class Ui_DnaSequenceEditor(PM_DockWidget):
"""
The Ui_DnaSequenceEditor class defines UI elements for the Sequence Editor
object. The sequence editor is usually visible while in while editing
a DnaStrand.
It is a DockWidget that is docked 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
# Should parentWidget for a docwidget always be win?
#Not necessary but most likely it will be the case.
parentWidget = win
_superclass.__init__(self, parentWidget, title=self._title)
#A flag used to restore the state of the Reports dock widget
#(which can be accessed through View > Reports) see self.show() and
#self.closeEvent() for more details.
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
#hide the history widget first
#(It will be shown back during self.close)
#The history widget is hidden or shown only when both
# 'View > Full Screen' and View > Semi Full Screen actions
# are *unchecked*
#Thus show or close methods won't do anything to history widget
# if either of the above mentioned actions is checked.
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.
"""
#Note: Find and replace widgets might be moved to their own class.
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)
# Only supporting 5' to 3' direction until bug 2956 is fixed.
# Mark 2008-12-19
editDirectionChoices = ["5' to 3'"] # , "3' to 5'"]
self.baseDirectionChoiceComboBox = \
PM_ComboBox( self,
choices = editDirectionChoices,
index = 0,
spanWidth = False )
#Find and replace widgets --
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(60)
self.replaceLineEdit = \
PM_LineEdit( self,
label = "",
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")
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()
# NOTE: Following needs cleanup in the PM_WidgetRow/ PM_WidgetGrid
# but this explanation is sufficient until thats done --
# When the widget type starts with the word 'PM_' , the
# PM_WidgetRow treats it as a well defined widget and thus doesn't try
# to create a QWidget object (or its subclasses)
# This is the reason why qLabels such as self.warningSign and
# self.phraseNotFoundLabel are defined as PM_Labels and not 'QLabels'
# If they were defined as 'QLabel'(s) then PM_WidgetRow would have
# recreated the label. Since we want to show/hide the above mentioned
# labels (and if they were recreated as mentioned above),
# we would have needed to define those something like this:
# self.phraseNotFoundLabel = widgetRow._widgetList[-2]
#Cleanup in PM_widgetGrid could be to check if the widget starts with
#'Q' instead of 'PM_'
#Widgets to include in the widget row.
widgetList = [('PM_ToolButton', self.loadSequenceButton, 0),
('PM_ToolButton', self.saveSequenceButton, 1),
('QLabel', " Sequence direction:", 2),
('PM_ComboBox', self.baseDirectionChoiceComboBox, 3),
('QLabel', " Find:", 4),
('PM_LineEdit', self.findLineEdit, 5),
('PM_ToolButton', self.findOptionsToolButton, 6),
('PM_ToolButton', self.findPreviousToolButton, 7),
('PM_ToolButton', self.findNextToolButton, 8),
('QLabel', " Replace:", 9),
('PM_TextEdit', self.replaceLineEdit, 10),
('PM_PushButton', self.replacePushButton, 11),
('PM_Label', self.warningSign, 12),
('PM_Label', self.phraseNotFoundLabel, 13),
('QSpacerItem', 5, 5, 14)]
widgetRow = PM_WidgetRow(self,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
return
def _loadTextEditWidget(self):
"""
Load the SequenceTexteditWidgets.
"""
self.sequenceTextEdit = \
PM_TextEdit( self,
label = " Sequence: ",
spanWidth = False,
permit_enter_keystroke = False)
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.sequenceTextEdit.setFixedHeight(20)
#The StrandSequence 'Mate' it is a read only etxtedit that shows
#the complementary strand sequence.
self.sequenceTextEdit_mate = \
PM_TextEdit(self,
label = "",
spanWidth = False,
permit_enter_keystroke = False
)
palette = getPalette(None, QPalette.Base,
sequenceEditStrandMateBaseColor)
self.sequenceTextEdit_mate.setPalette(palette)
self.sequenceTextEdit_mate.setFixedHeight(20)
self.sequenceTextEdit_mate.setReadOnly(True)
self.sequenceTextEdit_mate.setWordWrapMode(QTextOption.WrapAnywhere)
#Important to make sure that the horizontal and vertical scrollbars
#for these text edits are never displayed.
for textEdit in (self.sequenceTextEdit, self.sequenceTextEdit_mate):
textEdit.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
textEdit.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)"\
"}"
#Not used:
# background-color: rgb(217, 255, 216)\
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_DnaSequenceEditor
ToolTip_DnaSequenceEditor(self)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_DnaSequenceEditor
whatsThis_DnaSequenceEditor(self)
return
class Ui_DnaSequenceEditor(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
# Should parentWidget for a docwidget always be win?
#Not necessary but most likely it will be the case.
parentWidget = win
_superclass.__init__(self, parentWidget, title = self._title)
#A flag used to restore the state of the Reports dock widget
#(which can be accessed through View > Reports) see self.show() and
#self.closeEvent() for more details.
self._reportsDockWidget_closed_in_show_method = False
self.setFixedHeight(90)
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
#hide the history widget first
#(It will be shown back during self.close)
#The history widget is hidden or shown only when both
# 'View > Full Screen' and View > Semi Full Screen actions
# are *unchecked*
#Thus show or close methods won't do anything to history widget
# if either of the above mentioned actions is checked.
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)
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
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTextEditWidget()
def _loadMenuWidgets(self):
"""
Load the various menu widgets (e.g. Open, save sequence options,
Find and replace widgets etc.
