class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager):
"""
The DnaStrand_PropertyManager class provides a Property Manager
for the DnaStrand_EditCommand.
@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 = "DnaStrand Properties"
pmName = title
iconPath = "ui/actions/Properties Manager/Strand.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self.sequenceEditor = None
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
self.dnaModel = 'PAM3'
_superclass.__init__( self,
win,
editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self._loadSequenceEditor()
msg = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg)
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox1( self._pmGroupBox1 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Strand name:",
text = "",
setAsDefault = False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = self.basesPerTurn,
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.duplexRise,
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.disableStructHighlightingCheckbox = \
PM_CheckBox( pmGroupBox,
text = "Don't highlight while editing DNA",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
#As of 2008-03-31, the properties such as number of bases will be
#editable only by using the resize handles. post FNANO we will support
#the
self.numberOfBasesSpinBox.setEnabled(False)
self.basesPerTurnDoubleSpinBox.setEnabled(False)
self.duplexRiseDoubleSpinBox.setEnabled(False)
def _loadSequenceEditor(self):
"""
Temporary code that shows the Sequence editor ..a doc widget docked
at the bottom of the mainwindow. The implementation is going to change
before 'rattleSnake' product release.
As of 2007-11-20: This feature (sequence editor) is waiting
for the ongoing dna model work to complete.
"""
self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
self.sequenceEditor.hide()
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of bases",
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),
("Number of bases to be changed",
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
]
return params
def getParameters(self):
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
basesPerTurn = self.basesPerTurn
duplexRise = self.duplexRise
color = self._colorChooser.getColor()
return (numberOfBases,
dnaForm,
dnaModel,
basesPerTurn,
duplexRise,
color
)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
#Set the duplex rise and bases per turn spinbox values.
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
color = params
if numberOfBases is not None:
self.numberOfBasesSpinBox.setValue(numberOfBases)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if duplexRise is not None:
self.duplexRiseDoubleSpinBox.setValue(duplexRise)
if basesPerTurn is not None:
self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn)
if color is not None:
self._colorChooser.setColor(color)
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: This is a temporary fix for a 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 atucally 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
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
if self.sequenceEditor:
self.sequenceEditor.connect_or_disconnect_signals(isConnect)
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.disableStructHighlightingCheckbox,
SIGNAL('stateChanged(int)'),
self.change_struct_highlightPolicy)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def model_changed(self):
"""
@see: DnaStrand_EditCommand.model_changed()
@see: DnaStrand_EditCommand.hasResizableStructure()
"""
isStructResizable, why_not = self.editCommand.hasResizableStructure()
if not isStructResizable:
#disable all widgets
if self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(False)
msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name)
msg2 = redmsg("DnaStrand is not resizable. Reason: %s"%(why_not))
self.updateMessage(msg1 + msg2)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name)
msg2 = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg1 + msg2)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
This method also retrives the name information from the
editCommand's structure for its name line edit field.
@see: DnaStrand_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
self._showSequenceEditor()
if self.editCommand is not None:
name = self.editCommand.getStructureName()
if name is not None:
self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.editCommand's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.editCommand is not None:
name = str(self.nameLineEdit.text())
self.editCommand.setStructureName(name)
if self.sequenceEditor:
self.sequenceEditor.close()
_superclass.close(self)
def _showSequenceEditor(self):
if self.sequenceEditor:
if not self.sequenceEditor.isVisible():
#Show the sequence editor
#ATTENTION: the sequence editor also closes (temporarily) the
#reports dockwidget (if visible) Its state is later restored when
#the sequuence Editor is closed.
self.sequenceEditor.show()
self.updateSequence()
def updateSequence(self):
"""
Update the sequence string in the sequence editor
@see: DnaSequenceEditor.setSequence()
@see DnaSequenceEditor._determine_complementSequence()
@see: DnaSequenceEditor.setComplementSequence()
@see: DnaStrand.getStrandSequenceAndItsComplement()
"""
#Read in the strand sequence of the selected strand and
#show it in the text edit in the sequence editor.
##strand = self.strandListWidget.getPickedItem()
if not self.editCommand.hasValidStructure():
return
strand = self.editCommand.struct
titleString = 'Sequence Editor for ' + strand.name
self.sequenceEditor.setWindowTitle(titleString)
sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement()
if sequenceString:
sequenceString = QString(sequenceString)
sequenceString = sequenceString.toUpper()
#Set the initial sequence (read in from the file)
self.sequenceEditor.setSequence(sequenceString)
#Set the initial complement sequence for DnaSequence editor.
