class BreakStrands_PropertyManager(BreakOrJoinStrands_PropertyManager):
"""
The BreakStrands_PropertyManager class provides a Property Manager
for the B{Break Strands} 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 = "Break Strands"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/BreakStrand.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
self._previous_model_changed_params = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__(self, command)
msg = "Click on a strand's backbone bond to break a strand."
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
"""
#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
_superclass.connect_or_disconnect_signals(self, isConnect=isConnect)
if DEBUG_BREAK_OPTIONS_FEATURE:
self._dnaStrandChooserGroupBox.connect_or_disconnect_signals(
isConnect=isConnect)
change_connect(self.breakAllStrandsButton, SIGNAL("clicked()"),
self.command.breakStrandBonds)
change_connect(self.basesBeforeNextBreakSpinBox,
SIGNAL("valueChanged(int)"),
self.valueChanged_basesBeforeNextBreak)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.hasResizableStructure()
@see: self._current_model_changed_params()
"""
if not DEBUG_BREAK_OPTIONS_FEATURE:
return
currentParams = self._current_model_changed_params()
#Optimization. Return from the model_changed method if the
#params are the same.
if same_vals(currentParams, self._previous_model_changed_params):
return
basesBeforeNextBreak = currentParams
#update the self._previous_model_changed_params with this new param set.
self._previous_model_changed_params = currentParams
self.command.updateBreakSites()
def _current_model_changed_params(self):
"""
Returns a tuple containing the parameters that will be compared
against the previously stored parameters. This provides a quick test
to determine whether to do more things in self.model_changed()
@see: self.model_changed() which calls this
@see: self._previous_model_changed_params attr.
"""
params = None
if self.command:
params = (env.prefs[
breakStrandsCommand_numberOfBasesBeforeNextBreak_prefs_key])
return params
def valueChanged_basesBeforeNextBreak(self, val):
self.win.glpane.gl_update()
def getNumberOfBasesBeforeNextBreak(self):
return self.basesBeforeNextBreakSpinBox.value()
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._breakOptionsGroupbox = PM_GroupBox(self, title="Break Options")
self._loadBreakOptionsGroupbox(self._breakOptionsGroupbox)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
self._baseNumberLabelGroupBox = PM_GroupBox(self,
title="Base Number Labels")
self._loadBaseNumberLabelGroupBox(self._baseNumberLabelGroupBox)
def _loadBreakOptionsGroupbox(self, pmGroupBox):
"""
Load widgets in this group box.
"""
self.assignColorToBrokenDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Assign new color to broken strands',
widgetColumn = 0,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.assignColorToBrokenDnaStrandsCheckBox,
assignColorToBrokenDnaStrands_prefs_key)
self.basesBeforeNextBreakSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Break Every:",
value = 3,
setAsDefault = False,
minimum = 1,
maximum = 10000,
suffix = " bases"
)
connect_spinBox_with_pref(
self.basesBeforeNextBreakSpinBox,
breakStrandsCommand_numberOfBasesBeforeNextBreak_prefs_key)
self.breakAllStrandsButton = PM_PushButton(pmGroupBox,
label="",
text="do it")
self._dnaStrandChooserGroupBox = PM_ObjectChooser(
pmGroupBox,
self.command,
modelObjectType=self.win.assy.DnaStrand,
title="Choose strands ")
if not DEBUG_BREAK_OPTIONS_FEATURE:
self._dnaStrandChooserGroupBox.hide()
self.breakAllStrandsButton.hide()
self.basesBeforeNextBreakSpinBox.hide()
#Return varius prefs_keys for arrowhead display options ui elements =======
def _prefs_key_arrowsOnThreePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 3' strand ends of PAM DNA.
"""
return breakStrandsCommand_arrowsOnThreePrimeEnds_prefs_key
def _prefs_key_arrowsOnFivePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 5' strand ends of PAM DNA.