"""
#Note: Find and replace widgets might be moved to their own class.
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)
editDirectionChoices = ["5' to 3'", "3' to 5'"]
self.baseDirectionChoiceComboBox = \
PM_ComboBox( self,
choices = editDirectionChoices,
index = 0,
spanWidth = False )
#Find and replace widgets --
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(60)
self.replaceLineEdit = \
PM_LineEdit( self,
label = "",
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")
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()
# NOTE: Following needs cleanup in the PM_WidgetRow/ PM_WidgetGrid
# but this explanation is sufficient until thats done --
# When the widget type starts with the word 'PM_' , the
# PM_WidgetRow treats it as a well defined widget and thus doesn't try
# to create a QWidget object (or its subclasses)
# This is the reason why qLabels such as self.warningSign and
# self.phraseNotFoundLabel are defined as PM_Labels and not 'QLabels'
# If they were defined as 'QLabel'(s) then PM_WidgetRow would have
# recreated the label. Since we want to show/hide the above mentioned
# labels (and if they were recreated as mentioned above),
# we would have needed to define those something like this:
# self.phraseNotFoundLabel = widgetRow._widgetList[-2]
#Cleanup in PM_widgetGrid could be to check if the widget starts with
#'Q' instead of 'PM_'
#Widgets to include in the widget row.
widgetList = [('PM_ToolButton', self.loadSequenceButton, 0),
('PM_ToolButton', self.saveSequenceButton, 1),
('QLabel', " Sequence direction:", 2),
('PM_ComboBox', self.baseDirectionChoiceComboBox , 3),
('QLabel', " Find:", 4),
('PM_LineEdit', self.findLineEdit, 5),
('PM_ToolButton', self.findOptionsToolButton, 6),
('PM_ToolButton', self.findPreviousToolButton, 7),
('PM_ToolButton', self.findNextToolButton, 8),
('QLabel', " Replace:", 9),
('PM_TextEdit', self.replaceLineEdit, 10),
('PM_PushButton', self.replacePushButton, 11),
('PM_Label', self.warningSign, 12),
('PM_Label', self.phraseNotFoundLabel, 13),
('QSpacerItem', 5, 5, 14) ]
widgetRow = PM_WidgetRow(self,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def _loadTextEditWidget(self):
"""
Load the SequenceTexteditWidgets.
"""
self.sequenceTextEdit = \
PM_TextEdit( self,
label = " Sequence: ",
spanWidth = False,
permit_enter_keystroke = False)
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.sequenceTextEdit.setFixedHeight(20)
#The StrandSequence 'Mate' it is a read only etxtedit that shows
#the complementary strand sequence.
self.sequenceTextEdit_mate = \
PM_TextEdit(self,
label = "",
spanWidth = False,
permit_enter_keystroke = False
)
palette = getPalette(None,
QPalette.Base,
sequenceEditStrandMateBaseColor)
self.sequenceTextEdit_mate.setPalette(palette)
self.sequenceTextEdit_mate.setFixedHeight(20)
self.sequenceTextEdit_mate.setReadOnly(True)
self.sequenceTextEdit_mate.setWordWrapMode(QTextOption.WrapAnywhere)
#Important to make sure that the horizontal and vertical scrollbars
#for these text edits are never displayed.
for textEdit in (self.sequenceTextEdit, self.sequenceTextEdit_mate):
textEdit.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
textEdit.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
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)\
}"
#Not used:
# background-color: rgb(217, 255, 216)\
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)
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_SequenceEditor
ToolTip_SequenceEditor(self)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_SequenceEditor
whatsThis_SequenceEditor(self)
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
# Should parentWidget for a docwidget always be win?
#Not necessary but most likely it will be the case.
parentWidget = win
_superclass.__init__(self, parentWidget, title = self._title)
#A flag used to restore the state of the Reports dock widget
#(which can be accessed through View > Reports) see self.show() and
#self.closeEvent() for more details.
self._reportsDockWidget_closed_in_show_method = False
self.setFixedHeight(90)
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)
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
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTextEditWidget()
def _loadMenuWidgets(self):
"""
Load the various menu widgets (e.g. Open, save sequence options,
Find and replace widgets etc.
"""
#Note: Find and replace widgets might be moved to their own class.
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)
#Find and replace widgets --
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(60)
self.replaceLineEdit = \
PM_LineEdit( self,
label = "",
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")
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),
('QLabel', " Replace:", 9),
('PM_TextEdit', self.replaceLineEdit, 10),
('PM_PushButton', self.replacePushButton, 11),
('PM_Label', self.warningSign, 12),
('PM_Label', self.phraseNotFoundLabel, 13),
('QSpacerItem', 5, 5, 14) ]
widgetRow = PM_WidgetRow(self,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
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.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)
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)\
}"
#Not used:
# background-color: rgb(217, 255, 216)\
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)
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
pass
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
pass
class DnaGeneratorPropertyManager(PM_Dialog, DebugMenuMixin):
"""
The DnaGeneratorPropertyManager class provides a Property Manager
for the "Build > Atoms" command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
@ivar validSymbols: Miscellaneous symbols that may appear in the sequence
(but are ignored). The hyphen '-' is a special case
that must be dealt with individually; it is not
included because it can confuse regular expressions.