#do this independently because 'complementSequenceString' may have
#some characters (such as * ) that denote a missing base on the
#complementary strand. this information is used by the sequence
#editor. See DnaSequenceEditor._determine_complementSequence()
#for more details. See also bug 2787
self.sequenceEditor.setComplementSequence(complementSequenceString)
def change_struct_highlightPolicy(self,checkedState = False):
"""
Change the 'highlight policy' of the structure being edited
(i.e. self.editCommand.struct) .
@param checkedState: The checked state of the checkbox that says
'Don't highlight while editing DNA'. So, it
its True, the structure being edited won't get
highlighted.
@see: DnaStrand.setHighlightPolicy for more comments
"""
if self.editCommand and self.editCommand.hasValidStructure():
highlight = not checkedState
self.editCommand.struct.setHighlightPolicy(highlight = highlight)
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
class Ui_BuildAtomsPropertyManager(Command_PropertyManager):
"""
The Ui_BuildAtomsPropertyManager class defines UI elements for the Property
Manager of the B{Build Atoms 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
"""
# The title that appears in the Property Manager header
title = "Build Atoms"
# 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/Tools/Build Structures/BuildAtoms.png"
def __init__(self, command):
"""
Constructor for the B{Build Atoms} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{depositMode}
"""
self.previewGroupBox = None
self.regularElementChooser = None
self.PAM5Chooser = None
self.PAM3Chooser = None
self.elementChooser = None
self.advancedOptionsGroupBox = None
self.bondToolsGroupBox = None
self.selectionFilterCheckBox = None
self.filterlistLE = None
self.selectedAtomInfoLabel = None
#Initialize the following to None. (subclasses may not define this)
#Make sure you initialize it before adding groupboxes!
self.selectedAtomPosGroupBox = None
self.showSelectedAtomInfoCheckBox = None
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = ''
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
def _addGroupBoxes(self):
"""
Add various group boxes to the Build Atoms Property manager.
"""
self._addPreviewGroupBox()
self._addAtomChooserGroupBox()
self._addBondToolsGroupBox()
#@@@TODO HIDE the bonds tool groupbox initially as the
#by default, the atoms tool is active when BuildAtoms command is
#finist invoked.
self.bondToolsGroupBox.hide()
self._addSelectionOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addPreviewGroupBox(self):
"""
Adde the preview groupbox that shows the element selected in the
element chooser.
"""
self.previewGroupBox = PM_PreviewGroupBox(self, glpane=self.o)
def _addAtomChooserGroupBox(self):
"""
Add the Atom Chooser groupbox. This groupbox displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
@see: L{self.__updateAtomChooserGroupBoxes}
"""
self.atomChooserGroupBox = \
PM_GroupBox(self, title = "Atom Chooser")
self._loadAtomChooserGroupBox(self.atomChooserGroupBox)
self._updateAtomChooserGroupBoxes(currentIndex=0)
def _addElementChooserGroupBox(self, inPmGroupBox):
"""
Add the 'Element Chooser' groupbox. (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.regularElementChooser = \
PM_ElementChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM5_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM5 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM5Chooser = \
PM_PAM5_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM3_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM3 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM3Chooser = \
PM_PAM3_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _hideAllAtomChooserGroupBoxes(self):
"""
Hides all Atom Chooser group boxes.
"""
if self.regularElementChooser:
self.regularElementChooser.hide()
if self.PAM5Chooser:
self.PAM5Chooser.hide()
if self.PAM3Chooser:
self.PAM3Chooser.hide()
def _addBondToolsGroupBox(self):
"""
Add the 'Bond Tools' groupbox.
"""
self.bondToolsGroupBox = \
PM_GroupBox( self, title = "Bond Tools")
self._loadBondToolsGroupBox(self.bondToolsGroupBox)
def _addSelectionOptionsGroupBox(self):
"""
Add 'Selection Options' groupbox
"""
self.selectionOptionsGroupBox = \
PM_GroupBox( self, title = "Selection Options" )
self._loadSelectionOptionsGroupBox(self.selectionOptionsGroupBox)
def _loadAtomChooserGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Atom Chooser groupbox.