"""
return breakStrandsCommand_arrowsOnFivePrimeEnds_prefs_key
def _prefs_key_useCustomColorForThreePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 3' arrowheads (if they are drawn)
or for 3' strand end atoms (if arrowheads are not drawn)
"""
return breakStrandsCommand_useCustomColorForThreePrimeArrowheads_prefs_key
def _prefs_key_useCustomColorForFivePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 5' arrowheads (if they are drawn)
or for 5' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_useCustomColorForFivePrimeArrowheads_prefs_key
def _prefs_key_dnaStrandThreePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 3' arrowheads (if they are drawn)
or 3' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_dnaStrandThreePrimeArrowheadsCustomColor_prefs_key
def _prefs_key_dnaStrandFivePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 5' arrowheads (if they are drawn)
or 5' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_dnaStrandFivePrimeArrowheadsCustomColor_prefs_key
def _addWhatsThisText(self):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
class Ui_ProteinSequenceEditor(PM_DockWidget):
"""
The Ui_DnaSequenceEditor class defines UI elements for the Sequence Editor
object. The sequence editor is usually visible while in DNA edit mode.
It is a DockWidget that is doced at the bottom of the MainWindow
"""
_title = "Sequence Editor"
_groupBoxCount = 0
_lastGroupBox = None
def __init__(self, win):
"""
Constructor for the Ui_DnaSequenceEditor
@param win: The parentWidget (MainWindow) for the sequence editor
"""
self.win = win
parentWidget = win
_superclass.__init__(self, parentWidget, title = self._title)
self._reportsDockWidget_closed_in_show_method = False
self.setFixedHeight(90)
return
def show(self):
"""
Shows the sequence editor. While doing this, it also closes the reports
dock widget (if visible) the state of the reports dockwidget will be
restored when the sequence editor is closed.
@see:self.closeEvent()
"""
self._reportsDockWidget_closed_in_show_method = False
if self.win.viewFullScreenAction.isChecked() or \
self.win.viewSemiFullScreenAction.isChecked():
pass
else:
if self.win.reportsDockWidget.isVisible():
self.win.reportsDockWidget.close()
self._reportsDockWidget_closed_in_show_method = True
_superclass.show(self)
return
def closeEvent(self, event):
"""
Overrides close event. Makes sure that the visible state of the reports
widgetis restored when the sequence editor is closed.
@see: self.show()
"""
_superclass.closeEvent(self, event)
if self.win.viewFullScreenAction.isChecked() or \
self.win.viewSemiFullScreenAction.isChecked():
pass
else:
if self._reportsDockWidget_closed_in_show_method:
self.win.viewReportsAction.setChecked(True)
self._reportsDockWidget_closed_in_show_method = False
return
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTextEditWidget()
return
def _loadMenuWidgets(self):
"""
Load the various menu widgets (e.g. Open, save sequence options,
Find and replace widgets etc.
"""
self.loadSequenceButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Open.png")
self.saveSequenceButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Save_Strand_Sequence.png")
self.loadSequenceButton.setAutoRaise(True)
self.saveSequenceButton.setAutoRaise(True)
# Hide load and save buttons until they are implemented. -Mark 2008-12-20.
self.loadSequenceButton.hide()
self.saveSequenceButton.hide()
#Find and replace widgets --
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(60)
self.replaceLineEdit = \
PM_LineEdit( self,
label = " Replace:",
spanWidth = False)
self.replaceLineEdit.setMaximumWidth(60)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
self._setFindOptionsToolButtonMenu()
self.findNextToolButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Find_Next.png")
self.findNextToolButton.setAutoRaise(True)
self.findPreviousToolButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Find_Previous.png")
self.findPreviousToolButton.setAutoRaise(True)
self.replacePushButton = PM_PushButton(self, text = "Replace")
# Hide Replace widgets until we add support for transmuting residues.
# Mark 2008-12-19
#self.replaceLabel.hide()
self.replacePushButton.hide()
self.replaceLineEdit.hide()
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("Sequence Not Found")
self.phraseNotFoundLabel.hide()
#Widgets to include in the widget row.
