: PM_ComboBox.setCurrentIndex()
@note: This should be called each time the PM is displayed (see show()).
"""
self.dnaRenditionComboBox.setCurrentIndex(
env.prefs[dnaRendition_prefs_key],
blockSignals = blockSignals )
self.axisShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisShape_prefs_key], blockSignals = blockSignals)
self.axisScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleAxisScale_prefs_key], blockSignals = blockSignals)
self.axisColorComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisColor_prefs_key], blockSignals = blockSignals)
self.axisEndingStyleComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisEndingStyle_prefs_key], blockSignals = blockSignals)
self.strandsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsShape_prefs_key], blockSignals = blockSignals)
self.strandsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrandsScale_prefs_key], blockSignals = blockSignals)
self.strandsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsColor_prefs_key], blockSignals = blockSignals)
self.strandsArrowsComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsArrows_prefs_key], blockSignals = blockSignals)
self.strutsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsShape_prefs_key], blockSignals = blockSignals)
self.strutsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrutsScale_prefs_key], blockSignals = blockSignals)
self.strutsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsColor_prefs_key], blockSignals = blockSignals)
self.nucleotidesShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesShape_prefs_key], blockSignals = blockSignals)
self.nucleotidesScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleBasesScale_prefs_key], blockSignals = blockSignals)
self.nucleotidesColorComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesColor_prefs_key], blockSignals = blockSignals)
# DNA Strand label combobox.
if env.prefs[dnaStrandLabelsEnabled_prefs_key]:
_dnaStrandColorItem = env.prefs[dnaStrandLabelsColorMode_prefs_key] + 1
else:
_dnaStrandColorItem = 0
self.standLabelColorComboBox.setCurrentIndex(
_dnaStrandColorItem, blockSignals = blockSignals)
def change_dnaStrandLabelsDisplay(self, mode):
"""
Changes DNA Strand labels display (and color) mode.
@param mode: The display mode:
- 0 = hide all labels
- 1 = show (same color as chunk)
- 2 = show (black)
- 3 = show (white)
- 4 = show (custom color...)
@type mode: int
"""
if mode == 4:
self.win.userPrefs.change_dnaStrandLabelsColor()
if mode == 0:
#@ Fix this at the same time I (we) remove the DNA display style
# prefs options from the Preferences dialog. --Mark 2008-05-13
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(False)
else:
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(True)
self.win.userPrefs.change_dnaStrandLabelsColorMode(mode - 1)
def applyFavorite(self):
"""
Apply the DNA display style settings stored in the current favorite
(selected in the combobox) to the current DNA display style settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateDnaDisplayStyleWidgets()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current DNA display style
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The DNA display style settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/DnaDisplayStyle/$FAV_NAME.fav).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
#Check to see if favfilepath exists first
if not os.path.exists(favfilepath):
msg = "%s does not exist" % favfilepath
env.history.message(cmd + msg)
return
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
saveLocation, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir = None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir = None):
"""
[private method]
Set the working directory in the user preferences database.
@param workdir: The fullpath directory to write to the user pref db.
If I{workdir} is None (default), there is no change.
@type workdir: string
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message( redmsg(msg))
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile=loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateDnaDisplayStyleWidgets()
return
def change_dnaRendition(self, rendition):
"""
Sets the DNA rendition to 3D or one of the optional 2D styles.
@param rendition: The rendition mode, where:
- 0 = 3D (default)
- 1 = 2D with base letters
- 2 = 2D ball and stick
- 3 = 2D ladder
@type rendition: int
"""
if rendition == 0:
_enabled_flag = True
else:
_enabled_flag = False
self.dnaComponentComboBox.setEnabled(_enabled_flag)
self.dnaComponentStackedWidget.setEnabled(_enabled_flag)
self.standLabelColorComboBox.setEnabled(_enabled_flag)
env.prefs[dnaRendition_prefs_key] = rendition
self.o.gl_update() # Force redraw
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditDnaDisplayStyle_PropertyManager
ToolTip_EditDnaDisplayStyle_PropertyManager(self)
class TestGraphics_PropertyManager(Command_PropertyManager):
"""
The TestGraphics_PropertyManager class provides a Property Manager
for the Test Graphics command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Test Graphics"
pmName = title
iconPath = None ###k "ui/actions/View/Stereo_View.png" ### FIX - use some generic or default icon
def __init__(self, command):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = "Test the performance effect of graphics settings below. " \
"(To avoid bugs, choose testCase before bypassing paintGL.)"