@param inPmGroupBox: The Atom Chooser box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
atomChooserChoices = [
"Periodic Table Elements", "PAM5 Atoms", "PAM3 Atoms"
]
self.atomChooserComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = atomChooserChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
#Following fixes bug 2550
self.atomChooserComboBox.setFocusPolicy(Qt.NoFocus)
self._addElementChooserGroupBox(inPmGroupBox)
self._add_PAM5_AtomChooserGroupBox(inPmGroupBox)
self._add_PAM3_AtomChooserGroupBox(inPmGroupBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit(inPmGroupBox,
label="",
text="",
setAsDefault=False,
spanWidth=True)
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show=0)
self.enable_or_disable_selectedAtomPosGroupBox(bool_enable=False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref(self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key)
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadSelectedAtomPosGroupBox(self, inPmGroupBox):
"""
Load the selected Atoms position groupbox It is a sub-gropbox of
L{self.selectionOptionsGroupBox)
@param inPmGroupBox: 'The Selected Atom Position Groupbox'
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectedAtomLineEdit = PM_LineEdit(inPmGroupBox,
label="Selected Atom:",
text="",
setAsDefault=False,
spanWidth=False)
self.selectedAtomLineEdit.setReadOnly(True)
self.selectedAtomLineEdit.setEnabled(False)
self.coordinateSpinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
# User input to specify x-coordinate
self.xCoordOfSelectedAtom = self.coordinateSpinboxes.xSpinBox
# User input to specify y-coordinate
self.yCoordOfSelectedAtom = self.coordinateSpinboxes.ySpinBox
# User input to specify z-coordinate
self.zCoordOfSelectedAtom = self.coordinateSpinboxes.zSpinBox
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _loadBondToolsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Bond Tools group box.
@param inPmGroupBox: The Bond Tools box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BOND_TOOL_BUTTONS = \
[ ( "QToolButton", 0, "SINGLE", "", "", None, 0),
( "QToolButton", 1, "DOUBLE", "", "", None, 1),
( "QToolButton", 2, "TRIPLE", "", "", None, 2),
( "QToolButton", 3, "AROMATIC", "", "", None, 3),
( "QToolButton", 4, "GRAPHITIC", "", "", None, 4),
( "QToolButton", 5, "CUTBONDS", "", "", None, 5)
]
self.bondToolButtonRow = \
PM_ToolButtonRow(
inPmGroupBox,
title = "",
buttonList = BOND_TOOL_BUTTONS,
checkedId = None,
setAsDefault = True )
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager
whatsThis_BuildAtomsPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager
ToolTip_BuildAtomsPropertyManager(self)
def toggle_selectedAtomPosGroupBox(self, show=0):
"""
Show or hide L{self.selectedAtomPosGroupBox} depending on the state of
the checkbox (L{self.showSelectedAtomInfoCheckBox})
@param show: Flag that shows or hides the groupbox (can have values
0 or 1
@type show: int
"""
if show:
self.selectedAtomPosGroupBox.show()
else:
self.selectedAtomPosGroupBox.hide()
def enable_or_disable_selectedAtomPosGroupBox(self, bool_enable=False):
"""
Enable or disable Selected AtomPosGroupBox present within
'selection options' and also the checkbox that shows or hide this
groupbox. These two widgets are enabled when only a single atom is
selected from the 3D workspace.
@param bool_enable: Flag that enables or disables widgets
@type bool_enable: boolean
"""
if self.showSelectedAtomInfoCheckBox:
self.showSelectedAtomInfoCheckBox.setEnabled(bool_enable)
if self.selectedAtomPosGroupBox:
self.selectedAtomPosGroupBox.setEnabled(bool_enable)
def _updateAtomChooserGroupBoxes(self, currentIndex):
"""
Updates the Atom Chooser Groupbox. It displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
It also sets self.elementChooser to the current active Atom chooser
and updates the display accordingly in the Preview groupbox.
"""
self._hideAllAtomChooserGroupBoxes()
if currentIndex is 0:
self.elementChooser = self.regularElementChooser
self.regularElementChooser.show()
if currentIndex is 1:
self.elementChooser = self.PAM5Chooser
self.PAM5Chooser.show()
if currentIndex is 2:
self.elementChooser = self.PAM3Chooser
self.PAM3Chooser.show()
if self.elementChooser:
self.elementChooser.updateElementViewer()
self.updateMessage()
def updateMessage(self):
"""
Update the Message groupbox with informative message.
Subclasses should override this.
"""
pass
class Ui_BuildAtomsPropertyManager(Command_PropertyManager):
"""
The Ui_BuildAtomsPropertyManager class defines UI elements for the Property
Manager of the B{Build Atoms 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
"""
# The title that appears in the Property Manager header
title = "Build Atoms"
# 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/Tools/Build Structures/BuildAtoms.png"
def __init__(self, command):
"""
Constructor for the B{Build Atoms} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{depositMode}
"""
self.previewGroupBox = None
self.regularElementChooser = None
self.PAM5Chooser = None
self.PAM3Chooser = None
self.elementChooser = None
self.advancedOptionsGroupBox = None
self.bondToolsGroupBox = None
self.selectionFilterCheckBox = None
self.filterlistLE = None
self.selectedAtomInfoLabel = None
#Initialize the following to None. (subclasses may not define this)
#Make sure you initialize it before adding groupboxes!
self.selectedAtomPosGroupBox = None
self.showSelectedAtomInfoCheckBox = None
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = ''
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
def _addGroupBoxes(self):
"""
Add various group boxes to the Build Atoms Property manager.