@type validSymbols: QString
"""
title = "DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?')
# The following class variables guarantee the UI's menu items
# are synchronized with their action code. The arrays should
# not be changed, unless an item is removed or inserted.
# Changes should be made via only the _action... variables.
# e.g., Change _action_Complement from "Complement"
# to "Complement Sequences". The menu item will
# change and its related code will need no update.
_action_Complement = "Complement"
_action_Reverse = "Reverse"
_action_RemoveUnrecognized = 'Remove unrecognized letters'
_action_ConvertUnrecognized = 'Convert unrecognized letters to "N"'
_actionChoices = [
"Action", "---", _action_Complement, _action_Reverse,
_action_RemoveUnrecognized, _action_ConvertUnrecognized
]
_modeltype_PAM3 = "PAM3"
_modeltype_PAM5 = "PAM5"
_modeltype_Atomistic = "Atomistic" # deprecated
_modelChoices = [_modeltype_PAM3, _modeltype_PAM5]
def __init__(self):
"""
Constructor for the DNA Generator property manager.
"""
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
msg = "Edit the DNA parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into \
the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PM is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True)
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Strand Sequence")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="DNA Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox3(self._pmGroupBox3)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
# Duplex Length
self.duplexLengthSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Duplex Length: ",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 34000,
singleStep = self.getDuplexRise("B-DNA"),
decimals = 3,
suffix = ' Angstroms')
self.connect(self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Strand Length
self.strandLengthSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Strand Length :",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000,
suffix = ' bases' )
self.connect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
# New Base choices
newBaseChoices = []
for theBase in basesDict.keys():
newBaseChoices = newBaseChoices \
+ [ theBase + ' (' \
+ basesDict[theBase]['Name'] + ')' ]
try:
defaultBaseChoice = basesDict.keys().index('N')
except:
defaultBaseChoice = 0
# Strand Sequence
self.sequenceTextEdit = \
PM_TextEdit( pmGroupBox,
label = "",
spanWidth = True )
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.connect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
self.connect(self.sequenceTextEdit, SIGNAL("cursorPositionChanged()"),
self.cursorPosChanged)
# Actions
self.actionsComboBox = \
PM_ComboBox( pmGroupBox,
label = '',
choices = self._actionChoices,
index = 0,
setAsDefault = True,
spanWidth = True )
# If SIGNAL("activate(const QString&)") is used, we get a TypeError.
# This is a bug that needs Bruce. Using currentIndexChanged(int) as
# a workaround, but there is still a bug when the "Reverse" action
# is selected. Mark 2007-08-15
self.connect(self.actionsComboBox, SIGNAL("currentIndexChanged(int)"),
self.actionsComboBoxChanged)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
self.modelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model :",
choices = self._modelChoices,
setAsDefault = True)
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation :",
choices = ["B-DNA"],
setAsDefault = True)
self.connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
self.basesPerTurnComboBox= \
PM_ComboBox( pmGroupBox,
label = "Bases Per Turn :",
choices = ["10.0", "10.5", "10.67"],
setAsDefault = True)
# I may decide to reintroduce "base-pair chunks" at a later time.
# Please talk to me if you have a strong feeling about including
# this. Mark 2007-08-19.
createChoices = ["Strand chunks", \
"Single chunk" ]
#@ "Base-pair chunks"]
self.createComboBox = \
PM_ComboBox( pmGroupBox,
label = "Create :",
choices = createChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
self._endPoint1GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint1")
self._endPoint2GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint2")
# Point 1
self.x1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
# Point 2
self.x2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 10.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in the
DNA Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
self.conformationComboBox.setWhatsThis("""<b>Conformation</b>
<p>There are three DNA geometries, A-DNA, B-DNA,
and Z-DNA. Only B-DNA and Z-DNA are currently supported.</p>""")
self.sequenceTextEdit.setWhatsThis("""<b>Strand Sequence</b>
<p>Type in the strand sequence you want to generate here (5' => 3')<br>
<br>
Recognized base letters:<br>
<br>
A = Adenosine<br>
C = Cytosine<br>
G = Guanosine<br>
T = Thymidine<br>
N = aNy base<br>
X = Unassigned<br>
<br>
Other base letters currently recognized:<br>
<br>
B = C,G, or T<br>
D = A,G, or T<br>
H = A,C, or T<br>
V = A,C, or G<br>
R = A or G (puRine)<br>
Y = C or T (pYrimidine)<br>
K = G or T (Keto)<br>
M = A or C (aMino)<br>
S = G or C (Strong -3H bonds)<br>
W = A or T (Weak - 2H bonds)<br>
</p>""")
self.actionsComboBox.setWhatsThis("""<b>Action</b>
<p>Select an action to perform on the sequence.</p>""")
def conformationComboBoxChanged(self, inIndex):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.basesPerTurnComboBox.clear()
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnComboBox.insertItem(0, "10.0")
self.basesPerTurnComboBox.insertItem(1, "10.5")
self.basesPerTurnComboBox.insertItem(2, "10.67")
#10.5 is the default value for Bases per turn.
