def _loadAddRemoveButtons(self):
"""
"""
self._addToolButton = PM_ToolButton(self,
text="Add items to the list",
iconPath=self._addIcon,
spanWidth=True)
self._addToolButton.setCheckable(True)
self._addToolButton.setAutoRaise(True)
self._removeToolButton = PM_ToolButton(
self,
text="Remove items from the list",
iconPath=self._removeIcon,
spanWidth=True)
self._removeToolButton.setCheckable(True)
self._removeToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [('QLabel', " Add/Remove Items:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self._addToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self._removeToolButton, 4),
('QSpacerItem', 5, 5, 5)]
widgetRow = PM_WidgetRow(self,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
#Following toolbutton facilitates entering a temporary NanotubeLineMode
#to create a CNT using endpoints of the specified line.
self.specifyCntLineButton = PM_ToolButton(
pmGroupBox,
text="Specify Endpoints",
iconPath="ui/actions/Properties Manager/Pencil.png",
spanWidth=True)
self.specifyCntLineButton.setCheckable(True)
self.specifyCntLineButton.setAutoRaise(True)
self.specifyCntLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadAddRemoveButtons(self):
"""
"""
self._addToolButton = PM_ToolButton(
self,
text = "Add items to the list",
iconPath = self._addIcon,
spanWidth = True )
self._addToolButton.setCheckable(True)
self._addToolButton.setAutoRaise(True)
self._removeToolButton = PM_ToolButton(
self,
text = "Remove items from the list",
iconPath = self._removeIcon,
spanWidth = True )
self._removeToolButton.setCheckable(True)
self._removeToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [
('QLabel', " Add/Remove Items:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self._addToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self._removeToolButton, 4),
('QSpacerItem', 5, 5, 5) ]
widgetRow = PM_WidgetRow(self,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def _loadPM_ToolButton(self, inPmGroupBox):
"""
PM_ToolButton widgets.
"""
self.toolButton1 = \
PM_ToolButton( inPmGroupBox,
label = "",
text = "ToolButton 1" )
self.toolButton2 = \
PM_ToolButton( inPmGroupBox,
label = "",
text = "ToolButton 2",
spanWidth = True )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
#Following toolbutton facilitates entering a temporary NanotubeLineMode
#to create a CNT using endpoints of the specified line.
self.specifyCntLineButton = PM_ToolButton(
pmGroupBox,
text = "Specify Endpoints",
iconPath = "ui/actions/Properties Manager/Pencil.png",
spanWidth = True
)
self.specifyCntLineButton.setCheckable(True)
self.specifyCntLineButton.setAutoRaise(True)
self.specifyCntLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text = "Launch QuteMolX",
iconPath = "ui/actions/Properties Manager/QuteMol.png",
spanWidth = True )
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.segmentListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [
('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5) ]
widgetRow = PM_WidgetRow(pmGroupBox,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5)]
widgetRow = PM_WidgetRow(pmGroupBox,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
def _loadMovieFilesGroupBox(self, inPmGroupBox):
"""
Load widgets in the Open/Save Movie Files group box.
@param inPmGroupBox: The Open/Save Movie Files groupbox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
for action in self.fileOpenMovieAction, self.fileSaveMovieAction:
btn = PM_ToolButton(inPmGroupBox,
text = str(action.text()),
spanWidth = True)
btn.setDefaultAction(action)
btn.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = X_ROW_LABELS )
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Y_ROW_LABELS )
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Z_ROW_LABELS )
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
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.searchTypeComboBox = \
PM_ComboBox( self,
label = "Search options:",
choices = ["By node name", "By # of bases (DNA only)"],
setAsDefault = True)
#Find widgets --
self._nucleotidesSpinBox_1 = PM_SpinBox(self,
label="",
value=10,
setAsDefault=False,
singleStep=10,
minimum=1,
maximum=50000)
self._nucleotidesSpinBox_2 = PM_SpinBox(self,
label="",
value=50,
setAsDefault=False,
singleStep=10,
minimum=1,
maximum=50000)
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(80)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
##self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
##self._setFindOptionsToolButtonMenu()
self.searchToolButton = PM_ToolButton(
self, iconPath="ui/actions/Properties Manager/Find_Next.png")
self.searchToolButton.setAutoRaise(False)
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("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.
widgetList1 = [('QLabel', " Search for name:", 1),
('PM_LineEdit', self.findLineEdit, 2),
('PM_ToolButton', self.findOptionsToolButton, 3),
('PM_ToolButton', self.searchToolButton, 4),
('PM_Label', self.warningSign, 5),
('PM_Label', self.phraseNotFoundLabel, 6),
('QSpacerItem', 5, 5, 7)]
widgetList2 = [('QLabel', " Number of bases: >=", 1),
('PM_SpinBox', self._nucleotidesSpinBox_1, 2),
('QLabel', " <=", 3),
('PM_SpinBox', self._nucleotidesSpinBox_2, 4),
('QSpacerItem', 5, 5, 5)]
widgetList3 = [('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.searchToolButton, 2),
('PM_Label', self.warningSign, 3),
('PM_Label', self.phraseNotFoundLabel, 4),
('QSpacerItem', 5, 5, 5)]
self._widgetRow1 = PM_WidgetRow(self,
title='',
widgetList=widgetList1,
label="",
spanWidth=True)
self._widgetRow2 = PM_WidgetRow(self,
title='',
widgetList=widgetList2,
label="",
spanWidth=True)
self._widgetRow3 = PM_WidgetRow(self,
title='',
widgetList=widgetList3,
label="",
spanWidth=True)
class Ui_MovePropertyManager(Command_PropertyManager):
# The title that appears in the Property Manager header
title = "Move"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/Translate_Components.png"
# The title(s) that appear in the property manager header.
# (these are changed depending on the active group box)
translateTitle = "Translate"
rotateTitle = "Rotate"
# The full path to PNG file(s) that appears in the header.
translateIconPath = "ui/actions/Properties Manager/Translate_Components.png"
rotateIconPath = "ui/actions/Properties Manager/Rotate_Components.png"
def __init__(self, command):
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
def _addGroupBoxes(self):
"""
Add groupboxes to the Property Manager dialog.
"""
self.translateGroupBox = PM_GroupBox(self,
title="Translate",
connectTitleButton=False)
self.translateGroupBox.titleButton.setShortcut('T')
self._loadTranslateGroupBox(self.translateGroupBox)
self.rotateGroupBox = PM_GroupBox(self,
title="Rotate",
connectTitleButton=False)
self.rotateGroupBox.titleButton.setShortcut('R')
self._loadRotateGroupBox(self.rotateGroupBox)
self.translateGroupBox.collapse()
self.rotateGroupBox.collapse()
# == Begin Translate Group Box =====================
def _loadTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate group box.
@param inPmGroupBox: The Translate group box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
translateChoices = ["Free Drag", "By Delta XYZ", "To XYZ Position"]
self.translateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = translateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.freeDragTranslateGroupBox = PM_GroupBox(inPmGroupBox)
self._loadFreeDragTranslateGroupBox(self.freeDragTranslateGroupBox)
self.byDeltaGroupBox = PM_GroupBox(inPmGroupBox)
self._loadByDeltaGroupBox(self.byDeltaGroupBox)
self.toPositionGroupBox = PM_GroupBox(inPmGroupBox)
self._loadToPositionGroupBox(self.toPositionGroupBox)
self.updateTranslateGroupBoxes(0)
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton = self.freeDragTranslateButtonGroup.getButtonById(
1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
def _loadByDeltaGroupBox(self, inPmGroupBox):
"""
Load widgets in the translate By Delta group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Translate By Delta group box in the translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.moveDeltaXSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_X.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaYSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Y.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaZSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Z.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
DELTA_BUTTONS = [
("QToolButton", 1, "Delta Plus",
"ui/actions/Properties Manager/Move_Delta_Plus.png", "", "+", 0),
("QToolButton", 2, "Delta Minus",
"ui/actions/Properties Manager/Move_Delta_Minus.png", "", "-", 1)
]
self.translateDeltaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = DELTA_BUTTONS,
label = 'Translate:',
isAutoRaise = True,
isCheckable = False
)
self.transDeltaPlusButton = \
self.translateDeltaButtonRow.getButtonById(1)
self.transDeltaMinusButton = \
self.translateDeltaButtonRow.getButtonById(2)
def _loadToPositionGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate To a given Position group box, which is
present within the Translate groupbox.
@param inPmGroupBox: Translate To Position group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.toPositionspinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
self.moveXSpinBox = self.toPositionspinboxes.xSpinBox
self.moveYSpinBox = self.toPositionspinboxes.ySpinBox
self.moveZSpinBox = self.toPositionspinboxes.zSpinBox
self.moveAbsoluteButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Move Selection",
spanWidth = True )
# == Begin Rotate Group Box =====================
def _loadRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate group box,
@param inPmGroupBox: The Rotate GroupBox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
rotateChoices = ["Free Drag", "By Specified Angle"]
self.rotateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = rotateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.rotateAsUnitCB = \
PM_CheckBox( inPmGroupBox,
text = 'Rotate as a unit' ,
widgetColumn = 0,
state = Qt.Checked )
self.freeDragRotateGroupBox = PM_GroupBox(inPmGroupBox)
self._loadFreeDragRotateGroupBox(self.freeDragRotateGroupBox)
self.bySpecifiedAngleGroupBox = PM_GroupBox(inPmGroupBox)
self._loadBySpecifiedAngleGroupBox(self.bySpecifiedAngleGroupBox)
self.updateRotateGroupBoxes(0)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=X_ROW_LABELS)
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Y_ROW_LABELS)
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Z_ROW_LABELS)
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
def _loadBySpecifiedAngleGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate By Specified Angle group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: Rotate By Specified Angle group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
("QToolButton", 1, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png",
"Rotate about X axis", "X", 0),
("QToolButton", 2, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png",
"Rotate about Y axis", "Y", 1),
("QToolButton", 3, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png",
"Rotate about Z axis", "Z", 2),
]
self.rotateAroundAxisButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
alignment = 'Right',
label = 'Rotate Around:'
)
self.rotXaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(1)
self.rotYaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(2)
self.rotZaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(3)
self.rotateThetaSpinBox = \
PM_DoubleSpinBox(inPmGroupBox,
label = "Rotate By:",
value = 0.0,
setAsDefault = True,
minimum = 0,
maximum = 360.0,
singleStep = 1.0,
decimals = 2,
suffix = ' Degrees')
THETA_BUTTONS = [
("QToolButton", 1, "Theta Plus",
"ui/actions/Properties Manager/Move_Theta_Plus.png", "", "+", 0),
("QToolButton", 2, "Theta Minus",
"ui/actions/Properties Manager/Move_Theta_Minus.png", "", "-", 1)
]
self.rotateThetaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = THETA_BUTTONS,
label = 'Direction:',
isAutoRaise = True,
isCheckable = False
)
self.rotateThetaPlusButton = self.rotateThetaButtonRow.getButtonById(1)
self.rotateThetaMinusButton = self.rotateThetaButtonRow.getButtonById(
2)
# == End Rotate Group Box =====================
# == Slots for Translate group box
def _hideAllTranslateGroupBoxes(self):
"""
Hides all Translate group boxes.
"""
self.toPositionGroupBox.hide()
self.byDeltaGroupBox.hide()
self.freeDragTranslateGroupBox.hide()
def updateTranslateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Translate group box.
@type id: int
"""
self._hideAllTranslateGroupBoxes()
if id is 0:
self.freeDragTranslateGroupBox.show()
if id is 1:
self.byDeltaGroupBox.show()
if id is 2:
self.toPositionGroupBox.show()
self.updateMessage()
def changeMoveOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of translate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManager.changeMoveOption} which overrides this
method
"""
pass
# == Slots for Rotate group box
def updateRotateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Rotate group box.
@type id: int
"""
if id is 0:
self.bySpecifiedAngleGroupBox.hide()
self.freeDragRotateGroupBox.show()
if id is 1:
self.freeDragRotateGroupBox.hide()
self.bySpecifiedAngleGroupBox.show()
self.updateMessage()
def changeRotateOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of rotate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManage.changeRotateOption} which overrides this
method
"""
pass
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager
whatsThis_MovePropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager
ToolTip_MovePropertyManager(self)
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton = self.freeDragTranslateButtonGroup.getButtonById(
1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
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 _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 _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 )
class MultipleDnaSegmentResize_PropertyManager(DnaOrCnt_PropertyManager):
title = "Resize Dna Segments"
iconPath = "ui/actions/Properties Manager/Resize_Multiple_Segments.png"
def __init__(self, command):
"""
Constructor for the Build DNA property manager.
"""
self.endPoint1 = V(0, 0, 0)
self.endPoint2 = V(0, 0, 0)
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
self.dnaModel = 'PAM3'
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Use resize handles to resize the segments."
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
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.addSegmentsToolButton, SIGNAL("toggled(bool)"),
self.activateAddSegmentsTool)
change_connect(self.removeSegmentsToolButton, SIGNAL("toggled(bool)"),
self.activateRemoveSegmentsTool)
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.model_changed()
@see: DnaSegment_EditCommand.hasResizableStructure()
@see: self._current_model_changed_params()
"""
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
number_of_segments, isStructResizable, why_not = currentParams
#update the self._previous_model_changed_params with this new param set.
self._previous_model_changed_params = currentParams
if not isStructResizable:
if not number_of_segments == 0:
#disable all widgets
self._pmGroupBox1.setEnabled(False)
msg = redmsg("DnaSegment is not resizable. Reason: %s" % (why_not))
self.updateMessage(msg)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg = "Use resize handles to resize the segments"
self.updateMessage(msg)
self.updateListWidgets()
##self.command.updateHandlePositions()
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:
#update the list first.
self.command.updateResizeSegmentList()
number_of_segments = len(self.command.getResizeSegmentList())
isStructResizable, why_not = self.command.hasResizableStructure()
params = (number_of_segments, isStructResizable, why_not)
return params
def isAddSegmentsToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments to be resized) is active
"""
if self.addSegmentsToolButton.isChecked():
#For safety
if not self.removeSegmentsToolButton.isChecked():
return True
return False
def isRemoveSegmentsToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments to be resized) is active
"""
if self.removeSegmentsToolButton.isChecked():
if not self.addSegmentsToolButton.isChecked():
#For safety
return True
return False
def activateAddSegmentsTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
to be resized) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(True)
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightgreen_2)
else:
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def activateRemoveSegmentsTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
to be resized) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(True)
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightred_1)
else:
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def removeListWidgetItems(self):
"""
Removes selected atoms from the resize dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget (indicating its no longer being resized)
This is intentional.
"""
self.segmentListWidget.deleteSelection()
itemDict = self.segmentListWidget.getItemDictonary()
self.command.setResizeStructList(itemDict.values())
self.updateListWidgets()
self.win.win_update()
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Segments for Resizing")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5)]
widgetRow = PM_WidgetRow(pmGroupBox,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
def show(self):
"""
Overrides the superclass method
@see: self._deactivateAddRemoveSegmentsTool
"""
_superclass.show(self)
##self.updateListWidgets()
self._deactivateAddRemoveSegmentsTool()
def _deactivateAddRemoveSegmentsTool(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self.addSegmentsToolButton.setChecked(False)
self.removeSegmentsToolButton.setChecked(False)
def listWidgetHasFocus(self):
"""
Checks if the list widget that lists dnasegments to be resized has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self.segmentListWidget.hasFocus():
return True
return False
def setParameters(self, params):
pass
def getParameters(self):
return ()
def updateListWidgets(self):
self.updateSegmentListWidget()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
segmentList = self.command.getResizeSegmentList()
self.segmentListWidget.insertItems(row=0, items=segmentList)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaSegmentEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaSegmentEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Duplex length",
dnaSegmentEditCommand_cursorTextCheckBox_length_prefs_key),
("Number of basepairs to be changed",
dnaSegmentEditCommand_cursorTextCheckBox_changedBasePairs_prefs_key)
]
return params
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
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 )
class QuteMolPropertyManager(PM_Dialog):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = [ "Render axes",
"Hide axes" ]
_bases_display_choices = [ "Render bases",
"Hide bases" ]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__(self, win):
"""
Construct the QuteMolX Property Manager.
@param win: The main window.
@type win: QMainWindow
"""
self.win = win
self.pw = None
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
msg = "Select a QuteMolX rendering style and click the \
<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
# Hide Preview and Restore defaults button for Alpha9.
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON | PM_PREVIEW_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title = "DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title = "Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Axes: ',
choices = self._axes_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.basesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Bases: ',
choices = self._bases_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text = "Launch QuteMolX",
iconPath = "ui/actions/Properties Manager/QuteMol.png",
spanWidth = True )
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show)
"""
if self.isVisible(): # Fixes bug 2680. --Mark 2008-03-19
return
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect = True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
#First exit temporary modes (e.g. Pan mode) if any.
currentCommand = self.win.commandSequencer.currentCommand
if not currentCommand.command_has_its_own_gui:
currentCommand.Done()
self.connect_or_disconnect_signals(isConnect = False)
PM_Dialog.close(self)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.accept()
self.close() # Close the property manager.
# The following reopens the property manager of the mode after
# when the PM of the reference geometry is closed. -- Ninad 20070603
# Note: the value of self.modePropertyManager can be None
# @see: anyMode.propMgr
#
# (Note: once we have a real command sequencer, it will be
# handling this kind of thing itself, and the situation
# in which the currentCommand does not correspond to
# the current PM (as is true here while this separate PM
# is open, since it's not currentCommand.propMgr)
# will be deprecated or impossible. [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.reject()
self.close()
# The following reopens the property manager of the command after
# the PM of the reference geometry editCommand (i.e. Plane) is closed.
# Note: the value of self.modePropertyManager can be None.
# See anyMode.propMgr
# (See similar code in ok_btn_clicked [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton,
SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class QuteMolPropertyManager(PM_Dialog):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = ["Render axes", "Hide axes"]
_bases_display_choices = ["Render bases", "Hide bases"]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__(self, win):
"""
Construct the QuteMolX Property Manager.
@param win: The main window.
@type win: QMainWindow
"""
self.win = win
self.pw = None
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
msg = "Select a QuteMolX rendering style and click the \
<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
# Hide Preview and Restore defaults button for Alpha9.
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON | PM_PREVIEW_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title="DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title="Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(pmGroupBox,
label='Axes: ',
choices=self._axes_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
self.basesCombobox = PM_ComboBox(pmGroupBox,
label='Bases: ',
choices=self._bases_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text="Launch QuteMolX",
iconPath="ui/actions/Properties Manager/QuteMol.png",
spanWidth=True)
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show)
"""
if self.isVisible(): # Fixes bug 2680. --Mark 2008-03-19
return
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect=True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
#First exit temporary modes (e.g. Pan mode) if any.
currentCommand = self.win.commandSequencer.currentCommand
if not currentCommand.command_has_its_own_gui:
currentCommand.Done()
self.connect_or_disconnect_signals(isConnect=False)
PM_Dialog.close(self)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.accept()
self.close() # Close the property manager.
# The following reopens the property manager of the mode after
# when the PM of the reference geometry is closed. -- Ninad 20070603
# Note: the value of self.modePropertyManager can be None
# @see: anyMode.propMgr
#
# (Note: once we have a real command sequencer, it will be
# handling this kind of thing itself, and the situation
# in which the currentCommand does not correspond to
# the current PM (as is true here while this separate PM
# is open, since it's not currentCommand.propMgr)
# will be deprecated or impossible. [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.reject()
self.close()
# The following reopens the property manager of the command after
# the PM of the reference geometry editCommand (i.e. Plane) is closed.
# Note: the value of self.modePropertyManager can be None.
# See anyMode.propMgr
# (See similar code in ok_btn_clicked [bruce 071011 comment])
self.modePropertyManager = self.win.currentCommand.propMgr
if self.modePropertyManager:
# (re)open the PM of the current command (i.e. "Build > Atoms").
self.open(self.modePropertyManager)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton, SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg=''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault=False,
minLines=5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class Ui_MovePropertyManager(Command_PropertyManager):
# The title that appears in the Property Manager header
title = "Move"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/Translate_Components.png"
# The title(s) that appear in the property manager header.
# (these are changed depending on the active group box)
translateTitle = "Translate"
rotateTitle = "Rotate"
# The full path to PNG file(s) that appears in the header.
translateIconPath = "ui/actions/Properties Manager/Translate_Components.png"
rotateIconPath = "ui/actions/Properties Manager/Rotate_Components.png"
def __init__(self, command):
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
def _addGroupBoxes(self):
"""
Add groupboxes to the Property Manager dialog.
"""
self.translateGroupBox = PM_GroupBox( self,
title = "Translate",
connectTitleButton = False)
self.translateGroupBox.titleButton.setShortcut('T')
self._loadTranslateGroupBox(self.translateGroupBox)
self.rotateGroupBox = PM_GroupBox( self,
title = "Rotate",
connectTitleButton = False)
self.rotateGroupBox.titleButton.setShortcut('R')
self._loadRotateGroupBox(self.rotateGroupBox)
self.translateGroupBox.collapse()
self.rotateGroupBox.collapse()
# == Begin Translate Group Box =====================
def _loadTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate group box.
@param inPmGroupBox: The Translate group box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
translateChoices = [ "Free Drag",
"By Delta XYZ",
"To XYZ Position" ]
self.translateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = translateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.freeDragTranslateGroupBox = PM_GroupBox( inPmGroupBox )
self._loadFreeDragTranslateGroupBox(self.freeDragTranslateGroupBox)
self.byDeltaGroupBox = PM_GroupBox( inPmGroupBox )
self._loadByDeltaGroupBox(self.byDeltaGroupBox)
self.toPositionGroupBox = PM_GroupBox( inPmGroupBox )
self._loadToPositionGroupBox(self.toPositionGroupBox)
self.updateTranslateGroupBoxes(0)
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton =self.freeDragTranslateButtonGroup.getButtonById(1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
def _loadByDeltaGroupBox(self, inPmGroupBox):
"""
Load widgets in the translate By Delta group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Translate By Delta group box in the translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.moveDeltaXSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_X.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaYSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Y.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaZSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Z.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
DELTA_BUTTONS = [
("QToolButton",1, "Delta Plus",
"ui/actions/Properties Manager/Move_Delta_Plus.png",
"", "+", 0 ),
( "QToolButton", 2, "Delta Minus",
"ui/actions/Properties Manager/Move_Delta_Minus.png",
"", "-", 1 )
]
self.translateDeltaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = DELTA_BUTTONS,
label = 'Translate:',
isAutoRaise = True,
isCheckable = False
)
self.transDeltaPlusButton = \
self.translateDeltaButtonRow.getButtonById(1)
self.transDeltaMinusButton = \
self.translateDeltaButtonRow.getButtonById(2)
def _loadToPositionGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate To a given Position group box, which is
present within the Translate groupbox.
@param inPmGroupBox: Translate To Position group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.toPositionspinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
self.moveXSpinBox = self.toPositionspinboxes.xSpinBox
self.moveYSpinBox = self.toPositionspinboxes.ySpinBox
self.moveZSpinBox = self.toPositionspinboxes.zSpinBox
self.moveAbsoluteButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Move Selection",
spanWidth = True )
# == Begin Rotate Group Box =====================
def _loadRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate group box,
@param inPmGroupBox: The Rotate GroupBox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
rotateChoices = [ "Free Drag", "By Specified Angle"]
self.rotateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = rotateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.rotateAsUnitCB = \
PM_CheckBox( inPmGroupBox,
text = 'Rotate as a unit' ,
widgetColumn = 0,
state = Qt.Checked )
self.freeDragRotateGroupBox = PM_GroupBox( inPmGroupBox )
self._loadFreeDragRotateGroupBox(self.freeDragRotateGroupBox)
self.bySpecifiedAngleGroupBox = PM_GroupBox( inPmGroupBox )
self._loadBySpecifiedAngleGroupBox(self.bySpecifiedAngleGroupBox)
self.updateRotateGroupBoxes(0)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = X_ROW_LABELS )
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Y_ROW_LABELS )
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Z_ROW_LABELS )
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
def _loadBySpecifiedAngleGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate By Specified Angle group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: Rotate By Specified Angle group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png",
"Rotate about X axis", "X", 0 ),
( "QToolButton", 2, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png",
"Rotate about Y axis", "Y", 1 ),
( "QToolButton", 3, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png",
"Rotate about Z axis","Z", 2 ),
]
self.rotateAroundAxisButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
alignment = 'Right',
label = 'Rotate Around:'
)
self.rotXaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(1)
self.rotYaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(2)
self.rotZaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(3)
self.rotateThetaSpinBox = \
PM_DoubleSpinBox(inPmGroupBox,
label = "Rotate By:",
value = 0.0,
setAsDefault = True,
minimum = 0,
maximum = 360.0,
singleStep = 1.0,
decimals = 2,
suffix = ' Degrees')
THETA_BUTTONS = [
( "QToolButton", 1, "Theta Plus",
"ui/actions/Properties Manager/Move_Theta_Plus.png", "", "+", 0 ),
( "QToolButton", 2, "Theta Minus",
"ui/actions/Properties Manager/Move_Theta_Minus.png", "", "-", 1 )
]
self.rotateThetaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = THETA_BUTTONS,
label = 'Direction:',
isAutoRaise = True,
isCheckable = False
)
self.rotateThetaPlusButton = self.rotateThetaButtonRow.getButtonById(1)
self.rotateThetaMinusButton = self.rotateThetaButtonRow.getButtonById(2)
# == End Rotate Group Box =====================
# == Slots for Translate group box
def _hideAllTranslateGroupBoxes(self):
"""
Hides all Translate group boxes.
"""
self.toPositionGroupBox.hide()
self.byDeltaGroupBox.hide()
self.freeDragTranslateGroupBox.hide()
def updateTranslateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Translate group box.
@type id: int
"""
self._hideAllTranslateGroupBoxes()
if id is 0:
self.freeDragTranslateGroupBox.show()
if id is 1:
self.byDeltaGroupBox.show()
if id is 2:
self.toPositionGroupBox.show()
self.updateMessage()
def changeMoveOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of translate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManager.changeMoveOption} which overrides this
method
"""
pass
# == Slots for Rotate group box
def updateRotateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Rotate group box.
@type id: int
"""
if id is 0:
self.bySpecifiedAngleGroupBox.hide()
self.freeDragRotateGroupBox.show()
if id is 1:
self.freeDragRotateGroupBox.hide()
self.bySpecifiedAngleGroupBox.show()
self.updateMessage()
def changeRotateOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of rotate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManage.changeRotateOption} which overrides this
method
"""
pass
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager
whatsThis_MovePropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager
ToolTip_MovePropertyManager(self)
class SelectNodeByNameDockWidget(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 = "Select Node by Name"
_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)
win.addDockWidget(Qt.BottomDockWidgetArea, self)
self.setFixedHeight(120)
##self.setFixedWidth(90)
self.connect_or_disconnect_signals(True)
if not self.win.selectByNameAction.isChecked():
self.close()
def show(self):
"""
Overrides superclass method.
"""
_superclass.show(self)
val = env.prefs[dnaSearchTypeLabelChoice_prefs_key]
self.searchTypeComboBox_indexChanged(val)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self._listWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.searchToolButton, SIGNAL("clicked()"),
self.searchNodes)
prefs_key = dnaSearchTypeLabelChoice_prefs_key
connect_comboBox_with_pref(self.searchTypeComboBox, prefs_key)
change_connect(self.searchTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.searchTypeComboBox_indexChanged)
def searchTypeComboBox_indexChanged(self, val):
if val == 0:
##self._widgetRow1.show()
##self._widgetRow2.hide()
self._widgetRow1.setEnabled(True)
self._widgetRow2.setEnabled(False)
else:
##self._widgetRow2.show()
##self._widgetRow1.hide()
self._widgetRow2.setEnabled(True)
self._widgetRow1.setEnabled(False)
def searchNodes(self):
"""
ONLY implemented for DnaStrand or DnaSegments.
"""
assy = self.win.assy
topnode = assy.part.topnode
lst = []
def func(node):
if isinstance(node, assy.DnaStrandOrSegment):
lst.append(node)
topnode.apply2all(func)
choice = env.prefs[dnaSearchTypeLabelChoice_prefs_key]
if choice == 0:
nodes = self._searchNodesByName(lst)
elif choice == 1:
nodes = self._searchNodesByNucleotides(lst)
self._listWidget.insertItems(row=0, items=nodes)
def _searchNodesByNucleotides(self, nodeList):
lst = nodeList
min_val = self._nucleotidesSpinBox_1.value()
max_val = self._nucleotidesSpinBox_2.value()
if min_val > max_val:
print "Lower value for number of nucleotides exceeds max search value"
return ()
def func2(node):
n = node.getNumberOfNucleotides()
return (n >= min_val and n <= max_val)
return filter(lambda m: func2(m), lst)
def _searchNodesByName(self, nodeList):
nodeNameString = self.findLineEdit.text()
nodeNameString = str(nodeNameString)
lst = nodeList
def func2(node):
n = len(nodeNameString)
if len(node.name) < n:
return False
nameString = str(node.name[:n])
if nameString.lower() == nodeNameString.lower():
return True
return False
return filter(lambda m: func2(m), lst)
def closeEvent(self, event):
self.win.selectByNameAction.setChecked(False)
_superclass.closeEvent(self, event)
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTableWidget()
def _loadTableWidget(self):
self._listWidget = PM_DnaSearchResultTable(self, self.win)
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.searchTypeComboBox = \
PM_ComboBox( self,
label = "Search options:",
choices = ["By node name", "By # of bases (DNA only)"],
setAsDefault = True)
#Find widgets --
self._nucleotidesSpinBox_1 = PM_SpinBox(self,
label="",
value=10,
setAsDefault=False,
singleStep=10,
minimum=1,
maximum=50000)
self._nucleotidesSpinBox_2 = PM_SpinBox(self,
label="",
value=50,
setAsDefault=False,
singleStep=10,
minimum=1,
maximum=50000)
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(80)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
##self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
##self._setFindOptionsToolButtonMenu()
self.searchToolButton = PM_ToolButton(
self, iconPath="ui/actions/Properties Manager/Find_Next.png")
self.searchToolButton.setAutoRaise(False)
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("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.
widgetList1 = [('QLabel', " Search for name:", 1),
('PM_LineEdit', self.findLineEdit, 2),
('PM_ToolButton', self.findOptionsToolButton, 3),
('PM_ToolButton', self.searchToolButton, 4),
('PM_Label', self.warningSign, 5),
('PM_Label', self.phraseNotFoundLabel, 6),
('QSpacerItem', 5, 5, 7)]
widgetList2 = [('QLabel', " Number of bases: >=", 1),
('PM_SpinBox', self._nucleotidesSpinBox_1, 2),
('QLabel', " <=", 3),
('PM_SpinBox', self._nucleotidesSpinBox_2, 4),
('QSpacerItem', 5, 5, 5)]
widgetList3 = [('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.searchToolButton, 2),
('PM_Label', self.warningSign, 3),
('PM_Label', self.phraseNotFoundLabel, 4),
('QSpacerItem', 5, 5, 5)]
self._widgetRow1 = PM_WidgetRow(self,
title='',
widgetList=widgetList1,
label="",
spanWidth=True)
self._widgetRow2 = PM_WidgetRow(self,
title='',
widgetList=widgetList2,
label="",
spanWidth=True)
self._widgetRow3 = PM_WidgetRow(self,
title='',
widgetList=widgetList3,
label="",
spanWidth=True)
class DnaDuplexPropertyManager( DnaOrCnt_PropertyManager ):
"""
The DnaDuplexPropertyManager class provides a Property Manager
for the B{Build > DNA > Duplex} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Insert DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/InsertDsDna.png"
def __init__( self, win, editCommand ):
"""
Constructor for the DNA Duplex property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self._conformation = "B-DNA"
self._numberOfBases = 0
self._basesPerTurn = getDuplexBasesPerTurn(self._conformation)
self._duplexRise = getDuplexRise(self._conformation)
self._duplexLength = getDuplexLength(self._conformation,
self._numberOfBases)
_superclass.__init__( self,
win,
editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self._placementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.activateSpecifyReferencePlaneTool)
change_connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
change_connect( self.numberOfBasePairsSpinBox,
SIGNAL("valueChanged(int)"),
self.numberOfBasesChanged )
change_connect( self.basesPerTurnDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.basesPerTurnChanged )
change_connect( self.duplexRiseDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexRiseChanged )
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
self.duplexRiseDoubleSpinBox.connectWithState(
Preferences_StateRef_double( bdnaRise_prefs_key,
env.prefs[bdnaRise_prefs_key] )
)
self.basesPerTurnDoubleSpinBox.connectWithState(
Preferences_StateRef_double( bdnaBasesPerTurn_prefs_key,
env.prefs[bdnaBasesPerTurn_prefs_key] )
)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing = False)
##env.history.message(self.editCommand.logMessage)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides superclass method
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show where it is called.
"""
pass
def getFlyoutActionList(self):
""" returns custom actionlist that will be used in a specific mode
or editing a feature etc Example: while in movie mode,
the _createFlyoutToolBar method calls
this """
#'allActionsList' returns all actions in the flyout toolbar
#including the subcontrolArea actions
allActionsList = []
#Action List for subcontrol Area buttons.
#In this mode there is really no subcontrol area.
#We will treat subcontrol area same as 'command area'
#(subcontrol area buttons will have an empty list as their command area
#list). We will set the Comamnd Area palette background color to the
#subcontrol area.
subControlAreaActionList =[]
self.exitEditCommandAction.setChecked(True)
subControlAreaActionList.append(self.exitEditCommandAction)
separator = QAction(self.w)
separator.setSeparator(True)
subControlAreaActionList.append(separator)
allActionsList.extend(subControlAreaActionList)
#Empty actionlist for the 'Command Area'
commandActionLists = []
#Append empty 'lists' in 'commandActionLists equal to the
#number of actions in subControlArea
for i in range(len(subControlAreaActionList)):
lst = []
commandActionLists.append(lst)
params = (subControlAreaActionList, commandActionLists, allActionsList)
return params
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmReferencePlaneGroupBox = PM_GroupBox( self,
title = "Placement Options" )
self._loadReferencePlaneGroupBox( self._pmReferencePlaneGroupBox )
self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
#Folllowing toolbutton facilitates entering a temporary DnaLineMode
#to create a DNA using endpoints of the specified line.
self.specifyDnaLineButton = PM_ToolButton(
pmGroupBox,
text = "Specify Endpoints",
iconPath = "ui/actions/Properties Manager/Pencil.png",
spanWidth = True
)
self.specifyDnaLineButton.setCheckable(True)
self.specifyDnaLineButton.setAutoRaise(True)
self.specifyDnaLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation:",
choices = ["B-DNA"],
setAsDefault = True)
dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
choices = dnaModelChoices,
setAsDefault = True)
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = env.prefs[bdnaBasesPerTurn_prefs_key],
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = env.prefs[bdnaRise_prefs_key],
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfBasePairsSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(
pmGroupBox,
title = 'Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Number of turns",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),
("Duplex length",
dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),
("Angle",
dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
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
"""
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnDoubleSpinBox.setValue("10.0")
elif conformation == "Z-DNA":
self.basesPerTurnDoubleSpinBox.setValue("12.0")
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = "+ inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))
def numberOfBasesChanged( self, numberOfBases ):
"""
Slot for the B{Number of Bases} spinbox.
"""
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation,
numberOfBases,
self._duplexRise)) \
+ " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged( self, basesPerTurn ):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.editCommand.basesPerTurn = basesPerTurn
self._basesPerTurn = basesPerTurn
return
def duplexRiseChanged( self, rise ):
"""
Slot for the B{Rise} spinbox.
"""
self.editCommand.duplexRise = rise
self._duplexRise = rise
return
def getParameters(self):
"""
Return the parameters from this property manager
to be used to create the DNA duplex.
@return: A tuple containing the parameters
@rtype: tuple
@see: L{DnaDuplex_EditCommand._gatherParameters} where this is used
"""
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = str(self.conformationComboBox.currentText())
basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
duplexRise = self.duplexRiseDoubleSpinBox.value()
dnaModel = str(self.dnaModelComboBox.currentText())
# First endpoint (origin) of DNA duplex
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of DNA duplex.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
return (numberOfBases,
dnaForm,
dnaModel,
basesPerTurn,
duplexRise,
self.endPoint1,
self.endPoint2)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_DnaDuplexPropertyManager(self)
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)
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
class PM_ObjectChooser(PM_GroupBox):
def __init__(self,
parentWidget,
command,
modelObjectType,
title = '' ,
addIcon = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
removeIcon = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png"):
"""
"""
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__(self, parentWidget, title=title)
self.command = command
self.win = self.command.win
self._modelObjectType = modelObjectType
self._addIcon = addIcon
self._removeIcon = removeIcon
self._loadWidgets()
def getModelObjectType(self):
return self._modelObjectType
def setModelObjectType(self, modelObjtype):
self._modelObjectType = modelObjtype
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
self._listWidget.connect_or_disconnect_signals(isConnect)
change_connect(self._addToolButton, SIGNAL("toggled(bool)"),
self.activateAddTool)
change_connect(self._removeToolButton, SIGNAL("toggled(bool)"),
self.activateRemoveTool)
def _loadWidgets(self):
"""
"""
self._loadSelectionListWidget()
self._loadAddRemoveButtons()
def _loadSelectionListWidget(self):
"""
"""
self._listWidget = PM_SelectionListWidget(self,
self.win,
label="",
heightByRows=12)
self._listWidget.setFocusPolicy(Qt.StrongFocus)
self._listWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
def _loadAddRemoveButtons(self):
"""
"""
self._addToolButton = PM_ToolButton(self,
text="Add items to the list",
iconPath=self._addIcon,
spanWidth=True)
self._addToolButton.setCheckable(True)
self._addToolButton.setAutoRaise(True)
self._removeToolButton = PM_ToolButton(
self,
text="Remove items from the list",
iconPath=self._removeIcon,
spanWidth=True)
self._removeToolButton.setCheckable(True)
self._removeToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [('QLabel', " Add/Remove Items:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self._addToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self._removeToolButton, 4),
('QSpacerItem', 5, 5, 5)]
widgetRow = PM_WidgetRow(self,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
def isAddToolActive(self):
"""
Returns True if the add objects tool is active.
"""
if self._addToolButton.isChecked():
#For safety
if not self._removeToolButton.isChecked():
return True
return False
def isRemoveToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments ) is active
"""
if self._removeToolButton.isChecked():
if not self._addToolButton.isChecked():
#For safety
return True
return False
def hasFocus(self):
"""
Checks if the list widget that lists dnasegments (that will undergo
special operations such as 'resizing them at once or making
crossovers between the segments etc) has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self._listWidget.hasFocus():
return True
return False
def activateAddTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self._addToolButton.isChecked():
self._addToolButton.setChecked(True)
if self._removeToolButton.isChecked():
self._removeToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(False)
self._listWidget.setColor(lightgreen_2)
##objectType = self._modelObjectType
##objectChooserType = 'ADD'
##self.command.activateObjectChooser((objectType, objectChooserType))
##self.command.logMessage('ADD_SEGMENTS_ACTIVATED')
else:
if self._addToolButton.isChecked():
self._addToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(True)
self._listWidget.resetColor()
def activateRemoveTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self._removeToolButton.isChecked():
self._removeToolButton.setChecked(True)
if self._addToolButton.isChecked():
self._addToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(False)
##self.command.logMessage('REMOVE_SEGMENTS_ACTIVATED')
self._listWidget.setColor(lightred_1)
else:
if self._removeToolButton.isChecked():
self._removeToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(True)
self._listWidget.resetColor()
def _deactivateAddRemoveTools(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self._addToolButton.setChecked(False)
self._removeToolButton.setChecked(False)
def removeItems(self):
"""
Removes selected itoms from the dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget
This is intentional.
"""
self._listWidget.deleteSelection()
itemDict = self._listWidget.getItemDictonary()
self.command.setSegmentList(itemDict.values())
self.updateListWidget()
self.win.win_update()
def updateListWidget(self, objectList=[]):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
self._listWidget.insertItems(row=0, items=objectList)
class QuteMolPropertyManager(Command_PropertyManager):
"""
The QuteMolPropertyManager class provides a Property Manager for
QuteMolX, allowing its launch for external rendering of the model.
"""
# The title that appears in the Property Manager header.
title = "QuteMolX"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/QuteMol.png"
# DNA Display choices.
_axes_display_choices = [ "Render axes",
"Hide axes" ]
_bases_display_choices = [ "Render bases",
"Hide bases" ]
#"Color bases black",
#"Color bases by type" ]
# PDB exclude flags = _axesFlags | _basesFlags
_axesFlags = EXCLUDE_HIDDEN_ATOMS
_basesFlags = EXCLUDE_HIDDEN_ATOMS
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Select a QuteMolX rendering style and click the "\
"<b>Launch QuteMolX</b> button when ready."
# This causes the "Message" box to be displayed as well.
self.updateMessage(msg)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox(self, title = "DNA Display Options")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox(self, title = "Launch")
self._loadGroupBox2(self.pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Axes: ',
choices = self._axes_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.basesCombobox = PM_ComboBox(
pmGroupBox,
label = 'Bases: ',
choices = self._bases_display_choices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in 2nd group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.launchQuteMolButton = PM_ToolButton(
pmGroupBox,
text = "Launch QuteMolX",
iconPath = "ui/actions/Properties Manager/QuteMol.png",
spanWidth = True )
self.launchQuteMolButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager
whatsThis_QuteMolPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager
ToolTip_QuteMolPropertyManager(self)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.axesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeAxesDisplay)
change_connect(self.basesCombobox,
SIGNAL("currentIndexChanged(const QString&)"),
self.changeBasesDisplay)
change_connect(self.launchQuteMolButton,
SIGNAL("clicked()"),
self.launchQuteMol)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param msg: Message to be displayed in the Message groupbox of
the property manager
@type msg: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def changeAxesDisplay(self, optionText):
"""
Slot to change the axes display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._axes_display_choices[0]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS
# Cannot display axes if axis atoms are excluded.
self.basesCombobox.setCurrentIndex(0)
elif optionText == self._axes_display_choices[1]:
self._axesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_BONDS
else:
print "Unknown axes display option: ", optionText
#print "Axes display option=", optionText
#print "Axes Flags=", self._axesFlags
def changeBasesDisplay(self, optionText):
"""
Slot to change the bases display style.
@param optionText: The text of the combobox option selected.
@type optionText: str
"""
if optionText == self._bases_display_choices[0]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS
elif optionText == self._bases_display_choices[1]:
self._basesFlags = EXCLUDE_HIDDEN_ATOMS | EXCLUDE_DNA_AXIS_ATOMS
# Cannot display axesif axis atoms are excluded.
self.axesCombobox.setCurrentIndex(1)
else:
print "Unknown bases display option: ", optionText
#print "Bases display option=", optionText
#print "Bases Flags=", self._basesFlags
def launchQuteMol(self):
"""
Slot for 'Launch QuteMolX' button.
Opens the QuteMolX rendering program and loads a copy of the current
model.
Method:
1. Write a PDB file of the current part.
2. Write an atom attributes table text file containing atom radii and
color information.
3. Launches QuteMolX (with the PDB file as an argument).
"""
cmd = greenmsg("QuteMolX : ")
excludeFlags = self._axesFlags | self._basesFlags
#print "Exclude flags=", excludeFlags
pdb_file = write_qutemol_files(self.win.assy, excludeFlags)
# Launch QuteMolX. It will verify the plugin.
errorcode, msg = launch_qutemol(pdb_file)
# errorcode is ignored.
env.history.message(cmd + msg)
class InsertNanotube_PropertyManager(DnaOrCnt_PropertyManager):
"""
The InsertNanotube_PropertyManager class provides a Property Manager
for the B{Build > Nanotube > CNT} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Insert Nanotube"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png"
def __init__(self, win, editCommand):
"""
Constructor for the Nanotube property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self.nanotube = Nanotube() # A 5x5 CNT.
_superclass.__init__(self, win, editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.ntTypeComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._ntTypeComboBoxChanged)
change_connect(self.chiralityNSpinBox, SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.chiralityMSpinBox, SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.endingsComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._endingsComboBoxChanged)
# This spin box is currently hidden.
change_connect(self.bondLengthDoubleSpinBox,
SIGNAL("valueChanged(double)"), self._bondLengthChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing=False)
##env.history.message(self.editCommand.logMessage)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides MotorPropertyManager._update_widgets_in_PM_before_show.
The various widgets , (e.g. spinboxes) will get values from the
structure for which this propMgr is constructed for
(self.editcCntroller.struct)
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show where it is called.
"""
pass
def getFlyoutActionList(self):
"""
Returns custom actionlist that will be used in a specific mode
or editing a feature etc Example: while in movie mode,
the _createFlyoutToolBar method calls this.
"""
#'allActionsList' returns all actions in the flyout toolbar
#including the subcontrolArea actions
allActionsList = []
#Action List for subcontrol Area buttons.
#In this mode there is really no subcontrol area.
#We will treat subcontrol area same as 'command area'
#(subcontrol area buttons will have an empty list as their command area
#list). We will set the Comamnd Area palette background color to the
#subcontrol area.
subControlAreaActionList = []
self.exitEditCommandAction.setChecked(True)
subControlAreaActionList.append(self.exitEditCommandAction)
separator = QAction(self.w)
separator.setSeparator(True)
subControlAreaActionList.append(separator)
allActionsList.extend(subControlAreaActionList)
#Empty actionlist for the 'Command Area'
commandActionLists = []
#Append empty 'lists' in 'commandActionLists equal to the
#number of actions in subControlArea
for i in range(len(subControlAreaActionList)):
lst = []
commandActionLists.append(lst)
params = (subControlAreaActionList, commandActionLists, allActionsList)
return params
def _addGroupBoxes(self):
"""
Add the Insert Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
self._pmGroupBox3 = PM_GroupBox(self, title="Nanotube Distortion")
self._loadGroupBox3(self._pmGroupBox3)
self._pmGroupBox3.hide() #@ Temporary.
self._pmGroupBox4 = PM_GroupBox(self, title="Multi-Walled CNTs")
self._loadGroupBox4(self._pmGroupBox4)
self._pmGroupBox4.hide() #@ Temporary.
self._pmGroupBox5 = PM_GroupBox(self, title="Advanced Options")
self._loadGroupBox5(self._pmGroupBox5)
self._pmGroupBox5.hide() #@ Temporary.
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
#Following toolbutton facilitates entering a temporary NanotubeLineMode
#to create a CNT using endpoints of the specified line.
self.specifyCntLineButton = PM_ToolButton(
pmGroupBox,
text="Specify Endpoints",
iconPath="ui/actions/Properties Manager/Pencil.png",
spanWidth=True)
self.specifyCntLineButton.setCheckable(True)
self.specifyCntLineButton.setAutoRaise(True)
self.specifyCntLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
_ntTypeChoices = ['Carbon', 'Boron Nitride']
self.ntTypeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Type:",
choices = _ntTypeChoices,
setAsDefault = True)
self.ntRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.nanotube.getRise(),
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.ntRiseDoubleSpinBox.hide()
# Nanotube Length
self.ntLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Nanotube Length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.ntLengthLineEdit.setDisabled(True)
self.ntLengthLineEdit.hide()
# Nanotube diameter
self.ntDiameterLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Diameter: ",
setAsDefault = False)
self.ntDiameterLineEdit.setDisabled(True)
self.updateNanotubeDiameter()
self.chiralityNSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (n):",
value = self.nanotube.getChiralityN(),
minimum = 2,
maximum = 100,
setAsDefault = True )
self.chiralityMSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (m):",
value = self.nanotube.getChiralityM(),
minimum = 0,
maximum = 100,
setAsDefault = True )
# How about having user prefs for CNT and BNNT bond lengths?
# I'm guessing that if the user wants to set these values, they will
# do it once and would like those bond length values persist forever.
# Need to discuss with others to determine if this spinbox comes out.
# --Mark 2008-03-29
self.bondLengthDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bond length:",
value = self.nanotube.getBondLength(),
setAsDefault = True,
minimum = 1.0,
maximum = 3.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
#self.bondLengthDoubleSpinBox.hide()
endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"]
self.endingsComboBox= \
PM_ComboBox( pmGroupBox,
label = "Endings:",
choices = endingChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, inPmGroupBox):
"""
Load widgets in group box 3.
"""
self.zDistortionDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Z-distortion:",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.xyDistortionDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "XY-distortion:",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 2.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.twistSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Twist:",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 100, # What should maximum be?
suffix = " deg/A" )
self.bendSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Bend:",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 360,
suffix = " deg" )
def _loadGroupBox4(self, inPmGroupBox):
"""
Load widgets in group box 4.
"""
# "Number of Nanotubes" SpinBox
self.mwntCountSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Number:",
value = 1,
setAsDefault = True,
minimum = 1,
maximum = 10,
suffix = " nanotubes" )
self.mwntCountSpinBox.setSpecialValueText("SWNT")
# "Spacing" lineedit.
self.mwntSpacingDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Spacing:",
value = 2.46,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
def _loadGroupBox5(self, pmGroupBox):
"""
Load widgets in group box 5.
"""
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band Line:')
ntLineChoices = ['Ladder']
self.ntRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = ntLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Nanotube length",
insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ),
("Angle",
insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key )
]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Insert Nanotube Property Manager.
"""
pass
def _setEndPoints(self):
"""
Set the two endpoints of the nanotube using the values from the
X, Y, Z coordinate spinboxes in the property manager.
@note: The group box containing the 2 sets of XYZ spin boxes are
currently hidden.
"""
# First endpoint (origin) of nanotube
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of nanotube.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
self.nanotube.setEndPoints(self.endPoint1, self.endPoint2)
# Need arg "recompute=True", which will recompute the second
# endpoint (endPoint2) using the nanotube rise.
def getParameters(self):
"""
Return the parameters from this property manager to be used to create
the nanotube.
@return: A nanotube instance with its attrs set to the current
parameters in the property manager.
@rtype: L{Nanotube}
@see: L{InsertNanotube_EditCommand._gatherParameters} where this is used
"""
self._setEndPoints()
return (self.nanotube)
def _ntTypeComboBoxChanged(self, type):
"""
Slot for the Type combobox. It is called whenever the
Type choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.nanotube.setType(str(type))
print "Bond Length =", self.nanotube.getBondLength()
self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength())
#self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex])
def _bondLengthChanged(self, bondLength):
"""
Slot for the B{Bond Length} spinbox.
"""
self.nanotube.setBondLength(bondLength)
self.updateNanotubeDiameter()
return
def _chiralityFixup(self, spinBoxValueJunk=None):
"""
Slot for several validators for different parameters.
This gets called whenever the user changes the n, m chirality values.
@param spinBoxValueJunk: This is the Spinbox value from the valueChanged
signal. It is not used. We just want to know
that the spinbox value has changed.
@type spinBoxValueJunk: double or None
"""
_n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(),
self.chiralityMSpinBox.value())
#self.n, self.m = self.nanotube.getChirality()
self.connect_or_disconnect_signals(isConnect=False)
self.chiralityNSpinBox.setValue(_n)
self.chiralityMSpinBox.setValue(_m)
self.connect_or_disconnect_signals(isConnect=True)
self.updateNanotubeDiameter()
def updateNanotubeDiameter(self):
"""
Update the nanotube Diameter lineEdit widget.
"""
diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
self.ntDiameterLineEdit.setText(diameterText)
# ntRiseDoubleSpinBox is currently hidden.
self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise())
def _endingsComboBoxChanged(self, endings):
"""
Slot for the B{Ending} combobox.
@param endings: The option's text.
@type endings: string
"""
self.nanotube.setEndings(str(endings))
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_InsertNanotube_PropertyManager(self)
return
class InsertDna_PropertyManager(DnaOrCnt_PropertyManager):
"""
The InsertDna_PropertyManager class provides a Property Manager
for the B{Insert Dna} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Insert DNA"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/InsertDna.png"
def __init__(self, command):
"""
Constructor for the DNA Duplex property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self._conformation = "B-DNA"
self._numberOfBases = 0
self._basesPerTurn = getDuplexBasesPerTurn(self._conformation)
self._duplexRise = getDuplexRise(self._conformation)
self._duplexLength = getDuplexLength(self._conformation,
self._numberOfBases)
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self._placementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.activateSpecifyReferencePlaneTool)
change_connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
change_connect(self.numberOfBasePairsSpinBox,
SIGNAL("valueChanged(int)"), self.numberOfBasesChanged)
change_connect(self.basesPerTurnDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.basesPerTurnChanged)
change_connect(self.duplexRiseDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.duplexRiseChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
self.duplexRiseDoubleSpinBox.connectWithState(
Preferences_StateRef_double(bdnaRise_prefs_key,
env.prefs[bdnaRise_prefs_key]))
self.basesPerTurnDoubleSpinBox.connectWithState(
Preferences_StateRef_double(bdnaBasesPerTurn_prefs_key,
env.prefs[bdnaBasesPerTurn_prefs_key]))
def show(self):
_superclass.show(self)
self.updateMessage("Specify the DNA parameters below, then click "\
"two endpoints in the graphics area to insert a DNA duplex.")
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmReferencePlaneGroupBox = PM_GroupBox(self,
title="Placement Options")
self._loadReferencePlaneGroupBox(self._pmReferencePlaneGroupBox)
self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
#Folllowing toolbutton facilitates entering a temporary DnaLineMode
#to create a DNA using endpoints of the specified line.
self.specifyDnaLineButton = PM_ToolButton(
pmGroupBox,
text="Specify Endpoints",
iconPath="ui/actions/Properties Manager/Pencil.png",
spanWidth=True)
self.specifyDnaLineButton.setCheckable(True)
self.specifyDnaLineButton.setAutoRaise(True)
self.specifyDnaLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation:",
choices = ["B-DNA"],
setAsDefault = True)
dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
choices = dnaModelChoices,
setAsDefault = True)
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = env.prefs[bdnaBasesPerTurn_prefs_key],
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = env.prefs[bdnaRise_prefs_key],
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfBasePairsSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Number of turns",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),
("Duplex length",
dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),
("Angle",
dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
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
"""
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnDoubleSpinBox.setValue("10.0")
elif conformation == "Z-DNA":
self.basesPerTurnDoubleSpinBox.setValue("12.0")
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = " + inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))
def numberOfBasesChanged(self, numberOfBases):
"""
Slot for the B{Number of Bases} spinbox.
"""
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation,
numberOfBases,
self._duplexRise)) \
+ " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged(self, basesPerTurn):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.command.basesPerTurn = basesPerTurn
self._basesPerTurn = basesPerTurn
return
def duplexRiseChanged(self, rise):
"""
Slot for the B{Rise} spinbox.
"""
self.command.duplexRise = rise
self._duplexRise = rise
return
def getParameters(self):
"""
Return the parameters from this property manager
to be used to create the DNA duplex.
@return: A tuple containing the parameters
@rtype: tuple
@see: L{InsertDna_EditCommand._gatherParameters} where this is used
"""
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = str(self.conformationComboBox.currentText())
basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
duplexRise = self.duplexRiseDoubleSpinBox.value()
dnaModel = str(self.dnaModelComboBox.currentText())
# First endpoint (origin) of DNA duplex
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of DNA duplex.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise,
self.endPoint1, self.endPoint2)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_InsertDna_PropertyManager(self)
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 PM_ObjectChooser(PM_GroupBox):
def __init__(self,
parentWidget,
command,
modelObjectType,
title = '' ,
addIcon = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
removeIcon = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png"):
"""
"""
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__(self,
parentWidget,
title = title)
self.command = command
self.win = self.command.win
self._modelObjectType = modelObjectType
self._addIcon = addIcon
self._removeIcon = removeIcon
self._loadWidgets()
def getModelObjectType(self):
return self._modelObjectType
def setModelObjectType(self, modelObjtype):
self._modelObjectType = modelObjtype
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
self._listWidget.connect_or_disconnect_signals(isConnect)
change_connect(self._addToolButton,
SIGNAL("toggled(bool)"),
self.activateAddTool)
change_connect(self._removeToolButton,
SIGNAL("toggled(bool)"),
self.activateRemoveTool)
def _loadWidgets(self):
"""
"""
self._loadSelectionListWidget()
self._loadAddRemoveButtons()
def _loadSelectionListWidget(self):
"""
"""
self._listWidget = PM_SelectionListWidget(
self,
self.win,
label = "",
heightByRows = 12)
self._listWidget.setFocusPolicy(Qt.StrongFocus)
self._listWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
def _loadAddRemoveButtons(self):
"""
"""
self._addToolButton = PM_ToolButton(
self,
text = "Add items to the list",
iconPath = self._addIcon,
spanWidth = True )
self._addToolButton.setCheckable(True)
self._addToolButton.setAutoRaise(True)
self._removeToolButton = PM_ToolButton(
self,
text = "Remove items from the list",
iconPath = self._removeIcon,
spanWidth = True )
self._removeToolButton.setCheckable(True)
self._removeToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [
('QLabel', " Add/Remove Items:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self._addToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self._removeToolButton, 4),
('QSpacerItem', 5, 5, 5) ]
widgetRow = PM_WidgetRow(self,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def isAddToolActive(self):
"""
Returns True if the add objects tool is active.
"""
if self._addToolButton.isChecked():
#For safety
if not self._removeToolButton.isChecked():
return True
return False
def isRemoveToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments ) is active
"""
if self._removeToolButton.isChecked():
if not self._addToolButton.isChecked():
#For safety
return True
return False
def hasFocus(self):
"""
Checks if the list widget that lists dnasegments (that will undergo
special operations such as 'resizing them at once or making
crossovers between the segments etc) has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self._listWidget.hasFocus():
return True
return False
def activateAddTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self._addToolButton.isChecked():
self._addToolButton.setChecked(True)
if self._removeToolButton.isChecked():
self._removeToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(False)
self._listWidget.setColor(lightgreen_2)
##objectType = self._modelObjectType
##objectChooserType = 'ADD'
##self.command.activateObjectChooser((objectType, objectChooserType))
##self.command.logMessage('ADD_SEGMENTS_ACTIVATED')
else:
if self._addToolButton.isChecked():
self._addToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(True)
self._listWidget.resetColor()
def activateRemoveTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self._removeToolButton.isChecked():
self._removeToolButton.setChecked(True)
if self._addToolButton.isChecked():
self._addToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(False)
##self.command.logMessage('REMOVE_SEGMENTS_ACTIVATED')
self._listWidget.setColor(lightred_1)
else:
if self._removeToolButton.isChecked():
self._removeToolButton.setChecked(False)
self._listWidget.setAlternatingRowColors(True)
self._listWidget.resetColor()
def _deactivateAddRemoveTools(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self._addToolButton.setChecked(False)
self._removeToolButton.setChecked(False)
def removeItems(self):
"""
Removes selected itoms from the dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget
This is intentional.
"""
self._listWidget.deleteSelection()
itemDict = self._listWidget.getItemDictonary()
self.command.setSegmentList(itemDict.values())
self.updateListWidget()
self.win.win_update()
def updateListWidget(self, objectList = []):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
self._listWidget.insertItems(
row = 0,
items = objectList)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=X_ROW_LABELS)
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Y_ROW_LABELS)
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Z_ROW_LABELS)
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
class SelectNodeByNameDockWidget(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 = "Select Node by Name"
_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)
win.addDockWidget(Qt.BottomDockWidgetArea, self)
self.setFixedHeight(120)
##self.setFixedWidth(90)
self.connect_or_disconnect_signals(True)
if not self.win.selectByNameAction.isChecked():
self.close()
def show(self):
"""
Overrides superclass method.
"""
_superclass.show(self)
val = env.prefs[dnaSearchTypeLabelChoice_prefs_key]
self.searchTypeComboBox_indexChanged(val)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self._listWidget.connect_or_disconnect_signals(isConnect)
change_connect( self.searchToolButton,
SIGNAL("clicked()"),
self.searchNodes)
prefs_key = dnaSearchTypeLabelChoice_prefs_key
connect_comboBox_with_pref(self.searchTypeComboBox,
prefs_key )
change_connect( self.searchTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.searchTypeComboBox_indexChanged)
def searchTypeComboBox_indexChanged(self, val):
if val == 0:
##self._widgetRow1.show()
##self._widgetRow2.hide()
self._widgetRow1.setEnabled(True)
self._widgetRow2.setEnabled(False)
else:
##self._widgetRow2.show()
##self._widgetRow1.hide()
self._widgetRow2.setEnabled(True)
self._widgetRow1.setEnabled(False)
def searchNodes(self):
"""
ONLY implemented for DnaStrand or DnaSegments.
"""
assy = self.win.assy
topnode = assy.part.topnode
lst = []
def func(node):
if isinstance(node, assy.DnaStrandOrSegment):
lst.append(node)
topnode.apply2all(func)
choice = env.prefs[dnaSearchTypeLabelChoice_prefs_key]
if choice == 0:
nodes = self._searchNodesByName(lst)
elif choice == 1:
nodes = self._searchNodesByNucleotides(lst)
self._listWidget.insertItems(
row = 0,
items = nodes)
def _searchNodesByNucleotides(self, nodeList):
lst = nodeList
min_val = self._nucleotidesSpinBox_1.value()
max_val = self._nucleotidesSpinBox_2.value()
if min_val > max_val:
print "Lower value for number of nucleotides exceeds max search value"
return ()
def func2(node):
n = node.getNumberOfNucleotides()
return (n >= min_val and n <= max_val)
return filter(lambda m:func2(m), lst)
def _searchNodesByName(self, nodeList):
nodeNameString = self.findLineEdit.text()
nodeNameString = str(nodeNameString)
lst = nodeList
def func2(node):
n = len(nodeNameString)
if len(node.name)< n:
return False
nameString = str(node.name[:n])
if nameString.lower() == nodeNameString.lower():
return True
return False
return filter(lambda m:func2(m), lst)
def closeEvent(self, event):
self.win.selectByNameAction.setChecked(False)
_superclass.closeEvent(self, event)
def _loadWidgets(self):
"""
Overrides PM.PM_DockWidget._loadWidgets. Loads the widget in this
dockwidget.
"""
self._loadMenuWidgets()
self._loadTableWidget()
def _loadTableWidget(self):
self._listWidget = PM_DnaSearchResultTable(self, self.win)
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.searchTypeComboBox = \
PM_ComboBox( self,
label = "Search options:",
choices = ["By node name", "By # of bases (DNA only)"],
setAsDefault = True)
#Find widgets --
self._nucleotidesSpinBox_1 = PM_SpinBox(self,
label = "",
value = 10,
setAsDefault = False,
singleStep = 10,
minimum = 1,
maximum = 50000)
self._nucleotidesSpinBox_2 = PM_SpinBox(self,
label = "",
value = 50,
setAsDefault = False,
singleStep = 10,
minimum = 1,
maximum = 50000)
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(80)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
##self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
##self._setFindOptionsToolButtonMenu()
self.searchToolButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Find_Next.png")
self.searchToolButton.setAutoRaise(False)
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("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.
widgetList1 = [
('QLabel', " Search for name:", 1),
('PM_LineEdit', self.findLineEdit, 2),
('PM_ToolButton', self.findOptionsToolButton, 3),
('PM_ToolButton', self.searchToolButton, 4),
('PM_Label', self.warningSign, 5),
('PM_Label', self.phraseNotFoundLabel, 6),
('QSpacerItem', 5, 5, 7) ]
widgetList2 = [
('QLabel', " Number of bases: >=", 1),
('PM_SpinBox', self._nucleotidesSpinBox_1, 2),
('QLabel', " <=", 3),
('PM_SpinBox', self._nucleotidesSpinBox_2, 4),
('QSpacerItem', 5, 5, 5)]
widgetList3 = [
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.searchToolButton, 2),
('PM_Label', self.warningSign, 3),
('PM_Label', self.phraseNotFoundLabel, 4),
('QSpacerItem', 5, 5, 5) ]
self._widgetRow1 = PM_WidgetRow(self,
title = '',
widgetList = widgetList1,
label = "",
spanWidth = True )
self._widgetRow2 = PM_WidgetRow(self,
title = '',
widgetList = widgetList2,
label = "",
spanWidth = True )
self._widgetRow3 = PM_WidgetRow(self,
title = '',
widgetList = widgetList3,
label = "",
spanWidth = True )
class ListWidgetItems_PM_Mixin:
def _loadSegmentListWidget(self, pmGroupBox):
self.segmentListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [
('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5) ]
widgetRow = PM_WidgetRow(pmGroupBox,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def listWidgetHasFocus(self):
"""
Checks if the list widget that lists dnasegments (that will undergo
special operations such as 'resizing them at once or making
crossovers between the segments etc) has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self.segmentListWidget.hasFocus():
return True
return False
def updateListWidgets(self):
self.updateSegmentListWidget()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
segmentList = self.command.getSegmentList()
if segmentList:
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
else:
self.segmentListWidget.clear()
def isAddSegmentsToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments) is active
"""
if self.addSegmentsToolButton.isChecked():
#For safety
if not self.removeSegmentsToolButton.isChecked():
return True
return False
def isRemoveSegmentsToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments ) is active
"""
if self.removeSegmentsToolButton.isChecked():
if not self.addSegmentsToolButton.isChecked():
#For safety
return True
return False
def activateAddSegmentsTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(True)
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightgreen_2)
self.command.logMessage('ADD_SEGMENTS_ACTIVATED')
else:
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def activateRemoveSegmentsTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(True)
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.command.logMessage('REMOVE_SEGMENTS_ACTIVATED')
self.segmentListWidget.setColor(lightred_1)
else:
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def _deactivateAddRemoveSegmentsTool(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self.addSegmentsToolButton.setChecked(False)
self.removeSegmentsToolButton.setChecked(False)
def removeListWidgetItems(self):
"""
Removes selected itoms from the dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget
This is intentional.
"""
self.segmentListWidget.deleteSelection()
itemDict = self.segmentListWidget.getItemDictonary()
self.command.setSegmentList(itemDict.values())
self.updateListWidgets()
self.win.win_update()
class InsertNanotube_PropertyManager( DnaOrCnt_PropertyManager):
"""
The InsertNanotube_PropertyManager class provides a Property Manager
for the B{Build > Nanotube > CNT} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Insert Nanotube"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Nanotube property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self.nanotube = Nanotube() # A 5x5 CNT.
_superclass.__init__( self,
win,
editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect( self.ntTypeComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._ntTypeComboBoxChanged )
change_connect(self.chiralityNSpinBox,
SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.chiralityMSpinBox,
SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.endingsComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._endingsComboBoxChanged )
# This spin box is currently hidden.
change_connect(self.bondLengthDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self._bondLengthChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing = False)
##env.history.message(self.editCommand.logMessage)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides MotorPropertyManager._update_widgets_in_PM_before_show.
The various widgets , (e.g. spinboxes) will get values from the
structure for which this propMgr is constructed for
(self.editcCntroller.struct)
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show where it is called.
"""
pass
def getFlyoutActionList(self):
"""
Returns custom actionlist that will be used in a specific mode
or editing a feature etc Example: while in movie mode,
the _createFlyoutToolBar method calls this.
"""
#'allActionsList' returns all actions in the flyout toolbar
#including the subcontrolArea actions
allActionsList = []
#Action List for subcontrol Area buttons.
#In this mode there is really no subcontrol area.
#We will treat subcontrol area same as 'command area'
#(subcontrol area buttons will have an empty list as their command area
#list). We will set the Comamnd Area palette background color to the
#subcontrol area.
subControlAreaActionList =[]
self.exitEditCommandAction.setChecked(True)
subControlAreaActionList.append(self.exitEditCommandAction)
separator = QAction(self.w)
separator.setSeparator(True)
subControlAreaActionList.append(separator)
allActionsList.extend(subControlAreaActionList)
#Empty actionlist for the 'Command Area'
commandActionLists = []
#Append empty 'lists' in 'commandActionLists equal to the
#number of actions in subControlArea
for i in range(len(subControlAreaActionList)):
lst = []
commandActionLists.append(lst)
params = (subControlAreaActionList, commandActionLists, allActionsList)
return params
def _addGroupBoxes( self ):
"""
Add the Insert Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
self._pmGroupBox3 = PM_GroupBox( self, title = "Nanotube Distortion" )
self._loadGroupBox3( self._pmGroupBox3 )
self._pmGroupBox3.hide() #@ Temporary.
self._pmGroupBox4 = PM_GroupBox( self, title = "Multi-Walled CNTs" )
self._loadGroupBox4( self._pmGroupBox4 )
self._pmGroupBox4.hide() #@ Temporary.
self._pmGroupBox5 = PM_GroupBox( self, title = "Advanced Options" )
self._loadGroupBox5( self._pmGroupBox5 )
self._pmGroupBox5.hide() #@ Temporary.
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
#Following toolbutton facilitates entering a temporary NanotubeLineMode
#to create a CNT using endpoints of the specified line.
self.specifyCntLineButton = PM_ToolButton(
pmGroupBox,
text = "Specify Endpoints",
iconPath = "ui/actions/Properties Manager/Pencil.png",
spanWidth = True
)
self.specifyCntLineButton.setCheckable(True)
self.specifyCntLineButton.setAutoRaise(True)
self.specifyCntLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
_ntTypeChoices = ['Carbon',
'Boron Nitride']
self.ntTypeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Type:",
choices = _ntTypeChoices,
setAsDefault = True)
self.ntRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.nanotube.getRise(),
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.ntRiseDoubleSpinBox.hide()
# Nanotube Length
self.ntLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Nanotube Length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.ntLengthLineEdit.setDisabled(True)
self.ntLengthLineEdit.hide()
# Nanotube diameter
self.ntDiameterLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Diameter: ",
setAsDefault = False)
self.ntDiameterLineEdit.setDisabled(True)
self.updateNanotubeDiameter()
self.chiralityNSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (n):",
value = self.nanotube.getChiralityN(),
minimum = 2,
maximum = 100,
setAsDefault = True )
self.chiralityMSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (m):",
value = self.nanotube.getChiralityM(),
minimum = 0,
maximum = 100,
setAsDefault = True )
# How about having user prefs for CNT and BNNT bond lengths?
# I'm guessing that if the user wants to set these values, they will
# do it once and would like those bond length values persist forever.
# Need to discuss with others to determine if this spinbox comes out.
# --Mark 2008-03-29
self.bondLengthDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bond length:",
value = self.nanotube.getBondLength(),
setAsDefault = True,
minimum = 1.0,
maximum = 3.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
#self.bondLengthDoubleSpinBox.hide()
endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"]
self.endingsComboBox= \
PM_ComboBox( pmGroupBox,
label = "Endings:",
choices = endingChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, inPmGroupBox):
"""
Load widgets in group box 3.
"""
self.zDistortionDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Z-distortion:",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.xyDistortionDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "XY-distortion:",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 2.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.twistSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Twist:",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 100, # What should maximum be?
suffix = " deg/A" )
self.bendSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Bend:",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 360,
suffix = " deg" )
def _loadGroupBox4(self, inPmGroupBox):
"""
Load widgets in group box 4.
"""
# "Number of Nanotubes" SpinBox
self.mwntCountSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Number:",
value = 1,
setAsDefault = True,
minimum = 1,
maximum = 10,
suffix = " nanotubes" )
self.mwntCountSpinBox.setSpecialValueText("SWNT")
# "Spacing" lineedit.
self.mwntSpacingDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Spacing:",
value = 2.46,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
def _loadGroupBox5(self, pmGroupBox):
"""
Load widgets in group box 5.
"""
self._rubberbandLineGroupBox = PM_GroupBox(
pmGroupBox,
title = 'Rubber band Line:')
ntLineChoices = ['Ladder']
self.ntRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = ntLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key )
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Nanotube length",
insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ),
("Angle",
insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key )
]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Insert Nanotube Property Manager.
"""
pass
def _setEndPoints(self):
"""
Set the two endpoints of the nanotube using the values from the
X, Y, Z coordinate spinboxes in the property manager.
@note: The group box containing the 2 sets of XYZ spin boxes are
currently hidden.
"""
# First endpoint (origin) of nanotube
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of nanotube.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
self.nanotube.setEndPoints(self.endPoint1, self.endPoint2)
# Need arg "recompute=True", which will recompute the second
# endpoint (endPoint2) using the nanotube rise.
def getParameters(self):
"""
Return the parameters from this property manager to be used to create
the nanotube.
@return: A nanotube instance with its attrs set to the current
parameters in the property manager.
@rtype: L{Nanotube}
@see: L{InsertNanotube_EditCommand._gatherParameters} where this is used
"""
self._setEndPoints()
return (self.nanotube)
def _ntTypeComboBoxChanged( self, type ):
"""
Slot for the Type combobox. It is called whenever the
Type choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.nanotube.setType(str(type))
print "Bond Length =", self.nanotube.getBondLength()
self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength())
#self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex])
def _bondLengthChanged(self, bondLength):
"""
Slot for the B{Bond Length} spinbox.
"""
self.nanotube.setBondLength(bondLength)
self.updateNanotubeDiameter()
return
def _chiralityFixup(self, spinBoxValueJunk = None):
"""
Slot for several validators for different parameters.
This gets called whenever the user changes the n, m chirality values.
@param spinBoxValueJunk: This is the Spinbox value from the valueChanged
signal. It is not used. We just want to know
that the spinbox value has changed.
@type spinBoxValueJunk: double or None
"""
_n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(),
self.chiralityMSpinBox.value())
#self.n, self.m = self.nanotube.getChirality()
self.connect_or_disconnect_signals(isConnect = False)
self.chiralityNSpinBox.setValue(_n)
self.chiralityMSpinBox.setValue(_m)
self.connect_or_disconnect_signals(isConnect = True)
self.updateNanotubeDiameter()
def updateNanotubeDiameter(self):
"""
Update the nanotube Diameter lineEdit widget.
"""
diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
self.ntDiameterLineEdit.setText(diameterText)
# ntRiseDoubleSpinBox is currently hidden.
self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise())
def _endingsComboBoxChanged(self, endings):
"""
Slot for the B{Ending} combobox.
@param endings: The option's text.
@type endings: string
"""
self.nanotube.setEndings(str(endings))
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_InsertNanotube_PropertyManager(self)
return
class ListWidgetItems_PM_Mixin:
def _loadSegmentListWidget(self, pmGroupBox):
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5)]
widgetRow = PM_WidgetRow(pmGroupBox,
title='',
widgetList=widgetList,
label="",
spanWidth=True)
def listWidgetHasFocus(self):
"""
Checkes if the list widget that lists dnasegments (that will undergo
special operations such as 'resizing them at once or making
crossovers between the segments etc) has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self.segmentListWidget.hasFocus():
return True
return False
def updateListWidgets(self):
self.updateSegmentListWidget()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
segmentList = self.command.getSegmentList()
self.segmentListWidget.insertItems(row=0, items=segmentList)
def isAddSegmentsToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments) is active
"""
if self.addSegmentsToolButton.isChecked():
#For safety
if not self.removeSegmentsToolButton.isChecked():
return True
return False
def isRemoveSegmentsToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments ) is active
"""
if self.removeSegmentsToolButton.isChecked():
if not self.addSegmentsToolButton.isChecked():
#For safety
return True
return False
def activateAddSegmentsTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(True)
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightgreen_2)
self.command.logMessage('ADD_SEGMENTS_ACTIVATED')
else:
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def activateRemoveSegmentsTool(self, enable):
"""
Change the appearance of the list widget (that lists the dna segments
) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(True)
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.command.logMessage('REMOVE_SEGMENTS_ACTIVATED')
self.segmentListWidget.setColor(lightred_1)
else:
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def _deactivateAddRemoveSegmentsTool(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self.addSegmentsToolButton.setChecked(False)
self.removeSegmentsToolButton.setChecked(False)
def removeListWidgetItems(self):
"""
Removes selected itoms from the dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget
This is intentional.
"""
self.segmentListWidget.deleteSelection()
itemDict = self.segmentListWidget.getItemDictonary()
self.command.setSegmentList(itemDict.values())
self.updateListWidgets()
self.win.win_update()
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton =self.freeDragTranslateButtonGroup.getButtonById(1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
class MultipleDnaSegmentResize_PropertyManager( DnaOrCnt_PropertyManager ):
title = "Resize Dna Segments"
iconPath = "ui/actions/Properties Manager/Resize_Multiple_Segments.png"
def __init__( self, command ):
"""
Constructor for the Build DNA property manager.
"""
self.endPoint1 = V(0, 0, 0)
self.endPoint2 = V(0, 0, 0)
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
self.dnaModel = 'PAM3'
_superclass.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Use resize handles to resize the segments."
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
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.addSegmentsToolButton,
SIGNAL("toggled(bool)"),
self.activateAddSegmentsTool)
change_connect(self.removeSegmentsToolButton,
SIGNAL("toggled(bool)"),
self.activateRemoveSegmentsTool)
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.model_changed()
@see: DnaSegment_EditCommand.hasResizableStructure()
@see: self._current_model_changed_params()
"""
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
number_of_segments, isStructResizable, why_not = currentParams
#update the self._previous_model_changed_params with this new param set.
self._previous_model_changed_params = currentParams
if not isStructResizable:
if not number_of_segments == 0:
#disable all widgets
self._pmGroupBox1.setEnabled(False)
msg = redmsg("DnaSegment is not resizable. Reason: %s"%(why_not))
self.updateMessage(msg)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg = "Use resize handles to resize the segments"
self.updateMessage(msg)
self.updateListWidgets()
##self.command.updateHandlePositions()
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:
#update the list first.
self.command.updateResizeSegmentList()
number_of_segments = len(self.command.getResizeSegmentList())
isStructResizable, why_not = self.command.hasResizableStructure()
params = (number_of_segments, isStructResizable, why_not)
return params
def isAddSegmentsToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments to be resized) is active
"""
if self.addSegmentsToolButton.isChecked():
#For safety
if not self.removeSegmentsToolButton.isChecked():
return True
return False
def isRemoveSegmentsToolActive(self):
"""
Returns True if the remove segments tool (which removes the segments
from the list of segments to be resized) is active
"""
if self.removeSegmentsToolButton.isChecked():
if not self.addSegmentsToolButton.isChecked():
#For safety
return True
return False
def activateAddSegmentsTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
to be resized) so as to indicate that the add dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the add segments tool is active.
@type enable: bool
"""
if enable:
if not self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(True)
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightgreen_2)
else:
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def activateRemoveSegmentsTool(self,enable):
"""
Change the appearance of the list widget (that lists the dna segments
to be resized) so as to indicate that the REMOVE dna segments tool is
active
@param enable: If True, changes the appearance of list widget to
indicate that the REMOVE segments tool is active.
@type enable: bool
"""
if enable:
if not self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(True)
if self.addSegmentsToolButton.isChecked():
self.addSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(False)
self.segmentListWidget.setColor(lightred_1)
else:
if self.removeSegmentsToolButton.isChecked():
self.removeSegmentsToolButton.setChecked(False)
self.segmentListWidget.setAlternatingRowColors(True)
self.segmentListWidget.resetColor()
def removeListWidgetItems(self):
"""
Removes selected atoms from the resize dna segment list widget
Example: User selects a bunch of items in the list widget and hits
delete key to remove the selected items from the list
IMPORTANT NOTE: This method does NOT delete the correspoinging model
item in the GLPane (i.e. corresponding dnasegment). It just 'removes'
the item from the list widget (indicating its no longer being resized)
This is intentional.
"""
self.segmentListWidget.deleteSelection()
itemDict = self.segmentListWidget.getItemDictonary()
self.command.setResizeStructList(itemDict.values())
self.updateListWidgets()
self.win.win_update()
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Segments for Resizing" )
self._loadGroupBox1( self._pmGroupBox1 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.segmentListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.segmentListWidget.setFocusPolicy(Qt.StrongFocus)
self.segmentListWidget.setFocus()
self.setFocusPolicy(Qt.StrongFocus)
self.addSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Add segments to the list",
iconPath = "ui/actions/Properties Manager"\
"/AddSegment_To_ResizeSegmentList.png",
spanWidth = True )
self.addSegmentsToolButton.setCheckable(True)
self.addSegmentsToolButton.setAutoRaise(True)
self.removeSegmentsToolButton = PM_ToolButton(
pmGroupBox,
text = "Remove segments from the list",
iconPath = "ui/actions/Properties Manager"\
"/RemoveSegment_From_ResizeSegmentList.png",
spanWidth = True )
self.removeSegmentsToolButton.setCheckable(True)
self.removeSegmentsToolButton.setAutoRaise(True)
#Widgets to include in the widget row.
widgetList = [
('QLabel', " Add/Remove Segments:", 0),
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.addSegmentsToolButton, 2),
('QSpacerItem', 5, 5, 3),
('PM_ToolButton', self.removeSegmentsToolButton, 4),
('QSpacerItem', 5, 5, 5) ]
widgetRow = PM_WidgetRow(pmGroupBox,
title = '',
widgetList = widgetList,
label = "",
spanWidth = True )
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
def show(self):
"""
Overrides the superclass method
@see: self._deactivateAddRemoveSegmentsTool
"""
_superclass.show(self)
##self.updateListWidgets()
self._deactivateAddRemoveSegmentsTool()
def _deactivateAddRemoveSegmentsTool(self):
"""
Deactivate tools that allow adding or removing the segments to the
segment list in the Property manager. This can be simply done by
resetting the state of toolbuttons to False.
Example: toolbuttons that add or remove
segments to the segment list in the Property manager. When self.show
is called these need to be unchecked.
@see: self.isAddSegmentsToolActive()
@see:self.isRemoveSegmentsToolActive()
@see: self.show()
"""
self.addSegmentsToolButton.setChecked(False)
self.removeSegmentsToolButton.setChecked(False)
def listWidgetHasFocus(self):
"""
Checks if the list widget that lists dnasegments to be resized has the
Qt focus. This is used to just remove items from the list widget
(without actually 'deleting' the corresponding Dnasegment in the GLPane)
@see: MultipleDnaSegment_GraphicsMode.keyPressEvent() where it is called
"""
if self.segmentListWidget.hasFocus():
return True
return False
def setParameters(self, params):
pass
def getParameters(self):
return ()
def updateListWidgets(self):
self.updateSegmentListWidget()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
segmentList = self.command.getResizeSegmentList()
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
dnaSegmentEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaSegmentEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Duplex length",
dnaSegmentEditCommand_cursorTextCheckBox_length_prefs_key),
("Number of basepairs to be changed",
dnaSegmentEditCommand_cursorTextCheckBox_changedBasePairs_prefs_key)
]
return params
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.searchTypeComboBox = \
PM_ComboBox( self,
label = "Search options:",
choices = ["By node name", "By # of bases (DNA only)"],
setAsDefault = True)
#Find widgets --
self._nucleotidesSpinBox_1 = PM_SpinBox(self,
label = "",
value = 10,
setAsDefault = False,
singleStep = 10,
minimum = 1,
maximum = 50000)
self._nucleotidesSpinBox_2 = PM_SpinBox(self,
label = "",
value = 50,
setAsDefault = False,
singleStep = 10,
minimum = 1,
maximum = 50000)
self.findLineEdit = \
PM_LineEdit( self,
label = "",
spanWidth = False)
self.findLineEdit.setMaximumWidth(80)
self.findOptionsToolButton = PM_ToolButton(self)
self.findOptionsToolButton.setMaximumWidth(12)
self.findOptionsToolButton.setAutoRaise(True)
##self.findOptionsToolButton.setPopupMode(QToolButton.MenuButtonPopup)
##self._setFindOptionsToolButtonMenu()
self.searchToolButton = PM_ToolButton(
self,
iconPath = "ui/actions/Properties Manager/Find_Next.png")
self.searchToolButton.setAutoRaise(False)
self.warningSign = QLabel(self)
self.warningSign.setPixmap(
getpixmap('ui/actions/Properties Manager/Warning.png'))
self.warningSign.hide()
self.phraseNotFoundLabel = QLabel(self)
self.phraseNotFoundLabel.setText("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.
widgetList1 = [
('QLabel', " Search for name:", 1),
('PM_LineEdit', self.findLineEdit, 2),
('PM_ToolButton', self.findOptionsToolButton, 3),
('PM_ToolButton', self.searchToolButton, 4),
('PM_Label', self.warningSign, 5),
('PM_Label', self.phraseNotFoundLabel, 6),
('QSpacerItem', 5, 5, 7) ]
widgetList2 = [
('QLabel', " Number of bases: >=", 1),
('PM_SpinBox', self._nucleotidesSpinBox_1, 2),
('QLabel', " <=", 3),
('PM_SpinBox', self._nucleotidesSpinBox_2, 4),
('QSpacerItem', 5, 5, 5)]
widgetList3 = [
('QSpacerItem', 5, 5, 1),
('PM_ToolButton', self.searchToolButton, 2),
('PM_Label', self.warningSign, 3),
('PM_Label', self.phraseNotFoundLabel, 4),
('QSpacerItem', 5, 5, 5) ]
self._widgetRow1 = PM_WidgetRow(self,
title = '',
widgetList = widgetList1,
label = "",
spanWidth = True )
self._widgetRow2 = PM_WidgetRow(self,
title = '',
widgetList = widgetList2,
label = "",
spanWidth = True )
self._widgetRow3 = PM_WidgetRow(self,
title = '',
widgetList = widgetList3,
label = "",
spanWidth = True )