"""
self._addPreviewGroupBox()
self._addAtomChooserGroupBox()
self._addBondToolsGroupBox()
#@@@TODO HIDE the bonds tool groupbox initially as the
#by default, the atoms tool is active when BuildAtoms command is
#finist invoked.
self.bondToolsGroupBox.hide()
self._addSelectionOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addPreviewGroupBox(self):
"""
Adde the preview groupbox that shows the element selected in the
element chooser.
"""
self.previewGroupBox = PM_PreviewGroupBox( self, glpane = self.o )
def _addAtomChooserGroupBox(self):
"""
Add the Atom Chooser groupbox. This groupbox displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
@see: L{self.__updateAtomChooserGroupBoxes}
"""
self.atomChooserGroupBox = \
PM_GroupBox(self, title = "Atom Chooser")
self._loadAtomChooserGroupBox(self.atomChooserGroupBox)
self._updateAtomChooserGroupBoxes(currentIndex = 0)
def _addElementChooserGroupBox(self, inPmGroupBox):
"""
Add the 'Element Chooser' groupbox. (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.regularElementChooser = \
PM_ElementChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM5_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM5 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM5Chooser = \
PM_PAM5_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM3_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM3 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM3Chooser = \
PM_PAM3_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _hideAllAtomChooserGroupBoxes(self):
"""
Hides all Atom Chooser group boxes.
"""
if self.regularElementChooser:
self.regularElementChooser.hide()
if self.PAM5Chooser:
self.PAM5Chooser.hide()
if self.PAM3Chooser:
self.PAM3Chooser.hide()
def _addBondToolsGroupBox(self):
"""
Add the 'Bond Tools' groupbox.
"""
self.bondToolsGroupBox = \
PM_GroupBox( self, title = "Bond Tools")
self._loadBondToolsGroupBox(self.bondToolsGroupBox)
def _addSelectionOptionsGroupBox(self):
"""
Add 'Selection Options' groupbox
"""
self.selectionOptionsGroupBox = \
PM_GroupBox( self, title = "Selection Options" )
self._loadSelectionOptionsGroupBox(self.selectionOptionsGroupBox)
def _loadAtomChooserGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Atom Chooser groupbox.
@param inPmGroupBox: The Atom Chooser box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
atomChooserChoices = [ "Periodic Table Elements",
"PAM5 Atoms",
"PAM3 Atoms" ]
self.atomChooserComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = atomChooserChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
#Following fixes bug 2550
self.atomChooserComboBox.setFocusPolicy(Qt.NoFocus)
self._addElementChooserGroupBox(inPmGroupBox)
self._add_PAM5_AtomChooserGroupBox(inPmGroupBox)
self._add_PAM3_AtomChooserGroupBox(inPmGroupBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit( inPmGroupBox,
label = "",
text = "",
setAsDefault = False,
spanWidth = True )
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show = 0)
self.enable_or_disable_selectedAtomPosGroupBox( bool_enable = False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref( self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key )
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadSelectedAtomPosGroupBox(self, inPmGroupBox):
"""
Load the selected Atoms position groupbox It is a sub-gropbox of
L{self.selectionOptionsGroupBox)
@param inPmGroupBox: 'The Selected Atom Position Groupbox'
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectedAtomLineEdit = PM_LineEdit( inPmGroupBox,
label = "Selected Atom:",
text = "",
setAsDefault = False,
spanWidth = False )
self.selectedAtomLineEdit.setReadOnly(True)
self.selectedAtomLineEdit.setEnabled(False)
self.coordinateSpinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
# User input to specify x-coordinate
self.xCoordOfSelectedAtom = self.coordinateSpinboxes.xSpinBox
# User input to specify y-coordinate
self.yCoordOfSelectedAtom = self.coordinateSpinboxes.ySpinBox
# User input to specify z-coordinate
self.zCoordOfSelectedAtom = self.coordinateSpinboxes.zSpinBox
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _loadBondToolsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Bond Tools group box.