self.updateMessage(msg)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Settings") ### fix title
self._loadGroupBox1(self._pmGroupBox1)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
from widgets.prefs_widgets import ObjAttr_StateRef ### toplevel
self._cb2 = \
PM_CheckBox(pmGroupBox,
text = "redraw continuously",
)
self._cb2.connectWithState(
ObjAttr_StateRef(self.command, 'redraw_continuously'))
self._cb3 = \
PM_CheckBox(pmGroupBox,
text = "spin model",
)
self._cb3.connectWithState(ObjAttr_StateRef(self.command,
'spin_model'))
self._cb4 = \
PM_CheckBox(pmGroupBox,
text = "print fps to console",
)
self._cb4.connectWithState(ObjAttr_StateRef(self.command, 'print_fps'))
self._cb1 = \
PM_CheckBox(pmGroupBox,
text = "replace paintGL with testCase",
)
self._cb1.connectWithState(
ObjAttr_StateRef(self.command, 'bypass_paintgl'))
# note: this state (unlike the highest-quality staterefs)
# is not change-tracked [as of 081003], so nothing aside from
# user clicks on this checkbox should modify it after this runs,
# or our UI state will become out of sync with the state.
self.testCase_ComboBox = PM_ComboBox(
pmGroupBox,
label="testCase:",
labelColumn=0,
choices=self.command.testCaseChoicesText,
setAsDefault=False)
self.testCase_ComboBox.setCurrentIndex(self.command.testCaseIndex)
self.nSpheres_ComboBox = PM_ComboBox(
pmGroupBox,
label="n x n spheres:",
labelColumn=0,
choices=self.command._NSPHERES_CHOICES,
setAsDefault=False)
nSpheres_index = self.command._NSPHERES_CHOICES.index(
str(self.command.nSpheres))
self.nSpheres_ComboBox.setCurrentIndex(nSpheres_index)
self._set_nSpheresIndex(nSpheres_index)
self.detail_level_ComboBox = PM_ComboBox(
pmGroupBox,
label="Level of detail:",
labelColumn=0,
choices=["Low", "Medium", "High", "Variable"],
setAsDefault=False)
lod = env.prefs[levelOfDetail_prefs_key]
if lod > 2:
lod = 2
if lod < 0: # only lod == -1 is legal here
lod = 3
self.detail_level_ComboBox.setCurrentIndex(lod)
self.set_level_of_detail_index(lod)
self._updateWidgets()
## def updateUI(self): # BUG: this is not being called -- I guess the bypassed paintGL doesn't call it.
## self._updateWidgets() ### will this be too slow?
def _addWhatsThisText(self):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.testCase_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self.command._set_testCaseIndex)
change_connect(self.nSpheres_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self._set_nSpheresIndex)
change_connect(
self.detail_level_ComboBox,
SIGNAL("currentIndexChanged(int)"),
# in current code, SIGNAL("activated(int)")
self.set_level_of_detail_index)
return
# ==
def _set_nSpheresIndex(self, index):
self.command.nSpheres = int(self.command._NSPHERES_CHOICES[index])
def set_level_of_detail_index(
self,
level_of_detail_index): # copied from other code, renamed, revised
"""
Change the level of detail, where <level_of_detail_index> is a value
between 0 and 3 where:
- 0 = low
- 1 = medium
- 2 = high
- 3 = variable (based on number of atoms in the part)
@note: the prefs db value for 'variable' is -1, to allow for higher LOD
levels in the future.
"""
lod = level_of_detail_index
if lod == 3:
lod = -1
self.command.detailLevel = lod
def _updateWidgets(self):
"""
Update widget configuration based on state of prior widgets.
"""
## # presently, the LOD is not noticed by the test cases... oops, not true!
## self.detail_level_ComboBox.setEnabled( not self.command.bypass_paintgl )
return
pass
class DnaGeneratorPropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The DnaGeneratorPropertyManager class provides a Property Manager
for the "Build > Atoms" command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
@ivar validSymbols: Miscellaneous symbols that may appear in the sequence
(but are ignored). The hyphen '-' is a special case
that must be dealt with individually; it is not
included because it can confuse regular expressions.
@type validSymbols: QString
"""
title = "DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?')
# The following class variables guarantee the UI's menu items
# are synchronized with their action code. The arrays should
# not be changed, unless an item is removed or inserted.
# Changes should be made via only the _action... variables.
# e.g., Change _action_Complement from "Complement"
# to "Complement Sequences". The menu item will
# change and its related code will need no update.
_action_Complement = "Complement"
_action_Reverse = "Reverse"
_action_RemoveUnrecognized = 'Remove unrecognized letters'
_action_ConvertUnrecognized = 'Convert unrecognized letters to "N"'
_actionChoices = [ "Action",
"---",
_action_Complement,
_action_Reverse,
_action_RemoveUnrecognized,
_action_ConvertUnrecognized ]
_modeltype_PAM3 = "PAM3"
_modeltype_PAM5 = "PAM5"
_modeltype_Atomistic = "Atomistic" # deprecated
_modelChoices = [ _modeltype_PAM3,
_modeltype_PAM5 ]
def __init__( self ):
"""
Constructor for the DNA Generator property manager.