#So set the current index to 1
self.basesPerTurnComboBox.setCurrentIndex(1)
elif conformation == "Z-DNA":
self.basesPerTurnComboBox.insertItem(0, "12.0")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
conformation = "B-DNA" # Workaround for "Restore Defaults".
pass
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = " + inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(
self.getDuplexRise(conformation))
def modelComboBoxChanged(self, inIndex):
"""
Slot for the Model combobox. It is called whenever the
Model choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self._modelChoices[inIndex]
self.disconnect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
self.conformationComboBox.clear() # Generates signal!
if conformation == self._modeltype_PAM3:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_PAM5:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_Atomistic:
self.conformationComboBox.addItem("B-DNA")
self.conformationComboBox.addItem("Z-DNA")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
pass
else:
msg = "Error - unknown model representation. Index = " + inIndex
env.history.message(redmsg(msg))
self.connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
# GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox.
def getDuplexRise(self, inConformation):
"""
Return the 'rise' between base pairs of the
specified DNA type (conformation).
@param inConformation: The current conformation.
@type inConformation: int
"""
return dnaDict[str(inConformation)]['DuplexRise']
def synchronizeLengths(self):
"""
Guarantees the values of the duplex length and strand length
spinboxes agree with the strand sequence (textedit).
"""
self.updateStrandLength()
self.updateDuplexLength()
return
# Added :jbirac 20070613:
def duplexLengthChanged(self, inDuplexLength):
"""
Slot for the duplex length spinbox, called whenever the value of the
Duplex Length spinbox changes.
@param inDuplexLength: The duplex length.
@type inDuplexLength: float
"""
conformation = self.conformationComboBox.currentText()
duplexRise = self.getDuplexRise(conformation)
newStrandLength = inDuplexLength / duplexRise + 0.5
newStrandLength = int(newStrandLength)
self.strandLengthChanged(newStrandLength)
def updateDuplexLength(self): # Added :jbirac 20070615:
"""
Update the Duplex Length spinbox; always the length of the
strand sequence multiplied by the 'rise' of the duplex. This
method is called by slots of other controls (i.e., this itself
is not a slot.)
"""
conformation = self.conformationComboBox.currentText()
newDuplexLength = self.getDuplexRise( conformation ) \
* self.getSequenceLength()
self.disconnect(self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
self.duplexLengthSpinBox.setValue(newDuplexLength)
self.connect(self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Renamed from length_changed :jbirac 20070613:
def strandLengthChanged(self, inStrandLength):
"""
Slot for the Strand Length spin box, called whenever the value of the
Strand Length spin box changes.
@param inStrandLength: The number of bases in the strand sequence.
@type inStrandLength: int
"""
theSequence = self.getPlainSequence()
sequenceLen = len(theSequence)
lengthChange = inStrandLength - self.getSequenceLength()
# Preserve the cursor's position/selection
cursor = self.sequenceTextEdit.textCursor()
#cursorPosition = cursor.position()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStrandLength < 0:
return # Should never happen.
if lengthChange < 0:
# If length is less than the previous length,
# simply truncate the current sequence.
theSequence.chop(-lengthChange)
elif lengthChange > 0:
# If length has increased, add the correct number of base
# letters to the current strand sequence.
numNewBases = lengthChange
# Get current base selected in combobox.
chosenBase = 'X' # Unassigned.
basesToAdd = chosenBase * numNewBases
theSequence.append(basesToAdd)
else:
env.history.message(
orangemsg("strandLengthChanged(): Length has not changed."))
self.setSequence(theSequence)
return
# Renamed from updateLength :jbirac 20070613:
def updateStrandLength(self):
"""
Update the Strand Length spinbox; always the length of the strand
sequence.
"""
self.disconnect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
self.strandLengthSpinBox.setValue(self.getSequenceLength())
self.connect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
return
def sequenceChanged(self):
"""
Slot for the Strand Sequence textedit widget.
Assumes the sequence changed directly by user's keystroke in the
textedit. Other methods...
"""
cursorPosition = self.getCursorPosition()
theSequence = self.getPlainSequence()
# Disconnect while we edit the sequence.
self.disconnect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
# How has the text changed?
if theSequence.length() == 0: # There is no sequence.
self.updateStrandLength()
self.updateDuplexLength()
else:
# Insert the sequence; it will be "stylized" by setSequence().
self.setSequence(theSequence)
# Reconnect to respond when the sequence is changed.
self.connect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
self.synchronizeLengths()
return
def getPlainSequence(self, inOmitSymbols=False):
"""
Returns a plain text QString (without HTML stylization)
of the current sequence. All characters are preserved (unless
specified explicitly), including valid base letters, punctuation
symbols, whitespace and invalid letters.
@param inOmitSymbols: Omits characters listed in self.validSymbols.
@type inOmitSymbols: bool
@return: The current DNA sequence in the PM.
@rtype: QString
"""
outSequence = self.sequenceTextEdit.toPlainText()
if inOmitSymbols:
# This may look like a sloppy piece of code, but Qt's QRegExp
# class makes it pretty tricky to remove all punctuation.
theString = '[<>' \
+ str( QRegExp.escape(self.validSymbols) ) \
+ ']|-'
outSequence.remove(QRegExp(theString))
return outSequence
def stylizeSequence(self, inSequence):
"""
Converts a plain text string of a sequence (including optional
symbols) to an HTML rich text string.