@param inPmGroupBox: The Bond Tools box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BOND_TOOL_BUTTONS = \
[ ( "QToolButton", 0, "SINGLE", "", "", None, 0),
( "QToolButton", 1, "DOUBLE", "", "", None, 1),
( "QToolButton", 2, "TRIPLE", "", "", None, 2),
( "QToolButton", 3, "AROMATIC", "", "", None, 3),
( "QToolButton", 4, "GRAPHITIC", "", "", None, 4),
( "QToolButton", 5, "CUTBONDS", "", "", None, 5)
]
self.bondToolButtonRow = \
PM_ToolButtonRow(
inPmGroupBox,
title = "",
buttonList = BOND_TOOL_BUTTONS,
checkedId = None,
setAsDefault = True )
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager
whatsThis_BuildAtomsPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager
ToolTip_BuildAtomsPropertyManager(self)
def toggle_selectedAtomPosGroupBox(self, show = 0):
"""
Show or hide L{self.selectedAtomPosGroupBox} depending on the state of
the checkbox (L{self.showSelectedAtomInfoCheckBox})
@param show: Flag that shows or hides the groupbox (can have values
0 or 1
@type show: int
"""
if show:
self.selectedAtomPosGroupBox.show()
else:
self.selectedAtomPosGroupBox.hide()
def enable_or_disable_selectedAtomPosGroupBox(self, bool_enable = False):
"""
Enable or disable Selected AtomPosGroupBox present within
'selection options' and also the checkbox that shows or hide this
groupbox. These two widgets are enabled when only a single atom is
selected from the 3D workspace.
@param bool_enable: Flag that enables or disables widgets
@type bool_enable: boolean
"""
if self.showSelectedAtomInfoCheckBox:
self.showSelectedAtomInfoCheckBox.setEnabled(bool_enable)
if self.selectedAtomPosGroupBox:
self.selectedAtomPosGroupBox.setEnabled(bool_enable)
def _updateAtomChooserGroupBoxes(self, currentIndex):
"""
Updates the Atom Chooser Groupbox. It displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
It also sets self.elementChooser to the current active Atom chooser
and updates the display accordingly in the Preview groupbox.
"""
self._hideAllAtomChooserGroupBoxes()
if currentIndex is 0:
self.elementChooser = self.regularElementChooser
self.regularElementChooser.show()
if currentIndex is 1:
self.elementChooser = self.PAM5Chooser
self.PAM5Chooser.show()
if currentIndex is 2:
self.elementChooser = self.PAM3Chooser
self.PAM3Chooser.show()
if self.elementChooser:
self.elementChooser.updateElementViewer()
self.updateMessage()
def updateMessage(self):
"""
Update the Message groupbox with informative message.
Subclasses should override this.
"""
pass
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager):
"""
The DnaStrand_PropertyManager class provides a Property Manager
for the DnaStrand_EditCommand.
@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 = "DnaStrand Properties"
iconPath = "ui/actions/Properties Manager/Strand.png"
def __init__( self, command ):
"""
Constructor for the Build DNA property manager.
"""
self.sequenceEditor = None
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.dnaModel = 'PAM3'
_superclass.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def _addGroupBoxes( self ):
"""
Add group boxes to this PM.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox1( self._pmGroupBox1 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
#Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here
#so that the sequence editor gets connected! Perhaps
#superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03
self._loadSequenceEditor()
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Name:",
text = "",
setAsDefault = False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.disableStructHighlightingCheckbox = \
PM_CheckBox( pmGroupBox,
text = "Don't highlight while editing DNA",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
#As of 2008-03-31, the properties such as number of bases will be
#editable only by using the resize handles.
self.numberOfBasesSpinBox.setEnabled(False)
return
def _loadSequenceEditor(self):
"""
Temporary code that shows the Sequence editor ..a doc widget docked
at the bottom of the mainwindow. The implementation is going to change
before 'rattleSnake' product release.
As of 2007-11-20: This feature (sequence editor) is waiting
for the ongoing dna model work to complete.
"""
self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
self.sequenceEditor.hide()
return
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
return
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
return
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of bases",
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),
("Number of bases to be changed",
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
]
return params
def getParameters(self):
name = self.nameLineEdit.text()
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
color = self._colorChooser.getColor()
return (numberOfBases,
dnaForm,
dnaModel,
color,
name
)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
It also gets called when selecting a new strand (within this command).
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
numberOfBases, \
dnaForm, \
dnaModel, \
color, \
name = params
if numberOfBases is not None:
self.numberOfBasesSpinBox.setValue(numberOfBases)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if color is not None:
self._colorChooser.setColor(color)
if name: # Minimal test. Should add a validator. --Mark 2008-12-16
self.nameLineEdit.setText(name)
# This gets called when we enter the command *and* when selecting a new
# strand. In either case, we must update the sequence in the sequenece
# editor. Fixes bug 2951. --Mark 2008-12-16
if self.command and self.command.hasValidStructure():
#print "setParameters(): loading sequence in sequence editor for ", name
self.updateSequence(strand = self.command.struct)
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: This is a temporary fix for a 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 atucally 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
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
if self.sequenceEditor:
self.sequenceEditor.connect_or_disconnect_signals(isConnect)
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.disableStructHighlightingCheckbox,
SIGNAL('stateChanged(int)'),
self.change_struct_highlightPolicy)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
change_connect(self.nameLineEdit,
SIGNAL("editingFinished()"),
self._nameChanged)
return
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager. _update_UI_do_updates()
@see: DnaStrand_EditCommand.command_update_UI()
@see: DnaStrand_EditCommand.hasResizableStructure()
"""
if not self.command.hasValidStructure():
print "DnaStrand not a valid structure."