"""
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
DebugMenuMixin._init1( self )
msg = "Edit the DNA parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into \
the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PM is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = True )
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Strand Sequence" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "DNA Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
# Duplex Length
self.duplexLengthSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Duplex Length: ",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 34000,
singleStep = self.getDuplexRise("B-DNA"),
decimals = 3,
suffix = ' Angstroms')
self.connect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged )
# Strand Length
self.strandLengthSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Strand Length :",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000,
suffix = ' bases' )
self.connect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
# New Base choices
newBaseChoices = []
for theBase in basesDict.keys():
newBaseChoices = newBaseChoices \
+ [ theBase + ' (' \
+ basesDict[theBase]['Name'] + ')' ]
try:
defaultBaseChoice = basesDict.keys().index('N')
except:
defaultBaseChoice = 0
# Strand Sequence
self.sequenceTextEdit = \
PM_TextEdit( pmGroupBox,
label = "",
spanWidth = True )
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.connect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
self.connect( self.sequenceTextEdit,
SIGNAL("cursorPositionChanged()"),
self.cursorPosChanged )
# Actions
self.actionsComboBox = \
PM_ComboBox( pmGroupBox,
label = '',
choices = self._actionChoices,
index = 0,
setAsDefault = True,
spanWidth = True )
# If SIGNAL("activate(const QString&)") is used, we get a TypeError.
# This is a bug that needs Bruce. Using currentIndexChanged(int) as
# a workaround, but there is still a bug when the "Reverse" action
# is selected. Mark 2007-08-15
self.connect( self.actionsComboBox,
SIGNAL("currentIndexChanged(int)"),
self.actionsComboBoxChanged )
def _loadGroupBox2( self, pmGroupBox ):
"""
Load widgets in group box 2.
"""
self.modelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model :",
choices = self._modelChoices,
setAsDefault = True)
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation :",
choices = ["B-DNA"],
setAsDefault = True)
self.connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
self.basesPerTurnComboBox= \
PM_ComboBox( pmGroupBox,
label = "Bases Per Turn :",
choices = ["10.0", "10.5", "10.67"],
setAsDefault = True)
# I may decide to reintroduce "base-pair chunks" at a later time.
# Please talk to me if you have a strong feeling about including
# this. Mark 2007-08-19.
createChoices = ["Strand chunks", \
"Single chunk" ]
#@ "Base-pair chunks"]
self.createComboBox = \
PM_ComboBox( pmGroupBox,
label = "Create :",
choices = createChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
self._endPoint1GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint1" )
self._endPoint2GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint2" )
# Point 1
self.x1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
# Point 2
self.x2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 10.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
def _addWhatsThisText( self ):
"""
What's This text for some of the widgets in the
DNA Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
self.conformationComboBox.setWhatsThis("""<b>Conformation</b>
<p>There are three DNA geometries, A-DNA, B-DNA,
and Z-DNA. Only B-DNA and Z-DNA are currently supported.</p>""")
self.sequenceTextEdit.setWhatsThis("""<b>Strand Sequence</b>
<p>Type in the strand sequence you want to generate here (5' => 3')<br>
<br>
Recognized base letters:<br>
<br>
A = Adenosine<br>
C = Cytosine<br>
G = Guanosine<br>
T = Thymidine<br>
N = aNy base<br>
X = Unassigned<br>
<br>
Other base letters currently recognized:<br>
<br>
B = C,G, or T<br>
D = A,G, or T<br>
H = A,C, or T<br>
V = A,C, or G<br>
R = A or G (puRine)<br>
Y = C or T (pYrimidine)<br>
K = G or T (Keto)<br>
M = A or C (aMino)<br>
S = G or C (Strong -3H bonds)<br>
W = A or T (Weak - 2H bonds)<br>
</p>""")
self.actionsComboBox.setWhatsThis("""<b>Action</b>
<p>Select an action to perform on the sequence.</p>""")
def conformationComboBoxChanged( self, inIndex ):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.basesPerTurnComboBox.clear()
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnComboBox.insertItem(0, "10.0")
self.basesPerTurnComboBox.insertItem(1, "10.5")
self.basesPerTurnComboBox.insertItem(2, "10.67")
#10.5 is the default value for Bases per turn.
#So set the current index to 1
self.basesPerTurnComboBox.setCurrentIndex(1)
elif conformation == "Z-DNA":
self.basesPerTurnComboBox.insertItem(0, "12.0")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
conformation = "B-DNA" # Workaround for "Restore Defaults".
pass
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = "+ inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(
self.getDuplexRise(conformation) )
def modelComboBoxChanged( self, inIndex ):
"""
Slot for the Model combobox. It is called whenever the
Model choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self._modelChoices[ inIndex ]
self.disconnect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
self.conformationComboBox.clear() # Generates signal!
if conformation == self._modeltype_PAM3:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_PAM5:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_Atomistic:
self.conformationComboBox.addItem("B-DNA")
self.conformationComboBox.addItem("Z-DNA")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
pass
else:
msg = "Error - unknown model representation. Index = " + inIndex
env.history.message(redmsg(msg))
self.connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
# GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox.
def getDuplexRise( self, inConformation ):
"""
Return the 'rise' between base pairs of the
specified DNA type (conformation).
@param inConformation: The current conformation.
@type inConformation: int
"""
return dnaDict[str(inConformation)]['DuplexRise']
def synchronizeLengths( self ):
"""
Guarantees the values of the duplex length and strand length
spinboxes agree with the strand sequence (textedit).
"""
self.updateStrandLength()
self.updateDuplexLength()
return
# Added :jbirac 20070613:
def duplexLengthChanged( self, inDuplexLength ):
"""
Slot for the duplex length spinbox, called whenever the value of the
Duplex Length spinbox changes.