@param inSequence: A DNA sequence.
@type inSequence: QString
@return: The sequence.
@rtype: QString
"""
outSequence = str(inSequence)
# Verify that all characters (bases) in the sequence are "valid".
invalidSequence = False
basePosition = 0
sequencePosition = 0
invalidStartTag = "<b><font color=black>"
invalidEndTag = "</b>"
previousChar = chr(1) # Null character; may be revised.
# Some characters must be substituted to preserve
# whitespace and tags in HTML code.
substituteDict = {' ': ' ', '<': '<', '>': '>'}
while basePosition < len(outSequence):
theSeqChar = outSequence[basePosition]
if (theSeqChar in basesDict or theSeqChar in self.validSymbols):
# Close any preceding invalid sequence segment.
if invalidSequence == True:
outSequence = outSequence[:basePosition] \
+ invalidEndTag \
+ outSequence[basePosition:]
basePosition += len(invalidEndTag)
invalidSequence = False
# Color the valid characters.
if theSeqChar != previousChar:
# We only need to insert 'color' tags in places where
# the adjacent characters are different.
if theSeqChar in basesDict:
theTag = '<font color=' \
+ basesDict[ theSeqChar ]['Color'] \
+ '>'
elif not previousChar in self.validSymbols:
# The character is a 'valid' symbol to be greyed
# out. Only one 'color' tag is needed for a
# group of adjacent symbols.
theTag = '<font color=dimgrey>'
else:
theTag = ''
outSequence = outSequence[:basePosition] \
+ theTag + outSequence[basePosition:]
basePosition += len(theTag)
# Any <space> character must be substituted with an
# ASCII code tag because the HTML engine will collapse
# whitespace to a single <space> character; whitespace
# is truncated from the end of HTML by default.
# Also, many symbol characters must be substituted
# because they confuse the HTML syntax.
#if str( outSequence[basePosition] ) in substituteDict:
if outSequence[basePosition] in substituteDict:
#theTag = substituteDict[theSeqChar]
theTag = substituteDict[outSequence[basePosition]]
outSequence = outSequence[:basePosition] \
+ theTag \
+ outSequence[basePosition + 1:]
basePosition += len(theTag) - 1
else:
# The sequence character is invalid (but permissible).
# Tags (e.g., <b> and </b>) must be inserted at both the
# beginning and end of a segment of invalid characters.
if invalidSequence == False:
outSequence = outSequence[:basePosition] \
+ invalidStartTag \
+ outSequence[basePosition:]
basePosition += len(invalidStartTag)
invalidSequence = True
basePosition += 1
previousChar = theSeqChar
#basePosition += 1
# Specify that theSequence is definitely HTML format, because
# Qt can get confused between HTML and Plain Text.
outSequence = "<html>" + outSequence
outSequence += "</html>"
return outSequence
def setSequence(self, inSequence, inStylize=True, inRestoreCursor=True):
"""
Replace the current strand sequence with the new sequence text.
@param inSequence: The new sequence.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
text string (including optional symbols) to an HTML
rich text string.
@type inStylize: bool
@param inRestoreCursor: Not implemented yet.
@type inRestoreCursor: bool
@attention: Signals/slots must be managed before calling this method.
The textChanged() signal will be sent to any connected widgets.
"""
cursor = self.sequenceTextEdit.textCursor()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStylize:
inSequence = self.stylizeSequence(inSequence)
self.sequenceTextEdit.insertHtml(inSequence)
if inRestoreCursor:
cursor.setPosition(min(selectionStart, self.getSequenceLength()),
QTextCursor.MoveAnchor)
cursor.setPosition(min(selectionEnd, self.getSequenceLength()),
QTextCursor.KeepAnchor)
self.sequenceTextEdit.setTextCursor(cursor)
return
def getSequenceLength(self):
"""
Returns the number of characters in
the strand sequence textedit widget.
"""
theSequence = self.getPlainSequence(inOmitSymbols=True)
outLength = theSequence.length()
return outLength
def getCursorPosition(self):
"""
Returns the cursor position in the
strand sequence textedit widget.
"""
cursor = self.sequenceTextEdit.textCursor()
return cursor.position()
def cursorPosChanged(self):
"""
Slot called when the cursor position changes.
"""
cursor = self.sequenceTextEdit.textCursor()
if 0:
env.history.message(
greenmsg("cursorPosChanged: Selection (" +
str(cursor.selectionStart()) + " thru " +
str(cursor.selectionEnd()) + ')'))
return
def actionsComboBoxChanged(self, inIndex):
"""
Slot for the Actions combobox. It is called whenever the
Action choice is changed.
@param inIndex: The index of the selected action choice.
@type inIndex: int
"""
if inIndex == 0: # Very important.
return
actionName = str(self.actionsComboBox.currentText())
self.actionsComboBox.setCurrentIndex(0) # Generates signal!
self.invokeAction(actionName)
return
def invokeAction(self, inActionName):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='N')
self.setSequence(outResult)
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase='')
self.setSequence(outResult)
return
class DnaGeneratorPropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The DnaGeneratorPropertyManager class provides a Property Manager
for the "Build > Atoms" command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
@ivar validSymbols: Miscellaneous symbols that may appear in the sequence
(but are ignored). The hyphen '-' is a special case
that must be dealt with individually; it is not
included because it can confuse regular expressions.