widgetList = [('PM_ToolButton', self.loadSequenceButton, 0),
('PM_ToolButton', self.saveSequenceButton, 1),
('QLabel', " Find:", 4),
('PM_LineEdit', self.findLineEdit, 5),
('PM_ToolButton', self.findOptionsToolButton, 6),
('PM_ToolButton', self.findPreviousToolButton, 7),
('PM_ToolButton', self.findNextToolButton, 8),
#('PM_Label', self.replaceLabel, 9),
('PM_TextEdit', self.replaceLineEdit, 9),
('PM_PushButton', self.replacePushButton, 10),
('PM_Label', self.warningSign, 11),
('PM_Label', self.phraseNotFoundLabel, 12),
('QSpacerItem', 5, 5, 13) ]
widgetRow = PM_WidgetRow(self,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
return
def _loadTextEditWidget(self):
"""
Load the SequenceTexteditWidgets.
"""
self.aaRulerTextEdit = \
PM_TextEdit( self,
label = "",
spanWidth = False,
permit_enter_keystroke = False)
palette = getPalette(None,
QPalette.Base,
pmGrpBoxColor)
self.aaRulerTextEdit.setPalette(palette)
self.aaRulerTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.aaRulerTextEdit.setFixedHeight(20)
self.aaRulerTextEdit.setReadOnly(True)
self.sequenceTextEdit = \
PM_TextEdit( self,
label = " Sequence: ",
spanWidth = False,
permit_enter_keystroke = False)
#self.sequenceTextEdit.setReadOnly(True) #@@@
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.sequenceTextEdit.setFixedHeight(20)
self.secStrucTextEdit = \
PM_TextEdit( self,
label = " Secondary structure: ",
spanWidth = False,
permit_enter_keystroke = False)
palette = getPalette(None,
QPalette.Base,
sequenceEditStrandMateBaseColor)
self.secStrucTextEdit.setPalette(palette)
self.secStrucTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.secStrucTextEdit.setFixedHeight(20)
self.secStrucTextEdit.setReadOnly(True)
#Important to make sure that the horizontal and vertical scrollbars
#for these text edits are never displayed.
self.sequenceTextEdit.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.sequenceTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.secStrucTextEdit.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.secStrucTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.aaRulerTextEdit.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.aaRulerTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
return
def _getFindLineEditStyleSheet(self):
"""
Return the style sheet for the findLineEdit. This sets the following
properties only:
- background-color
This style is set whenever the searchStrig can't be found (sets
a light red color background to the lineedit when this happens)
@return: The line edit style sheet.
@rtype: str
"""
styleSheet = "QLineEdit {"\
"background-color: rgb(255, 102, 102)"\
"}"
return styleSheet
def _setFindOptionsToolButtonMenu(self):
"""
Sets the menu for the findOptionstoolbutton that appears a small
menu button next to the findLineEdit.
"""
self.findOptionsMenu = QMenu(self.findOptionsToolButton)
self.caseSensitiveFindAction = QAction(self.findOptionsToolButton)
self.caseSensitiveFindAction.setText('Match Case')
self.caseSensitiveFindAction.setCheckable(True)
self.caseSensitiveFindAction.setChecked(False)
self.findOptionsMenu.addAction(self.caseSensitiveFindAction)
self.findOptionsMenu.addSeparator()
self.findOptionsToolButton.setMenu(self.findOptionsMenu)
return
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_ProteinSequenceEditor
ToolTip_ProteinSequenceEditor(self)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_ProteinSequenceEditor
whatsThis_ProteinSequenceEditor(self)
return
class Ui_ProteinSequenceEditor(PM_DockWidget):
"""
The Ui_DnaSequenceEditor class defines UI elements for the Sequence Editor
object. The sequence editor is usually visible while in DNA edit mode.