@param inDuplexLength: The duplex length.
@type inDuplexLength: float
"""
conformation = self.conformationComboBox.currentText()
duplexRise = self.getDuplexRise( conformation )
newStrandLength = inDuplexLength / duplexRise + 0.5
newStrandLength = int( newStrandLength )
self.strandLengthChanged( newStrandLength )
def updateDuplexLength( self ): # Added :jbirac 20070615:
"""
Update the Duplex Length spinbox; always the length of the
strand sequence multiplied by the 'rise' of the duplex. This
method is called by slots of other controls (i.e., this itself
is not a slot.)
"""
conformation = self.conformationComboBox.currentText()
newDuplexLength = self.getDuplexRise( conformation ) \
* self.getSequenceLength()
self.disconnect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
self.duplexLengthSpinBox.setValue( newDuplexLength )
self.connect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Renamed from length_changed :jbirac 20070613:
def strandLengthChanged( self, inStrandLength ):
"""
Slot for the Strand Length spin box, called whenever the value of the
Strand Length spin box changes.
@param inStrandLength: The number of bases in the strand sequence.
@type inStrandLength: int
"""
theSequence = self.getPlainSequence()
sequenceLen = len( theSequence )
lengthChange = inStrandLength - self.getSequenceLength()
# Preserve the cursor's position/selection
cursor = self.sequenceTextEdit.textCursor()
#cursorPosition = cursor.position()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStrandLength < 0:
return # Should never happen.
if lengthChange < 0:
# If length is less than the previous length,
# simply truncate the current sequence.
theSequence.chop( -lengthChange )
elif lengthChange > 0:
# If length has increased, add the correct number of base
# letters to the current strand sequence.
numNewBases = lengthChange
# Get current base selected in combobox.
chosenBase = 'X' # Unassigned.
basesToAdd = chosenBase * numNewBases
theSequence.append( basesToAdd )
else:
env.history.message(
orangemsg( "strandLengthChanged(): Length has not changed." ))
self.setSequence( theSequence )
return
# Renamed from updateLength :jbirac 20070613:
def updateStrandLength( self ):
"""
Update the Strand Length spinbox; always the length of the strand
sequence.
"""
self.disconnect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
self.strandLengthSpinBox.setValue( self.getSequenceLength() )
self.connect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
return
def sequenceChanged( self ):
"""
Slot for the Strand Sequence textedit widget.
Assumes the sequence changed directly by user's keystroke in the
textedit. Other methods...
"""
cursorPosition = self.getCursorPosition()
theSequence = self.getPlainSequence()
# Disconnect while we edit the sequence.
self.disconnect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
# How has the text changed?
if theSequence.length() == 0: # There is no sequence.
self.updateStrandLength()
self.updateDuplexLength()
else:
# Insert the sequence; it will be "stylized" by setSequence().
self.setSequence( theSequence )
# Reconnect to respond when the sequence is changed.
self.connect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
self.synchronizeLengths()
return
def getPlainSequence( self, inOmitSymbols = False ):
"""
Returns a plain text QString (without HTML stylization)
of the current sequence. All characters are preserved (unless
specified explicitly), including valid base letters, punctuation
symbols, whitespace and invalid letters.
@param inOmitSymbols: Omits characters listed in self.validSymbols.
@type inOmitSymbols: bool
@return: The current DNA sequence in the PM.
@rtype: QString
"""
outSequence = self.sequenceTextEdit.toPlainText()
if inOmitSymbols:
# This may look like a sloppy piece of code, but Qt's QRegExp
# class makes it pretty tricky to remove all punctuation.
theString = '[<>' \
+ str( QRegExp.escape(self.validSymbols) ) \
+ ']|-'
outSequence.remove(QRegExp( theString ))
return outSequence
def stylizeSequence( self, inSequence ):
"""
Converts a plain text string of a sequence (including optional
symbols) to an HTML rich text string.
@param inSequence: A DNA sequence.
@type inSequence: QString
@return: The sequence.
@rtype: QString
"""
outSequence = str(inSequence)
# Verify that all characters (bases) in the sequence are "valid".
invalidSequence = False
basePosition = 0
sequencePosition = 0
invalidStartTag = "<b><font color=black>"
invalidEndTag = "</b>"
previousChar = chr(1) # Null character; may be revised.
# Some characters must be substituted to preserve
# whitespace and tags in HTML code.
substituteDict = { ' ':' ', '<':'<', '>':'>' }
while basePosition < len(outSequence):
theSeqChar = outSequence[basePosition]
if ( theSeqChar in basesDict
or theSeqChar in self.validSymbols ):
# Close any preceding invalid sequence segment.
if invalidSequence == True:
outSequence = outSequence[:basePosition] \
+ invalidEndTag \
+ outSequence[basePosition:]
basePosition += len(invalidEndTag)
invalidSequence = False
# Color the valid characters.
if theSeqChar != previousChar:
# We only need to insert 'color' tags in places where
# the adjacent characters are different.
if theSeqChar in basesDict:
theTag = '<font color=' \
+ basesDict[ theSeqChar ]['Color'] \
+ '>'
elif not previousChar in self.validSymbols:
# The character is a 'valid' symbol to be greyed
# out. Only one 'color' tag is needed for a
# group of adjacent symbols.
theTag = '<font color=dimgrey>'
else:
theTag = ''
outSequence = outSequence[:basePosition] \
+ theTag + outSequence[basePosition:]
basePosition += len(theTag)