@type validSymbols: QString
"""
title = "DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?')
# The following class variables guarantee the UI's menu items
# are synchronized with their action code. The arrays should
# not be changed, unless an item is removed or inserted.
# Changes should be made via only the _action... variables.
# e.g., Change _action_Complement from "Complement"
# to "Complement Sequences". The menu item will
# change and its related code will need no update.
_action_Complement = "Complement"
_action_Reverse = "Reverse"
_action_RemoveUnrecognized = 'Remove unrecognized letters'
_action_ConvertUnrecognized = 'Convert unrecognized letters to "N"'
_actionChoices = [ "Action",
"---",
_action_Complement,
_action_Reverse,
_action_RemoveUnrecognized,
_action_ConvertUnrecognized ]
_modeltype_PAM3 = "PAM3"
_modeltype_PAM5 = "PAM5"
_modeltype_Atomistic = "Atomistic" # deprecated
_modelChoices = [ _modeltype_PAM3,
_modeltype_PAM5 ]
def __init__( self ):
"""
Constructor for the DNA Generator property manager.
"""
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
DebugMenuMixin._init1( self )
msg = "Edit the DNA parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into \
the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PM is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = True )
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Strand Sequence" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "DNA Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
# Duplex Length
self.duplexLengthSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Duplex Length: ",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 34000,
singleStep = self.getDuplexRise("B-DNA"),
decimals = 3,
suffix = ' Angstroms')
self.connect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged )
# Strand Length
self.strandLengthSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Strand Length :",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000,
suffix = ' bases' )
self.connect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
# New Base choices
newBaseChoices = []
for theBase in basesDict.keys():
newBaseChoices = newBaseChoices \
+ [ theBase + ' (' \
+ basesDict[theBase]['Name'] + ')' ]
try:
defaultBaseChoice = basesDict.keys().index('N')
except:
defaultBaseChoice = 0
# Strand Sequence
self.sequenceTextEdit = \
PM_TextEdit( pmGroupBox,
label = "",
spanWidth = True )
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode( QTextOption.WrapAnywhere )
self.connect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
self.connect( self.sequenceTextEdit,
SIGNAL("cursorPositionChanged()"),
self.cursorPosChanged )
# Actions
self.actionsComboBox = \
PM_ComboBox( pmGroupBox,
label = '',
choices = self._actionChoices,
index = 0,
setAsDefault = True,
spanWidth = True )
# If SIGNAL("activate(const QString&)") is used, we get a TypeError.
# This is a bug that needs Bruce. Using currentIndexChanged(int) as
# a workaround, but there is still a bug when the "Reverse" action
# is selected. Mark 2007-08-15
self.connect( self.actionsComboBox,
SIGNAL("currentIndexChanged(int)"),
self.actionsComboBoxChanged )
def _loadGroupBox2( self, pmGroupBox ):
"""
Load widgets in group box 2.
"""
self.modelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model :",
choices = self._modelChoices,
setAsDefault = True)
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation :",
choices = ["B-DNA"],
setAsDefault = True)
self.connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
self.basesPerTurnComboBox= \
PM_ComboBox( pmGroupBox,
label = "Bases Per Turn :",
choices = ["10.0", "10.5", "10.67"],
setAsDefault = True)
# I may decide to reintroduce "base-pair chunks" at a later time.
# Please talk to me if you have a strong feeling about including
# this. Mark 2007-08-19.
createChoices = ["Strand chunks", \
"Single chunk" ]
#@ "Base-pair chunks"]
self.createComboBox = \
PM_ComboBox( pmGroupBox,
label = "Create :",
choices = createChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
self._endPoint1GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint1" )
self._endPoint2GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint2" )
# Point 1
self.x1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
# Point 2
self.x2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 10.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
def _addWhatsThisText( self ):
"""
What's This text for some of the widgets in the
DNA Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
self.conformationComboBox.setWhatsThis("""<b>Conformation</b>
<p>There are three DNA geometries, A-DNA, B-DNA,
and Z-DNA. Only B-DNA and Z-DNA are currently supported.</p>""")
self.sequenceTextEdit.setWhatsThis("""<b>Strand Sequence</b>
<p>Type in the strand sequence you want to generate here (5' => 3')<br>
<br>
Recognized base letters:<br>
<br>
A = Adenosine<br>
C = Cytosine<br>
G = Guanosine<br>
T = Thymidine<br>
N = aNy base<br>
X = Unassigned<br>
<br>
Other base letters currently recognized:<br>
<br>
B = C,G, or T<br>
D = A,G, or T<br>
H = A,C, or T<br>
V = A,C, or G<br>
R = A or G (puRine)<br>
Y = C or T (pYrimidine)<br>
K = G or T (Keto)<br>
M = A or C (aMino)<br>
S = G or C (Strong -3H bonds)<br>
W = A or T (Weak - 2H bonds)<br>
</p>""")
self.actionsComboBox.setWhatsThis("""<b>Action</b>
<p>Select an action to perform on the sequence.</p>""")
def conformationComboBoxChanged( self, inIndex ):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.basesPerTurnComboBox.clear()
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnComboBox.insertItem(0, "10.0")
self.basesPerTurnComboBox.insertItem(1, "10.5")
self.basesPerTurnComboBox.insertItem(2, "10.67")
#10.5 is the default value for Bases per turn.