It is a DockWidget that is doced at the bottom of the MainWindow
"""
_title = "Sequence Editor"
_groupBoxCount = 0
_lastGroupBox = None
def __init__(self, win):
"""
Constructor for the Ui_DnaSequenceEditor
@param win: The parentWidget (MainWindow) for the sequence editor
"""
self.win = win
parentWidget = win
_superclass.__init__(self, parentWidget, title=self._title)
self._reportsDockWidget_closed_in_show_method = False
self.setFixedHeight(90)
return
def show(self):
"""
Shows the sequence editor. While doing this, it also closes the reports
dock widget (if visible) the state of the reports dockwidget will be
restored when the sequence editor is closed.
@see:self.closeEvent()
"""
self._reportsDockWidget_closed_in_show_method = False
if self.win.viewFullScreenAction.isChecked() or \
self.win.viewSemiFullScreenAction.isChecked():
pass
else:
if self.win.reportsDockWidget.isVisible():
self.win.reportsDockWidget.close()
self._reportsDockWidget_closed_in_show_method = True
_superclass.show(self)
return
def closeEvent(self, event):
"""
Overrides close event. Makes sure that the visible state of the reports
widgetis restored when the sequence editor is closed.
@see: self.show()
"""
_superclass.closeEvent(self, event)
if self.win.viewFullScreenAction.isChecked() or \
self.win.viewSemiFullScreenAction.isChecked():
pass
else:
if self._reportsDockWidget_closed_in_show_method:
self.win.viewReportsAction.setChecked(True)
self._reportsDockWidget_closed_in_show_method = False
return
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTextEditWidget()
return
def _loadMenuWidgets(self):
"""
Load the various menu widgets (e.g. Open, save sequence options,
Find and replace widgets etc.
"""
self.loadSequenceButton = PM_ToolButton(
self, iconPath="ui/actions/Properties Manager/Open.png")
self.saveSequenceButton = PM_ToolButton(
self,
iconPath="ui/actions/Properties Manager/Save_Strand_Sequence.png")
self.loadSequenceButton.setAutoRaise(True)
self.saveSequenceButton.setAutoRaise(True)
# Hide load and save buttons until they are implemented. -Mark 2008-12-20.
self.loadSequenceButton.hide()
self.saveSequenceButton.hide()
#Find and replace widgets --
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(60)
self.replaceLineEdit = \
PM_LineEdit( self,
label = " Replace:",
spanWidth = False)
self.replaceLineEdit.setMaximumWidth(60)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
self._setFindOptionsToolButtonMenu()
self.findNextToolButton = PM_ToolButton(
self, iconPath="ui/actions/Properties Manager/Find_Next.png")
self.findNextToolButton.setAutoRaise(True)
self.findPreviousToolButton = PM_ToolButton(
self, iconPath="ui/actions/Properties Manager/Find_Previous.png")
self.findPreviousToolButton.setAutoRaise(True)
self.replacePushButton = PM_PushButton(self, text="Replace")
# Hide Replace widgets until we add support for transmuting residues.
# Mark 2008-12-19
#self.replaceLabel.hide()
self.replacePushButton.hide()
self.replaceLineEdit.hide()
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("Sequence Not Found")
self.phraseNotFoundLabel.hide()
#Widgets to include in the widget row.
widgetList = [
('PM_ToolButton', self.loadSequenceButton, 0),
('PM_ToolButton', self.saveSequenceButton, 1),
('QLabel', " Find:", 4),
('PM_LineEdit', self.findLineEdit, 5),
('PM_ToolButton', self.findOptionsToolButton, 6),
('PM_ToolButton', self.findPreviousToolButton, 7),
('PM_ToolButton', self.findNextToolButton, 8),
#('PM_Label', self.replaceLabel, 9),
('PM_TextEdit', self.replaceLineEdit, 9),
('PM_PushButton', self.replacePushButton, 10),
('PM_Label', self.warningSign, 11),
('PM_Label', self.phraseNotFoundLabel, 12),
('QSpacerItem', 5, 5, 13)
]
widgetRow = PM_WidgetRow(self,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
return
def _loadTextEditWidget(self):
"""
Load the SequenceTexteditWidgets.