self._pmGroupBox1.setEnabled(False)
self._displayOptionsGroupBox.setEnabled(False)
self.sequenceEditor.updateSequence(strand = " ")
self.sequenceEditor.setEnabled(False)
self.nameLineEdit.setText("")
self.numberOfBasesSpinBox.setValue(0)
return
else:
self._pmGroupBox1.setEnabled(True)
self._displayOptionsGroupBox.setEnabled(True)
self.sequenceEditor.setEnabled(True)
isStructResizable, why_not = self.command.hasResizableStructure()
if not isStructResizable:
#disable all widgets
if self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(False)
msg1 = ("Attention: ") % (self.command.struct.name)
msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \
(self.command.struct.name, why_not))
self.updateMessage(msg1 + msg2)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name)
msg2 = "Use resize handles to resize the strand. "\
"Use the <i>Sequence Editor</i> to edit the sequence."
self.updateMessage(msg1 + msg2)
return
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
if self.sequenceEditor:
self.sequenceEditor.close()
_superclass.close(self)
return
def updateSequence(self, strand = None):
"""
Public method provided for convenience. If any callers outside of this
command need to update the sequence in the sequence editor, they can simply
do DnaStrand_ProprtyManager.updateSequence() rather than
DnaStrand_ProprtyManager.sequenceEditor.updateSequence()
@see: Ui_DnaSequenceEditor.updateSequence()
"""
if self.sequenceEditor:
self.sequenceEditor.updateSequence(strand = strand)
return
def change_struct_highlightPolicy(self,checkedState = False):
"""
Change the 'highlight policy' of the structure being edited
(i.e. self.command.struct) .
@param checkedState: The checked state of the checkbox that says
'Don't highlight while editing DNA'. So, it
its True, the structure being edited won't get
highlighted.
@see: DnaStrand.setHighlightPolicy for more comments
"""
if self.command and self.command.hasValidStructure():
highlight = not checkedState
self.command.struct.setHighlightPolicy(highlight = highlight)
return
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
def _nameChanged(self): # Added by Mark. 2008-12-16
"""
Slot for "Name" field. Changes the name of the strand if the user types
in a new name.
@warning: this lacks a validator. User can type in a name with invalid
characters.
"""
if not self.command.hasValidStructure():
return
name = str(self.nameLineEdit.text())
if not name: # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16
if self.command.hasValidStructure():
self.nameLineEdit.setText(self.command.getStructureName())
return
self.command.setStructureName(name)
self._update_UI_do_updates() # Updates the message box.
return
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager):
"""
The DnaStrand_PropertyManager class provides a Property Manager
for the DnaStrand_EditCommand.
@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 = "DnaStrand Properties"
iconPath = "ui/actions/Properties Manager/Strand.png"
def __init__(self, command):
"""
Constructor for the Build DNA property manager.
"""
self.sequenceEditor = None
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.dnaModel = 'PAM3'
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def _addGroupBoxes(self):
"""
Add group boxes to this PM.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
#Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here
#so that the sequence editor gets connected! Perhaps
#superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03
self._loadSequenceEditor()
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Name:",
text="",
setAsDefault=False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.disableStructHighlightingCheckbox = \
PM_CheckBox( pmGroupBox,
text = "Don't highlight while editing DNA",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
#As of 2008-03-31, the properties such as number of bases will be
#editable only by using the resize handles.
self.numberOfBasesSpinBox.setEnabled(False)
return
def _loadSequenceEditor(self):
"""
Temporary code that shows the Sequence editor ..a doc widget docked
at the bottom of the mainwindow. The implementation is going to change
before 'rattleSnake' product release.
As of 2007-11-20: This feature (sequence editor) is waiting
for the ongoing dna model work to complete.
"""
self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
self.sequenceEditor.hide()
return
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
return
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
return
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of bases",
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),
("Number of bases to be changed",
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
]
return params
def getParameters(self):
name = self.nameLineEdit.text()
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
color = self._colorChooser.getColor()
return (numberOfBases, dnaForm, dnaModel, color, name)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
It also gets called when selecting a new strand (within this command).