# Any <space> character must be substituted with an
# ASCII code tag because the HTML engine will collapse
# whitespace to a single <space> character; whitespace
# is truncated from the end of HTML by default.
# Also, many symbol characters must be substituted
# because they confuse the HTML syntax.
#if str( outSequence[basePosition] ) in substituteDict:
if outSequence[basePosition] in substituteDict:
#theTag = substituteDict[theSeqChar]
theTag = substituteDict[ outSequence[basePosition] ]
outSequence = outSequence[:basePosition] \
+ theTag \
+ outSequence[basePosition + 1:]
basePosition += len(theTag) - 1
else:
# The sequence character is invalid (but permissible).
# Tags (e.g., <b> and </b>) must be inserted at both the
# beginning and end of a segment of invalid characters.
if invalidSequence == False:
outSequence = outSequence[:basePosition] \
+ invalidStartTag \
+ outSequence[basePosition:]
basePosition += len(invalidStartTag)
invalidSequence = True
basePosition += 1
previousChar = theSeqChar
#basePosition += 1
# Specify that theSequence is definitely HTML format, because
# Qt can get confused between HTML and Plain Text.
outSequence = "<html>" + outSequence
outSequence += "</html>"
return outSequence
def setSequence( self,
inSequence,
inStylize = True,
inRestoreCursor = True ):
"""
Replace the current strand sequence with the new sequence text.
@param inSequence: The new sequence.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
text string (including optional symbols) to an HTML
rich text string.
@type inStylize: bool
@param inRestoreCursor: Not implemented yet.
@type inRestoreCursor: bool
@attention: Signals/slots must be managed before calling this method.
The textChanged() signal will be sent to any connected widgets.
"""
cursor = self.sequenceTextEdit.textCursor()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStylize:
inSequence = self.stylizeSequence( inSequence )
self.sequenceTextEdit.insertHtml( inSequence )
if inRestoreCursor:
cursor.setPosition( min(selectionStart, self.getSequenceLength()),
QTextCursor.MoveAnchor )
cursor.setPosition( min(selectionEnd, self.getSequenceLength()),
QTextCursor.KeepAnchor )
self.sequenceTextEdit.setTextCursor( cursor )
return
def getSequenceLength( self ):
"""
Returns the number of characters in
the strand sequence textedit widget.
"""
theSequence = self.getPlainSequence( inOmitSymbols = True )
outLength = theSequence.length()
return outLength
def getCursorPosition( self ):
"""
Returns the cursor position in the
strand sequence textedit widget.
"""
cursor = self.sequenceTextEdit.textCursor()
return cursor.position()
def cursorPosChanged( self ):
"""
Slot called when the cursor position changes.
"""
cursor = self.sequenceTextEdit.textCursor()
if 0:
env.history.message( greenmsg( "cursorPosChanged: Selection ("
+ str(cursor.selectionStart())
+ " thru "
+ str(cursor.selectionEnd())+')' ) )
return
def actionsComboBoxChanged( self, inIndex ):
"""
Slot for the Actions combobox. It is called whenever the
Action choice is changed.
@param inIndex: The index of the selected action choice.
@type inIndex: int
"""
if inIndex == 0: # Very important.
return
actionName = str(self.actionsComboBox.currentText())
self.actionsComboBox.setCurrentIndex( 0 ) # Generates signal!
self.invokeAction( actionName )
return
def invokeAction( self, inActionName ):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = 'N')
self.setSequence( outResult )
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = '')
self.setSequence( outResult )
return
class StereoProperties_PropertyManager(Command_PropertyManager):
"""
The StereoProperties_PropertyManager class provides a Property Manager
for the Stereo View command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Stereo View"
pmName = title
iconPath = "ui/actions/View/Stereo_View.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the Stereo View settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.stereoEnabledCheckBox,
SIGNAL("toggled(bool)"),
self._enableStereo )
change_connect( self.stereoModeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._stereoModeComboBoxChanged )
change_connect(self.stereoSeparationSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeSeparationSliderChanged )
change_connect(self.stereoAngleSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeAngleSliderChanged )
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Settings")
self._loadGroupBox1( self._pmGroupBox1 )
#@ self._pmGroupBox1.hide()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = ['Relaxed view',
'Cross-eyed view',
'Red/blue anaglyphs',
'Red/cyan anaglyphs',
'Red/green anaglyphs']
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(env.prefs[stereoViewMode_prefs_key]-1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def _enableStereo(self, enabled):
"""
Enable stereo view.
"""
glpane = self.o
if glpane:
glpane.set_stereo_enabled( enabled)
# switch to perspective mode
if enabled:
# store current projection mode
glpane.__StereoProperties_last_ortho = glpane.ortho
if glpane.ortho:
# dont use glpane.setViewProjection
# because we don't want to modify
# default projection setting
glpane.ortho = 0
else:
# restore default mode
if hasattr(glpane, "__StereoProperties_last_ortho"):
projection = glpane.__StereoProperties_last_ortho
if glpane.ortho != projection:
glpane.ortho = projection
self._updateWidgets()
glpane.gl_update()
def _stereoModeComboBoxChanged(self, mode):
"""
Change stereo mode.