#So set the current index to 1
self.basesPerTurnComboBox.setCurrentIndex(1)
elif conformation == "Z-DNA":
self.basesPerTurnComboBox.insertItem(0, "12.0")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
conformation = "B-DNA" # Workaround for "Restore Defaults".
pass
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = "+ inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(
self.getDuplexRise(conformation) )
def modelComboBoxChanged( self, inIndex ):
"""
Slot for the Model combobox. It is called whenever the
Model choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self._modelChoices[ inIndex ]
self.disconnect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
self.conformationComboBox.clear() # Generates signal!
if conformation == self._modeltype_PAM3:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_PAM5:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_Atomistic:
self.conformationComboBox.addItem("B-DNA")
self.conformationComboBox.addItem("Z-DNA")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
pass
else:
msg = "Error - unknown model representation. Index = " + inIndex
env.history.message(redmsg(msg))
self.connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
# GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox.
def getDuplexRise( self, inConformation ):
"""
Return the 'rise' between base pairs of the
specified DNA type (conformation).
@param inConformation: The current conformation.
@type inConformation: int
"""
return dnaDict[str(inConformation)]['DuplexRise']
def synchronizeLengths( self ):
"""
Guarantees the values of the duplex length and strand length
spinboxes agree with the strand sequence (textedit).
"""
self.updateStrandLength()
self.updateDuplexLength()
return
# Added :jbirac 20070613:
def duplexLengthChanged( self, inDuplexLength ):
"""
Slot for the duplex length spinbox, called whenever the value of the
Duplex Length spinbox changes.
@param inDuplexLength: The duplex length.
@type inDuplexLength: float
"""
conformation = self.conformationComboBox.currentText()
duplexRise = self.getDuplexRise( conformation )
newStrandLength = inDuplexLength / duplexRise + 0.5
newStrandLength = int( newStrandLength )
self.strandLengthChanged( newStrandLength )
def updateDuplexLength( self ): # Added :jbirac 20070615:
"""
Update the Duplex Length spinbox; always the length of the
strand sequence multiplied by the 'rise' of the duplex. This
method is called by slots of other controls (i.e., this itself
is not a slot.)
"""
conformation = self.conformationComboBox.currentText()
newDuplexLength = self.getDuplexRise( conformation ) \
* self.getSequenceLength()
self.disconnect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
self.duplexLengthSpinBox.setValue( newDuplexLength )
self.connect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Renamed from length_changed :jbirac 20070613:
def strandLengthChanged( self, inStrandLength ):
"""
Slot for the Strand Length spin box, called whenever the value of the
Strand Length spin box changes.
@param inStrandLength: The number of bases in the strand sequence.
@type inStrandLength: int
"""
theSequence = self.getPlainSequence()
sequenceLen = len( theSequence )
lengthChange = inStrandLength - self.getSequenceLength()
# Preserve the cursor's position/selection
cursor = self.sequenceTextEdit.textCursor()
#cursorPosition = cursor.position()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStrandLength < 0:
return # Should never happen.
if lengthChange < 0:
# If length is less than the previous length,
# simply truncate the current sequence.
theSequence.chop( -lengthChange )
elif lengthChange > 0:
# If length has increased, add the correct number of base
# letters to the current strand sequence.
numNewBases = lengthChange
# Get current base selected in combobox.
chosenBase = 'X' # Unassigned.
basesToAdd = chosenBase * numNewBases
theSequence.append( basesToAdd )
else:
env.history.message(
orangemsg( "strandLengthChanged(): Length has not changed." ))
self.setSequence( theSequence )
return
# Renamed from updateLength :jbirac 20070613:
def updateStrandLength( self ):
"""
Update the Strand Length spinbox; always the length of the strand
sequence.
"""
self.disconnect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
self.strandLengthSpinBox.setValue( self.getSequenceLength() )
self.connect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
return
def sequenceChanged( self ):
"""
Slot for the Strand Sequence textedit widget.
Assumes the sequence changed directly by user's keystroke in the
textedit. Other methods...
"""
cursorPosition = self.getCursorPosition()
theSequence = self.getPlainSequence()
# Disconnect while we edit the sequence.
self.disconnect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
# How has the text changed?
if theSequence.length() == 0: # There is no sequence.
self.updateStrandLength()
self.updateDuplexLength()
else:
# Insert the sequence; it will be "stylized" by setSequence().
self.setSequence( theSequence )
# Reconnect to respond when the sequence is changed.
self.connect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
self.synchronizeLengths()
return
def getPlainSequence( self, inOmitSymbols = False ):
"""
Returns a plain text QString (without HTML stylization)
of the current sequence. All characters are preserved (unless
specified explicitly), including valid base letters, punctuation
symbols, whitespace and invalid letters.
@param inOmitSymbols: Omits characters listed in self.validSymbols.
@type inOmitSymbols: bool
@return: The current DNA sequence in the PM.
@rtype: QString
"""
outSequence = self.sequenceTextEdit.toPlainText()
if inOmitSymbols:
# This may look like a sloppy piece of code, but Qt's QRegExp
# class makes it pretty tricky to remove all punctuation.
theString = '[<>' \
+ str( QRegExp.escape(self.validSymbols) ) \
+ ']|-'
outSequence.remove(QRegExp( theString ))
return outSequence
def stylizeSequence( self, inSequence ):
"""
Converts a plain text string of a sequence (including optional
symbols) to an HTML rich text string.
@param inSequence: A DNA sequence.
@type inSequence: QString
@return: The sequence.
@rtype: QString
"""
outSequence = str(inSequence)
# Verify that all characters (bases) in the sequence are "valid".
invalidSequence = False
basePosition = 0
sequencePosition = 0
invalidStartTag = "<b><font color=black>"
invalidEndTag = "</b>"
previousChar = chr(1) # Null character; may be revised.
# Some characters must be substituted to preserve
# whitespace and tags in HTML code.
substituteDict = { ' ':' ', '<':'<', '>':'>' }
while basePosition < len(outSequence):
theSeqChar = outSequence[basePosition]
if ( theSeqChar in basesDict
or theSeqChar in self.validSymbols ):
# Close any preceding invalid sequence segment.
if invalidSequence == True:
outSequence = outSequence[:basePosition] \
+ invalidEndTag \
+ outSequence[basePosition:]
basePosition += len(invalidEndTag)
invalidSequence = False
# Color the valid characters.
if theSeqChar != previousChar:
# We only need to insert 'color' tags in places where
# the adjacent characters are different.
if theSeqChar in basesDict:
theTag = '<font color=' \
+ basesDict[ theSeqChar ]['Color'] \
+ '>'
elif not previousChar in self.validSymbols:
# The character is a 'valid' symbol to be greyed
# out. Only one 'color' tag is needed for a
# group of adjacent symbols.
theTag = '<font color=dimgrey>'
else:
theTag = ''
outSequence = outSequence[:basePosition] \
+ theTag + outSequence[basePosition:]
basePosition += len(theTag)
# Any <space> character must be substituted with an
# ASCII code tag because the HTML engine will collapse
# whitespace to a single <space> character; whitespace
# is truncated from the end of HTML by default.
# Also, many symbol characters must be substituted
# because they confuse the HTML syntax.
#if str( outSequence[basePosition] ) in substituteDict:
if outSequence[basePosition] in substituteDict:
#theTag = substituteDict[theSeqChar]
theTag = substituteDict[ outSequence[basePosition] ]
outSequence = outSequence[:basePosition] \
+ theTag \
+ outSequence[basePosition + 1:]
basePosition += len(theTag) - 1
else:
# The sequence character is invalid (but permissible).
# Tags (e.g., <b> and </b>) must be inserted at both the
# beginning and end of a segment of invalid characters.
if invalidSequence == False:
outSequence = outSequence[:basePosition] \
+ invalidStartTag \
+ outSequence[basePosition:]
basePosition += len(invalidStartTag)
invalidSequence = True
basePosition += 1
previousChar = theSeqChar
#basePosition += 1
# Specify that theSequence is definitely HTML format, because
# Qt can get confused between HTML and Plain Text.
outSequence = "<html>" + outSequence
outSequence += "</html>"
return outSequence
def setSequence( self,
inSequence,
inStylize = True,
inRestoreCursor = True ):
"""
Replace the current strand sequence with the new sequence text.
@param inSequence: The new sequence.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
text string (including optional symbols) to an HTML
rich text string.
@type inStylize: bool
@param inRestoreCursor: Not implemented yet.
@type inRestoreCursor: bool
@attention: Signals/slots must be managed before calling this method.
The textChanged() signal will be sent to any connected widgets.
"""
cursor = self.sequenceTextEdit.textCursor()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStylize:
inSequence = self.stylizeSequence( inSequence )
self.sequenceTextEdit.insertHtml( inSequence )
if inRestoreCursor:
cursor.setPosition( min(selectionStart, self.getSequenceLength()),
QTextCursor.MoveAnchor )
cursor.setPosition( min(selectionEnd, self.getSequenceLength()),
QTextCursor.KeepAnchor )
self.sequenceTextEdit.setTextCursor( cursor )
return
def getSequenceLength( self ):
"""
Returns the number of characters in
the strand sequence textedit widget.
"""
theSequence = self.getPlainSequence( inOmitSymbols = True )
outLength = theSequence.length()
return outLength
def getCursorPosition( self ):
"""
Returns the cursor position in the
strand sequence textedit widget.
"""
cursor = self.sequenceTextEdit.textCursor()
return cursor.position()
def cursorPosChanged( self ):
"""
Slot called when the cursor position changes.
"""
cursor = self.sequenceTextEdit.textCursor()
if 0:
env.history.message( greenmsg( "cursorPosChanged: Selection ("
+ str(cursor.selectionStart())
+ " thru "
+ str(cursor.selectionEnd())+')' ) )
return
def actionsComboBoxChanged( self, inIndex ):
"""
Slot for the Actions combobox. It is called whenever the
Action choice is changed.
@param inIndex: The index of the selected action choice.
@type inIndex: int
"""
if inIndex == 0: # Very important.
return
actionName = str(self.actionsComboBox.currentText())
self.actionsComboBox.setCurrentIndex( 0 ) # Generates signal!
self.invokeAction( actionName )
return
def invokeAction( self, inActionName ):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = 'N')
self.setSequence( outResult )
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = '')
self.setSequence( outResult )
return