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
numberOfBases, \
dnaForm, \
dnaModel, \
color, \
name = params
if numberOfBases is not None:
self.numberOfBasesSpinBox.setValue(numberOfBases)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if color is not None:
self._colorChooser.setColor(color)
if name: # Minimal test. Should add a validator. --Mark 2008-12-16
self.nameLineEdit.setText(name)
# This gets called when we enter the command *and* when selecting a new
# strand. In either case, we must update the sequence in the sequenece
# editor. Fixes bug 2951. --Mark 2008-12-16
if self.command and self.command.hasValidStructure():
#print "setParameters(): loading sequence in sequence editor for ", name
self.updateSequence(strand=self.command.struct)
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: This is a temporary fix for a 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 atucally 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
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
if self.sequenceEditor:
self.sequenceEditor.connect_or_disconnect_signals(isConnect)
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.disableStructHighlightingCheckbox,
SIGNAL('stateChanged(int)'),
self.change_struct_highlightPolicy)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
change_connect(self.nameLineEdit, SIGNAL("editingFinished()"),
self._nameChanged)
return
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager. _update_UI_do_updates()
@see: DnaStrand_EditCommand.command_update_UI()
@see: DnaStrand_EditCommand.hasResizableStructure()
"""
if not self.command.hasValidStructure():
print "DnaStrand not a valid structure."
self._pmGroupBox1.setEnabled(False)
self._displayOptionsGroupBox.setEnabled(False)
self.sequenceEditor.updateSequence(strand=" ")
self.sequenceEditor.setEnabled(False)
self.nameLineEdit.setText("")
self.numberOfBasesSpinBox.setValue(0)
return
else:
self._pmGroupBox1.setEnabled(True)
self._displayOptionsGroupBox.setEnabled(True)
self.sequenceEditor.setEnabled(True)
isStructResizable, why_not = self.command.hasResizableStructure()
if not isStructResizable:
#disable all widgets
if self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(False)
msg1 = ("Attention: ") % (self.command.struct.name)
msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \
(self.command.struct.name, why_not))
self.updateMessage(msg1 + msg2)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name)
msg2 = "Use resize handles to resize the strand. "\
"Use the <i>Sequence Editor</i> to edit the sequence."
self.updateMessage(msg1 + msg2)
return
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
if self.sequenceEditor:
self.sequenceEditor.close()
_superclass.close(self)
return
def updateSequence(self, strand=None):
"""
Public method provided for convenience. If any callers outside of this
command need to update the sequence in the sequence editor, they can simply
do DnaStrand_ProprtyManager.updateSequence() rather than
DnaStrand_ProprtyManager.sequenceEditor.updateSequence()
@see: Ui_DnaSequenceEditor.updateSequence()
"""
if self.sequenceEditor:
self.sequenceEditor.updateSequence(strand=strand)
return
def change_struct_highlightPolicy(self, checkedState=False):
"""
Change the 'highlight policy' of the structure being edited
(i.e. self.command.struct) .
@param checkedState: The checked state of the checkbox that says
'Don't highlight while editing DNA'. So, it
its True, the structure being edited won't get
highlighted.
@see: DnaStrand.setHighlightPolicy for more comments
"""
if self.command and self.command.hasValidStructure():
highlight = not checkedState
self.command.struct.setHighlightPolicy(highlight=highlight)
return
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
def _nameChanged(self): # Added by Mark. 2008-12-16
"""
Slot for "Name" field. Changes the name of the strand if the user types
in a new name.
@warning: this lacks a validator. User can type in a name with invalid
characters.
"""
if not self.command.hasValidStructure():
return
name = str(self.nameLineEdit.text())
if not name: # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16
if self.command.hasValidStructure():
self.nameLineEdit.setText(self.command.getStructureName())
return
self.command.setStructureName(name)
self._update_UI_do_updates() # Updates the message box.
return
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager):
"""
The DnaStrand_PropertyManager class provides a Property Manager
for the DnaStrand_EditCommand.
@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 = "DnaStrand Properties"
pmName = title
iconPath = "ui/actions/Properties Manager/Strand.png"
def __init__(self, win, editCommand):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self.sequenceEditor = None
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
self.dnaModel = 'PAM3'
_superclass.__init__(self, win, editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self._loadSequenceEditor()
msg = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg)
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Strand name:",
text="",
setAsDefault=False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = self.basesPerTurn,
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.duplexRise,
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.disableStructHighlightingCheckbox = \
PM_CheckBox( pmGroupBox,
text = "Don't highlight while editing DNA",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
#As of 2008-03-31, the properties such as number of bases will be
#editable only by using the resize handles. post FNANO we will support
#the
self.numberOfBasesSpinBox.setEnabled(False)
self.basesPerTurnDoubleSpinBox.setEnabled(False)
self.duplexRiseDoubleSpinBox.setEnabled(False)
def _loadSequenceEditor(self):
"""
Temporary code that shows the Sequence editor ..a doc widget docked
at the bottom of the mainwindow. The implementation is going to change
before 'rattleSnake' product release.