@param mode: stereo mode (0=relaxed, 1=cross-eyed, 2=red/blue,
3=red/cyan, 4=red/green)
@type value: int
"""
env.prefs[stereoViewMode_prefs_key] = mode + 1
self._updateSeparationSlider()
def _stereoModeSeparationSliderChanged(self, value):
"""
Change stereo view separation.
@param value: separation (0..300)
@type value: int
"""
env.prefs[stereoViewSeparation_prefs_key] = value
def _stereoModeAngleSliderChanged(self, value):
"""
Change stereo view angle.
@param value: stereo angle (0..100)
@type value: int
"""
env.prefs[stereoViewAngle_prefs_key] = value
def _updateSeparationSlider(self):
"""
Update the separation slider widget.
"""
if self.stereoModeComboBox.currentIndex() >= 2:
# for anaglyphs disable the separation slider
self.stereoSeparationSlider.setEnabled(False)
else:
# otherwise, enable the separation slider
self.stereoSeparationSlider.setEnabled(True)
def _updateWidgets(self):
"""
Update stereo PM widgets.
"""
if self.stereoEnabledCheckBox.isChecked():
self.stereoModeComboBox.setEnabled(True)
self.stereoSeparationSlider.setEnabled(True)
self.stereoAngleSlider.setEnabled(True)
self._updateSeparationSlider()
else:
self.stereoModeComboBox.setEnabled(False)
self.stereoSeparationSlider.setEnabled(False)
self.stereoAngleSlider.setEnabled(False)
class ProteinDisplayStyle_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Edit Protein Display Style"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__(self, parentCommand):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = "Modify the protein display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# Favorite buttons signal-slot connections.
change_connect(self.applyFavoriteButton, SIGNAL("clicked()"), self.applyFavorite)
change_connect(self.addFavoriteButton, SIGNAL("clicked()"), self.addFavorite)
change_connect(self.deleteFavoriteButton, SIGNAL("clicked()"), self.deleteFavorite)
change_connect(self.saveFavoriteButton, SIGNAL("clicked()"), self.saveFavorite)
change_connect(self.loadFavoriteButton, SIGNAL("clicked()"), self.loadFavorite)
# Display group box signal slot connections
change_connect(self.proteinStyleComboBox, SIGNAL("currentIndexChanged(int)"), self.changeProteinDisplayStyle)
change_connect(self.smoothingCheckBox, SIGNAL("stateChanged(int)"), self.smoothProteinDisplay)
change_connect(self.scaleComboBox, SIGNAL("currentIndexChanged(int)"), self.changeProteinDisplayScale)
change_connect(self.splineDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeProteinSplineValue)
change_connect(self.scaleFactorDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeProteinScaleFactor)
# color groupbox
change_connect(self.proteinComponentComboBox, SIGNAL("currentIndexChanged(int)"), self.chooseProteinComponent)
change_connect(
self.proteinAuxComponentComboBox, SIGNAL("currentIndexChanged(int)"), self.chooseAuxilliaryProteinComponent
)
change_connect(self.customColorComboBox, SIGNAL("editingFinished()"), self.chooseCustomColor)
change_connect(self.auxColorComboBox, SIGNAL("editingFinished()"), self.chooseAuxilliaryColor)
change_connect(self.discColorCheckBox, SIGNAL("stateChanged(int)"), self.setDiscreteColors)
change_connect(self.helixColorComboBox, SIGNAL("editingFinished()"), self.chooseHelixColor)
change_connect(self.strandColorComboBox, SIGNAL("editingFinished()"), self.chooseStrandColor)
change_connect(self.coilColorComboBox, SIGNAL("editingFinished()"), self.chooseCoilColor)
# Protein Display methods
def changeProteinDisplayStyle(self, idx):
env.prefs[proteinStyle_prefs_key] = idx
return
def changeProteinDisplayQuality(self, idx):
env.prefs[proteinStyleQuality_prefs_key] = idx
return
def smoothProteinDisplay(self, state):
if state == Qt.Checked:
env.prefs[proteinStyleSmooth_prefs_key] = True
else:
env.prefs[proteinStyleSmooth_prefs_key] = False
return
def changeProteinDisplayScale(self, idx):
env.prefs[proteinStyleScaling_prefs_key] = idx
return
def changeProteinSplineValue(self, val):
env.prefs[proteinStyleQuality_prefs_key] = val
return
def changeProteinScaleFactor(self, val):
env.prefs[proteinStyleScaleFactor_prefs_key] = val
return
def chooseProteinComponent(self, idx):
env.prefs[proteinStyleColors_prefs_key] = idx
return
def chooseAuxilliaryProteinComponent(self, idx):
env.prefs[proteinStyleAuxColors_prefs_key] = idx - 1
return
def chooseCustomColor(self):
color = self.customColorComboBox.getColor()
env.prefs[proteinStyleCustomColor_prefs_key] = color
return
def chooseAuxilliaryColor(self):
color = self.auxColorComboBox.getColor()
env.prefs[proteinStyleAuxCustomColor_prefs_key] = color
return
def chooseHelixColor(self):
color = self.helixColorComboBox.getColor()
env.prefs[proteinStyleHelixColor_prefs_key] = color
return
def chooseStrandColor(self):
color = self.strandColorComboBox.getColor()
env.prefs[proteinStyleStrandColor_prefs_key] = color
return
def chooseCoilColor(self):
color = self.coilColorComboBox.getColor()
env.prefs[proteinStyleCoilColor_prefs_key] = color
return
def setDiscreteColors(self, state):
if state == Qt.Checked:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = True
else:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = False
return
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
# TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
# Not required for Proteins
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
# self.originalDisplayStyle = self.o.getGlobalDisplayStyle()
# self.o.setGlobalDisplayStyle(diDNACYLINDER)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self.updateProteinDisplayStyleWidgets()