"""
self.aaRulerTextEdit = \
PM_TextEdit( self,
label = "",
spanWidth = False,
permit_enter_keystroke = False)
palette = getPalette(None, QPalette.Base, pmGrpBoxColor)
self.aaRulerTextEdit.setPalette(palette)
self.aaRulerTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.aaRulerTextEdit.setFixedHeight(20)
self.aaRulerTextEdit.setReadOnly(True)
self.sequenceTextEdit = \
PM_TextEdit( self,
label = " Sequence: ",
spanWidth = False,
permit_enter_keystroke = False)
#self.sequenceTextEdit.setReadOnly(True) #@@@
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.sequenceTextEdit.setFixedHeight(20)
self.secStrucTextEdit = \
PM_TextEdit( self,
label = " Secondary structure: ",
spanWidth = False,
permit_enter_keystroke = False)
palette = getPalette(None, QPalette.Base,
sequenceEditStrandMateBaseColor)
self.secStrucTextEdit.setPalette(palette)
self.secStrucTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.secStrucTextEdit.setFixedHeight(20)
self.secStrucTextEdit.setReadOnly(True)
#Important to make sure that the horizontal and vertical scrollbars
#for these text edits are never displayed.
self.sequenceTextEdit.setHorizontalScrollBarPolicy(
Qt.ScrollBarAlwaysOff)
self.sequenceTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.secStrucTextEdit.setHorizontalScrollBarPolicy(
Qt.ScrollBarAlwaysOff)
self.secStrucTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.aaRulerTextEdit.setHorizontalScrollBarPolicy(
Qt.ScrollBarAlwaysOff)
self.aaRulerTextEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
return
def _getFindLineEditStyleSheet(self):
"""
Return the style sheet for the findLineEdit. This sets the following
properties only:
- background-color
This style is set whenever the searchStrig can't be found (sets
a light red color background to the lineedit when this happens)
@return: The line edit style sheet.
@rtype: str
"""
styleSheet = "QLineEdit {"\
"background-color: rgb(255, 102, 102)"\
"}"
return styleSheet
def _setFindOptionsToolButtonMenu(self):
"""
Sets the menu for the findOptionstoolbutton that appears a small
menu button next to the findLineEdit.
"""
self.findOptionsMenu = QMenu(self.findOptionsToolButton)
self.caseSensitiveFindAction = QAction(self.findOptionsToolButton)
self.caseSensitiveFindAction.setText('Match Case')
self.caseSensitiveFindAction.setCheckable(True)
self.caseSensitiveFindAction.setChecked(False)
self.findOptionsMenu.addAction(self.caseSensitiveFindAction)
self.findOptionsMenu.addSeparator()
self.findOptionsToolButton.setMenu(self.findOptionsMenu)
return
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_ProteinSequenceEditor
ToolTip_ProteinSequenceEditor(self)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_ProteinSequenceEditor
whatsThis_ProteinSequenceEditor(self)
return
class BreakStrands_PropertyManager( BreakOrJoinStrands_PropertyManager):
"""
The BreakStrands_PropertyManager class provides a Property Manager
for the B{Break Strands} 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 = "Break Strands"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/BreakStrand.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self._previous_model_changed_params = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__(self, command)
msg = "Click on a strand's backbone bond to break a strand."