As of 2007-11-20: This feature (sequence editor) is waiting
for the ongoing dna model work to complete.
"""
self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
self.sequenceEditor.hide()
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of bases",
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),
("Number of bases to be changed",
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
]
return params
def getParameters(self):
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
basesPerTurn = self.basesPerTurn
duplexRise = self.duplexRise
color = self._colorChooser.getColor()
return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise,
color)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
#Set the duplex rise and bases per turn spinbox values.
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
color = params
if numberOfBases is not None:
self.numberOfBasesSpinBox.setValue(numberOfBases)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if duplexRise is not None:
self.duplexRiseDoubleSpinBox.setValue(duplexRise)
if basesPerTurn is not None:
self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn)
if color is not None:
self._colorChooser.setColor(color)
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: This is a temporary fix for a 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 atucally 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
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
if self.sequenceEditor:
self.sequenceEditor.connect_or_disconnect_signals(isConnect)
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.disableStructHighlightingCheckbox,
SIGNAL('stateChanged(int)'),
self.change_struct_highlightPolicy)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def model_changed(self):
"""
@see: DnaStrand_EditCommand.model_changed()
@see: DnaStrand_EditCommand.hasResizableStructure()
"""
isStructResizable, why_not = self.editCommand.hasResizableStructure()
if not isStructResizable:
#disable all widgets
if self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(False)
msg1 = ("Viewing properties of %s <br>") % (
self.editCommand.struct.name)
msg2 = redmsg("DnaStrand is not resizable. Reason: %s" %
(why_not))
self.updateMessage(msg1 + msg2)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg1 = ("Viewing properties of %s <br>") % (
self.editCommand.struct.name)
msg2 = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg1 + msg2)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
This method also retrives the name information from the
editCommand's structure for its name line edit field.
@see: DnaStrand_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
self._showSequenceEditor()
if self.editCommand is not None:
name = self.editCommand.getStructureName()
if name is not None:
self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.editCommand's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.editCommand is not None:
name = str(self.nameLineEdit.text())
self.editCommand.setStructureName(name)
if self.sequenceEditor:
self.sequenceEditor.close()
_superclass.close(self)
def _showSequenceEditor(self):
if self.sequenceEditor:
if not self.sequenceEditor.isVisible():
#Show the sequence editor
#ATTENTION: the sequence editor also closes (temporarily) the
#reports dockwidget (if visible) Its state is later restored when
#the sequuence Editor is closed.
self.sequenceEditor.show()
self.updateSequence()
def updateSequence(self):
"""
Update the sequence string in the sequence editor
@see: DnaSequenceEditor.setSequence()
@see DnaSequenceEditor._determine_complementSequence()
@see: DnaSequenceEditor.setComplementSequence()
@see: DnaStrand.getStrandSequenceAndItsComplement()
"""
#Read in the strand sequence of the selected strand and
#show it in the text edit in the sequence editor.
##strand = self.strandListWidget.getPickedItem()
if not self.editCommand.hasValidStructure():
return
strand = self.editCommand.struct
titleString = 'Sequence Editor for ' + strand.name
self.sequenceEditor.setWindowTitle(titleString)
sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement(
)
if sequenceString:
sequenceString = QString(sequenceString)
sequenceString = sequenceString.toUpper()
#Set the initial sequence (read in from the file)
self.sequenceEditor.setSequence(sequenceString)
#Set the initial complement sequence for DnaSequence editor.
#do this independently because 'complementSequenceString' may have
#some characters (such as * ) that denote a missing base on the
#complementary strand. this information is used by the sequence
#editor. See DnaSequenceEditor._determine_complementSequence()
#for more details. See also bug 2787
self.sequenceEditor.setComplementSequence(complementSequenceString)
def change_struct_highlightPolicy(self, checkedState=False):
"""
Change the 'highlight policy' of the structure being edited
(i.e. self.editCommand.struct) .
@param checkedState: The checked state of the checkbox that says
'Don't highlight while editing DNA'. So, it
its True, the structure being edited won't get
highlighted.
@see: DnaStrand.setHighlightPolicy for more comments
"""
if self.editCommand and self.editCommand.hasValidStructure():
highlight = not checkedState
self.editCommand.struct.setHighlightPolicy(highlight=highlight)
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