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
# Not required for proteins
# Restore the original global display style.
# self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Favorites")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Display")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Color")
self._loadGroupBox3(self._pmGroupBox3)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/ProteinDisplayStyle directory
favoriteChoices = ["Factory default settings"]
# look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir("Favorites/ProteinDisplayStyle")
for file in os.listdir(_dir):
fullname = os.path.join(_dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch(file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0 : len(file) - 4])
self.favoritesComboBox = PM_ComboBox(pmGroupBox, choices=favoriteChoices, spanWidth=True)
self.favoritesComboBox.setWhatsThis(
"""<b> List of Favorites </b>
<p>
Creates a list of favorite Protein display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button."""
)
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
(
"QToolButton",
1,
"APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyPeptideDisplayStyleFavorite.png",
"Apply Favorite",
"",
0,
),
("QToolButton", 2, "ADD_FAVORITE", "ui/actions/Properties Manager/AddFavorite.png", "Add Favorite", "", 1),
(
"QToolButton",
3,
"DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite",
"",
2,
),
(
"QToolButton",
4,
"SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite",
"",
3,
),
(
"QToolButton",
5,
"LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite",
"",
4,
),
]
self.favsButtonGroup = PM_ToolButtonRow(
pmGroupBox,
title="",
buttonList=BUTTON_LIST,
spanWidth=True,
isAutoRaise=False,
isCheckable=False,
setAsDefault=True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
proteinStyleChoices = [
"CA trace (wire)",
"CA trace (cylinders)",
"CA trace (ball and stick)",
"Tube",
"Ladder",
"Zigzag",
"Flat ribbon",
"Solid ribbon",
"Cartoons",
"Fancy cartoons",
"Peptide tiles",
]
self.proteinStyleComboBox = PM_ComboBox(
pmGroupBox, label="Style:", choices=proteinStyleChoices, setAsDefault=True
)
scaleChoices = ["Constant", "Secondary structure", "B-factor"]
self.scaleComboBox = PM_ComboBox(pmGroupBox, label="Scaling:", choices=scaleChoices, setAsDefault=True)
self.scaleFactorDoubleSpinBox = PM_DoubleSpinBox(
pmGroupBox,
label="Scaling factor:",
value=1.00,
setAsDefault=True,
minimum=0.1,
maximum=3.0,
decimals=1,
singleStep=0.1,
)
self.splineDoubleSpinBox = PM_DoubleSpinBox(
pmGroupBox, label="Resolution:", value=4, setAsDefault=True, minimum=2, maximum=8, decimals=0, singleStep=1
)
self.smoothingCheckBox = PM_CheckBox(pmGroupBox, text="Smoothing", setAsDefault=True)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
colorChoices = [
"Chunk",
"Chain",
"Order",
"Hydropathy",
"Polarity",
"Acidity",
"Size",
"Character",
"Number of contacts",
"Secondary structure type",
"Secondary structure order",
"B-factor",
"Occupancy",
"Custom",
]
self.proteinComponentComboBox = PM_ComboBox(
pmGroupBox, label="Color by:", choices=colorChoices, setAsDefault=True
)
colorList = [orange, yellow, red, magenta, cyan, blue, white, black, gray]
colorNames = ["Orange(default)", "Yellow", "Red", "Magenta", "Cyan", "Blue", "White", "Black", "Other color..."]
self.customColorComboBox = PM_ColorComboBox(
pmGroupBox, colorList=colorList, colorNames=colorNames, label="Custom:", color=orange, setAsDefault=True
)
colorChoices1 = [
"Same as main color",
"Chunk",
"Chain",
"Order",
"Hydropathy",
"Polarity",
"Acidity",
"Size",
"Character",
"Number of contacts",
"Secondary structure type",
"Secondary structure order",
"B-factor",
"Occupancy",
"Custom",
]
self.proteinAuxComponentComboBox = PM_ComboBox(
pmGroupBox, label="Aux:", choices=colorChoices1, setAsDefault=True
)
colorListAux = [orange, yellow, red, magenta, cyan, blue, white, black, gray]
colorNamesAux = [
"Orange(default)",
"Yellow",
"Red",
"Magenta",
"Cyan",
"Blue",
"White",
"Black",
"Other color...",
]
self.auxColorComboBox = PM_ColorComboBox(
pmGroupBox,
colorList=colorListAux,
colorNames=colorNamesAux,
label="Custom aux:",
color=gray,
setAsDefault=True,
)
self.discColorCheckBox = PM_CheckBox(pmGroupBox, text="Discretize colors", setAsDefault=True)
colorListHelix = [red, yellow, gray, magenta, cyan, blue, white, black, orange]
colorNamesHelix = [
"Red(default)",
"Yellow",
"Gray",
"Magenta",
"Cyan",
"Blue",
"White",
"Black",
"Other color...",
]
self.helixColorComboBox = PM_ColorComboBox(
pmGroupBox,
colorList=colorListHelix,
colorNames=colorNamesHelix,
label="Helix:",
color=red,
setAsDefault=True,
)
colorListStrand = [cyan, yellow, gray, magenta, red, blue, white, black, orange]
colorNamesStrand = [
"Cyan(default)",
"Yellow",
"Gray",
"Magenta",
"Red",
"Blue",
"White",
"Black",
"Other color...",
]
self.strandColorComboBox = PM_ColorComboBox(
pmGroupBox,
colorList=colorListStrand,
colorNames=colorNamesStrand,
label="Strand:",
color=cyan,
setAsDefault=True,
)
self.coilColorComboBox = PM_ColorComboBox(
pmGroupBox, colorList=colorListAux, colorNames=colorNamesAux, label="Coil:", color=orange, setAsDefault=True
)
def updateProteinDisplayStyleWidgets(self):
"""
Updates all the Protein Display style widgets based on the current pref keys
values
"""
self.proteinStyleComboBox.setCurrentIndex(env.prefs[proteinStyle_prefs_key])
self.splineDoubleSpinBox.setValue(env.prefs[proteinStyleQuality_prefs_key])
if env.prefs[proteinStyleSmooth_prefs_key] == True:
self.smoothingCheckBox.setCheckState(Qt.Checked)
else:
self.smoothingCheckBox.setCheckState(Qt.Unchecked)
self.scaleComboBox.setCurrentIndex(env.prefs[proteinStyleScaling_prefs_key])
self.scaleFactorDoubleSpinBox.setValue(env.prefs[proteinStyleScaleFactor_prefs_key])
self.proteinComponentComboBox.setCurrentIndex(env.prefs[proteinStyleColors_prefs_key])
self.customColorComboBox.setColor(env.prefs[proteinStyleCustomColor_prefs_key])
self.proteinAuxComponentComboBox.setCurrentIndex(env.prefs[proteinStyleAuxColors_prefs_key])
self.auxColorComboBox.setColor(env.prefs[proteinStyleAuxCustomColor_prefs_key])
if env.prefs[proteinStyleColorsDiscrete_prefs_key] == True:
self.discColorCheckBox.setCheckState(Qt.Checked)
else:
self.discColorCheckBox.setCheckState(Qt.Unchecked)
self.helixColorComboBox.setColor(env.prefs[proteinStyleHelixColor_prefs_key])
self.strandColorComboBox.setColor(env.prefs[proteinStyleStrandColor_prefs_key])
self.coilColorComboBox.setColor(env.prefs[proteinStyleCoilColor_prefs_key])
return
def applyFavorite(self):
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == "Factory default settings":
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateProteinDisplayStyleWidgets()
return
def addFavorite(self):
# Rules and other info:
# - The new favorite is defined by the current Protein display style
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The DNA display style settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/ProteinDisplayStyle/$FAV_NAME.txt).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = grab_text_line_using_dialog(
title="Add new favorite",
label="favorite name:",
iconPath="ui/actions/Properties Manager/AddFavorite.png",
default="",
)
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename(name)
if os.path.exists(fname):
# favorite file already exists!
_ext = ".txt"
ret = QMessageBox.warning(
self,
"Warning!",
'The favorite file "' + name + _ext + '"already exists.\n'
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Cancel",
"",
0, # Enter == button 0
1,
) # Escape == button 1
if ret == 0:
# overwrite favorite file
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile = getFavoritePathFromBasename(currentText)
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" "and the favorite file [%s.txt]." % (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = "Favorite (*.txt);;" "All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, # where to save
formats, # file format options
QString("Favorite (*.txt)"), # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir=None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir=None):
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message(redmsg(msg))
return
def loadFavorite(self):
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = "Favorite (*.txt);;" "All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == "":
directory = getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self, "Choose a file to load", directory, formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile = loadFavoriteFile(fname)
if canLoadFile == 1:
# get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0 : len(favName) - 4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
# duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning(
self,
"Warning!",
'The favorite file "' + name + '"already exists.\n'
"Do you want to overwrite the existing file?",
"&Overwrite",
"&Rename",
"&Cancel",
0, # Enter == button 0
1, # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
# reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText("Factory default settings")
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateProteinDisplayStyleWidgets()
return
def _addWhatsThisText(self):
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
ToolTip_EditProteinDisplayStyle_PropertyManager(self)