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
"""
#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
_superclass.connect_or_disconnect_signals(self, isConnect = isConnect)
if DEBUG_BREAK_OPTIONS_FEATURE:
self._dnaStrandChooserGroupBox.connect_or_disconnect_signals(isConnect = isConnect)
change_connect(self.breakAllStrandsButton,
SIGNAL("clicked()"),
self.command.breakStrandBonds)
change_connect(self.basesBeforeNextBreakSpinBox,
SIGNAL("valueChanged(int)"),
self.valueChanged_basesBeforeNextBreak)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.hasResizableStructure()
@see: self._current_model_changed_params()
"""
if not DEBUG_BREAK_OPTIONS_FEATURE:
return
currentParams = self._current_model_changed_params()
#Optimization. Return from the model_changed method if the
#params are the same.
if same_vals(currentParams, self._previous_model_changed_params):
return
basesBeforeNextBreak = currentParams
#update the self._previous_model_changed_params with this new param set.
self._previous_model_changed_params = currentParams
self.command.updateBreakSites()
def _current_model_changed_params(self):
"""
Returns a tuple containing the parameters that will be compared
against the previously stored parameters. This provides a quick test
to determine whether to do more things in self.model_changed()
@see: self.model_changed() which calls this
@see: self._previous_model_changed_params attr.
"""
params = None
if self.command:
params = (env.prefs[breakStrandsCommand_numberOfBasesBeforeNextBreak_prefs_key])
return params
def valueChanged_basesBeforeNextBreak(self, val):
self.win.glpane.gl_update()
def getNumberOfBasesBeforeNextBreak(self):
return self.basesBeforeNextBreakSpinBox.value()
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._breakOptionsGroupbox = PM_GroupBox( self, title = "Break Options" )
self._loadBreakOptionsGroupbox( self._breakOptionsGroupbox )
self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
self._baseNumberLabelGroupBox = PM_GroupBox( self, title = "Base Number Labels" )
self._loadBaseNumberLabelGroupBox(self._baseNumberLabelGroupBox)
def _loadBreakOptionsGroupbox(self, pmGroupBox):
"""
Load widgets in this group box.
"""
self.assignColorToBrokenDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Assign new color to broken strands',
widgetColumn = 0,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.assignColorToBrokenDnaStrandsCheckBox,
assignColorToBrokenDnaStrands_prefs_key )
self.basesBeforeNextBreakSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Break Every:",
value = 3,
setAsDefault = False,
minimum = 1,
maximum = 10000,
suffix = " bases"
)
connect_spinBox_with_pref(
self.basesBeforeNextBreakSpinBox,
breakStrandsCommand_numberOfBasesBeforeNextBreak_prefs_key)
self.breakAllStrandsButton = PM_PushButton(
pmGroupBox,
label = "",
text = "do it" )
self._dnaStrandChooserGroupBox = PM_ObjectChooser(
pmGroupBox,
self.command,
modelObjectType = self.win.assy.DnaStrand,
title = "Choose strands " )
if not DEBUG_BREAK_OPTIONS_FEATURE:
self._dnaStrandChooserGroupBox.hide()
self.breakAllStrandsButton.hide()
self.basesBeforeNextBreakSpinBox.hide()
#Return varius prefs_keys for arrowhead display options ui elements =======
def _prefs_key_arrowsOnThreePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 3' strand ends of PAM DNA.
"""
return breakStrandsCommand_arrowsOnThreePrimeEnds_prefs_key
def _prefs_key_arrowsOnFivePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 5' strand ends of PAM DNA.
"""
return breakStrandsCommand_arrowsOnFivePrimeEnds_prefs_key
def _prefs_key_useCustomColorForThreePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 3' arrowheads (if they are drawn)
or for 3' strand end atoms (if arrowheads are not drawn)
"""
return breakStrandsCommand_useCustomColorForThreePrimeArrowheads_prefs_key
def _prefs_key_useCustomColorForFivePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 5' arrowheads (if they are drawn)
or for 5' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_useCustomColorForFivePrimeArrowheads_prefs_key
def _prefs_key_dnaStrandThreePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 3' arrowheads (if they are drawn)
or 3' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_dnaStrandThreePrimeArrowheadsCustomColor_prefs_key
def _prefs_key_dnaStrandFivePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 5' arrowheads (if they are drawn)
or 5' strand end atoms (if arrowheads are not drawn).
"""
return breakStrandsCommand_dnaStrandFivePrimeArrowheadsCustomColor_prefs_key
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass