def _loadReferencePlaneGroupBox(self, pmGroupBox):
"""
Load widgets in reference plane groupbox
@see: InsertDna_PropertyManager._addGroupBoxes where this groupbox
is added.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen (default)", "Parallel to screen" ),
( 1, "On the specified plane:", "On specified plane" )]
self._placementOptions = \
PM_RadioButtonList( pmGroupBox,
##label = "Duplex Placement Options:",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 0,
spanWidth = True,
borders = False)
self._specifyReferencePlane_radioButton = self._placementOptions.getButtonById(
1)
self.referencePlaneListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=2)
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 _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=9)
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
def _loadReferencePlaneGroupBox(self, pmGroupBox):
"""
Load widgets in reference plane groupbox
@see: InsertDna_PropertyManager._addGroupBoxes where this groupbox
is added.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen (default)", "Parallel to screen" ),
( 1, "On the specified plane:", "On specified plane" )]
self._placementOptions = \
PM_RadioButtonList( pmGroupBox,
##label = "Duplex Placement Options:",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 0,
spanWidth = True,
borders = False)
self._specifyReferencePlane_radioButton = self._placementOptions.getButtonById(1)
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
heightByRows = 2)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in groupbox 3.
This is the default implementation. Can be overridden in subclasses.
"""
self.attachedAtomsListWidget = \
PM_SelectionListWidget(pmGroupBox,
self.win,
heightByRows = 6 )
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.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
color = pmReferencesListWidgetColor,
heightByRows = 2)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.nanotubeListWidget = PM_SelectionListWidget(pmGroupBox, self.win, label="", heightByRows=12)
self.nanotubeListWidget.setObjectName("nanotubeListWidget")
self.nanotubeListWidget.setTagInstruction("PICK_ITEM_IN_GLPANE")
self.editNanotubePropertiesButton = PM_PushButton(pmGroupBox, label="", text="Edit Properties...")
self.editNanotubePropertiesButton.setEnabled(False)
return
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 _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=6)
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label="",
text="Compare Proteins...")
self.compareProteinsButton.setEnabled(False)
return
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 9 )
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editStrandPropertiesButton.setEnabled(False)
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 _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editSegmentPropertiesButton.setEnabled(False)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 6 )
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label = "",
text = "Compare Proteins..." )
self.compareProteinsButton.setEnabled(False)
return
class BuildNanotube_PropertyManager(EditCommand_PM):
"""
The BuildNanotube_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Nanotube"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/BuildNanotube.png"
def __init__(self, command):
"""
Constructor for the Build Nanotube property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
#TODO: This is a temporary fix for a bug. When you invoke a temporary
#mode, entering such a temporary mode keeps the signals of PM from the
#previous mode connected (but while exiting that temporary mode and
#reentering the previous mode, it actually reconnects the signal!
#This gives rise to lots of bugs. This needs a more general fix in
#the Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
if isConnect and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self.nanotubeListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editNanotubePropertiesButton, SIGNAL("clicked()"),
self._editNanotube)
return
def enable_or_disable_gui_actions(self, bool_enable=False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and \
structure_params_unchanged and \
command_stack_params_unchanged:
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the nanotube list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateNanotubesListWidget()
selectedNanotubeSegments = newSelectionParams
self.nanotubeListWidget.updateSelection(selectedNanotubeSegments)
self.updateNanotubePropertiesButton()
return
self.updateNanotubesListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_NANOTUBE command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_NANOTUBE'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_NANOTUBE to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_NANOTUBE command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_NANOTUBE')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected nanotubes.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedNanotubeSegments = []
if self.command is not None: # and self.command.hasValidStructure():
selectedNanotubeSegments = self.win.assy.getSelectedNanotubeSegments(
)
return (selectedNanotubeSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of nanotubes within the structure
(or None). This is a good enough check (and no need to compare
each and every nanotube within the structure with a previously stored
set of strands).
"""
params = None
if self.command: # and self.command.hasValidStructure():
nanotubeSegmentList = []
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
params = len(nanotubeSegmentList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.nanotubeListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Nanotube</b> to create a nanotube or "\
"select an existing nantube to modify it."
self.updateMessage(msg)
return
def _editNanotube(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
nanotubeSegment = self.win.assy.getSelectedNanotubeSegment()
if nanotubeSegment:
nanotubeSegment.edit()
return
def _addWhatsThisText(self):
"""
What's This text for widgets in the CNT Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the CNT Property Manager.
"""
pass
def _addGroupBoxes(self):
"""
Add the Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Nanotubes")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.nanotubeListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.nanotubeListWidget.setObjectName('nanotubeListWidget')
self.nanotubeListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editNanotubePropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editNanotubePropertiesButton.setEnabled(False)
return
def updateNanotubesListWidget(self):
"""
Updates the nanotubes (selection) groupbox. This includes both the
nanotube selection list widget (showing all nanotubes in the part)
and the B{Edit Properties} button just below it (enabled if only
one of the nanotubes is selected).
"""
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
if nanotubeSegmentList:
self.nanotubeListWidget.insertItems(row=0,
items=nanotubeSegmentList)
else:
self.nanotubeListWidget.clear()
self.updateNanotubePropertiesButton()
return
def updateNanotubePropertiesButton(self):
"""
Enables the B{Edit Properties} button if a single nanotube is currently
selected. Otherwise, the button is disabled.
"""
self.editNanotubePropertiesButton.setEnabled(
bool(self.win.assy.getSelectedNanotubeSegment()))
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 BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildProtein_PropertyManager class provides a Property Manager
for the B{Build Protein} 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 = "Build Protein"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/BuildProtein.png"
current_protein = "" # name of the single selected peptide. To be deprecated soon. --Mark 2008-12-14
def __init__( self, command):
"""
Constructor for the Build Protein property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self.proteinListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editPeptidePropertiesButton,
SIGNAL("clicked()"),
self._editPeptide)
change_connect(self.compareProteinsButton,
SIGNAL("clicked()"),
self._compareProteins)
return
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
if 0:
print "Build Protein: _update_UI_do_updates() - DO NOTHING"
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the protein list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateProteinListWidget()
selectedProteins = newSelectionParams
self.proteinListWidget.updateSelection(selectedProteins)
# Enable/disable "Edit Sequence" button.
if len(selectedProteins) == 1:
self.editPeptidePropertiesButton.setEnabled(True)
else:
self.editPeptidePropertiesButton.setEnabled(False)
# Enable/disable "Compare Proteins" button.
if len(selectedProteins) == 2:
self.compareProteinsButton.setEnabled(True)
else:
self.compareProteinsButton.setEnabled(False)
return
self.updateProteinListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_PROTEIN command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_PROTEIN'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_PROTEIN to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_PROTEIN command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_PROTEIN')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected peptides.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedProteins = []
if self.command is not None: # and self.command.hasValidStructure():
selectedProteins = self.win.assy.getSelectedProteinChunks()
return (selectedProteins)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of peptides within the structure
(or None). This is a good enough check (and no need to compare
each and every peptide within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of peptides remains the same even
#after some alterations to the peptides? Unlikely. (Example: a single
#(future) Break peptide operation will increase the number of peptides
#by one. Or Join peptides decrease it by 1)
params = None
if self.command: # and self.command.hasValidStructure():
proteinList = []
proteinList = getAllProteinChunksInPart(self.win.assy)
params = len(proteinList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.proteinListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Peptide</b> to create a peptide chain or "\
"select another modeling tool to modify an existing protein."
self.updateMessage(msg)
return
def _editPeptide(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
proteinChunk = self.win.assy.getSelectedProteinChunk()
if proteinChunk:
proteinChunk.protein.edit(self.win)
return
def _compareProteins(self):
"""
Slot for the "Compare Proteins" button.
"""
self.win.commandSequencer.userEnterCommand('COMPARE_PROTEINS')
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
def _addGroupBoxes(self):
"""
Add the Build Protein Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title = "Peptides")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 6 )
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label = "",
text = "Compare Proteins..." )
self.compareProteinsButton.setEnabled(False)
return
def updateProteinListWidget(self):
"""
Update the peptide list widget. It shows all peptides in the part.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
if proteinChunkList:
self.proteinListWidget.insertItems(
row = 0,
items = proteinChunkList)
else:
self.proteinListWidget.clear()
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):
"""
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 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 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 BuildDna_PropertyManager(EditCommand_PM):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
sponsor_keyword = None # Nanorex is the sponsor. Change to 'DNA' to the
# the NUPACK logo.
def __init__( self, command ):
"""
Constructor for the Build DNA property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__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
"""
#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.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton,
SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton,
SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton,
SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
self._baseNumberLabelGroupBox.connect_or_disconnect_signals(isConnect)
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the list widgets *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateListWidgets()
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..." % len(selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
return
# Calling updateListWidgets() here fixes bug 2950 without undoing the
# fix to bug 2940. --Mark 2008-12-13.
self.updateListWidgets()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_DNA command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current scommand stack change indicator and
the name of the command 'BUILD_DNA'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_DNA to the tuple to be returned. This is just to remind
#us that this method is meant for BUIL_DNA command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_DNA')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.command is not None and self.command.hasValidStructure():
selectedStrands = self.command.struct.getSelectedStrands()
selectedSegments = self.command.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None). This is a good enough check (and no need to compare
each and every strand within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.command and self.command.hasValidStructure():
strandList = []
strandList = self.command.struct.getStrands()
params = len(strandList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
"""
EditCommand_PM.show(self)
self.updateMessage("Use appropriate command in the command "\
"toolbar to create or modify a DNA Object"\
"<br>" )
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.command.hasValidStructure():
return
selectedStrandList = self.command.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.command is not None and self.command.hasValidStructure():
selectedSegments = self.command.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dna data model yet. Until that's implemented, we
#will do an isinstance(node, Chunk) check. Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.command.hasValidStructure():
strandChunkList = self.command.struct.getStrands()
self.strandListWidget.insertItems(
row = 0,
items = strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.command.isCurrentCommand():
if self.command.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.command.struct.apply2all(func)
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "Strands" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Segments" )
self._loadGroupBox3( self._pmGroupBox3 )
self._loadBaseNumberLabelGroupBox(self)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
color = pmReferencesListWidgetColor,
heightByRows = 2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 9 )
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 4 )
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Search For Crossovers..." )
self.searchForCrossoversButton.setEnabled(False)
def _loadBaseNumberLabelGroupBox(self, pmGroupBox):
"""
"""
self._baseNumberLabelGroupBox = PM_DnaBaseNumberLabelsGroupBox(pmGroupBox,
self.command)
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
class BuildDna_PropertyManager( EditCommand_PM, DebugMenuMixin ):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self._previousSelectionParams = None
self._previousStructureParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__( self,
win,
editCommand)
DebugMenuMixin._init1( self )
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
"""
#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.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton,
SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton,
SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton,
SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#TODO: This is bad. It would have been much better to enable/disable
#gui actions using a API method in command/commandSequencer which gets
#called when you enter another command exiting or suspending the
#previous one. . At present. it doesn't exist (first needs cleanup in
#command/command sequencer (Done and other methods._)-- Ninad 2008-01-09
if hasattr(self.editCommand, 'flyoutToolbar') and \
self.editCommand.flyoutToolbar:
self.editCommand.flyoutToolbar.exitDnaAction.setEnabled(not bool_enable)
def model_changed(self):
"""
When the editCommand is treated as a 'command' by the
commandSequencer. this method will override basicCommand.model_changed.
@WARNING: Ideally this property manager should implement both
model_changed and selection_changed methods in the mode/command
API.
model_changed method will be used here when the selected atom is
dragged, transmuted etc. The selection_changed method will be
used when the selection (picking/ unpicking) changes.
At present, selection_changed and model_changed methods are
called too frequently that it doesn't matter which one you use.
Its better to use only a single method for preformance reasons
(at the moment). This should change when the original
methods in the API are revised to be called at appropiraite
time.
"""
newSelectionParams = self._currentSelectionParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introduing self._previousStructureParams and adding structure_params_unchanged
#check to the if condition below fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
self._currentStructureParams())
if selection_params_unchanged and \
structure_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = self._currentStructureParams()
if not selection_params_unchanged and structure_params_unchanged:
self._previousSelectionParams = newSelectionParams
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..."%len(selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
#Update the strand and segmment list widgets.
#Ideally it should only update when the structure is modified
#example --when structure is deleted. But as of 2008-02-21
#this feature is not easily available in the API method.
#see Command class for some proposed methods such as 'something_changed'
#etc. The list widgets are updated even when selection changes.
#NOTE: If this is called before listwidget's 'updateSelection' call,
#done above, it 'may give' (as of 2008-02-25, it is unlikely to happen
#because of a better implementation) C/C++ object deleted errors.
#So better to do it in the end. Cause -- unknown.
#Guess : something to do with clearing the widget list and them readding
#items (done by self.updateListWidgets)
#..This probably interferes with the selection
#within that list. So better to do it after updating the selection.
if not structure_params_unchanged:
self.updateListWidgets()
def _currentSelectionParams(self):
"""
This needs commandSequencer to treat various
edit controllers as commands. Until then, the 'model_changed' method
(and thus this method) will never be called.
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed} or
L{self.selection_changed} methods are called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: The method name may be renamed in future.
Its possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.editCommand is not None and self.editCommand.hasValidStructure():
selectedStrands = self.editCommand.struct.getSelectedStrands()
selectedSegments = self.editCommand.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None) . This is a good enough check (and no need to compare
each and evry strand within the structure with a previously stored
set of strands)
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.editCommand and self.editCommand.hasValidStructure():
strandList = []
strandList = self.editCommand.struct.getStrands()
params = len(strandList)
return params
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing = False)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
"""
EditCommand_PM.show(self)
self.updateListWidgets()
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.editCommand.hasValidStructure():
return
selectedStrandList = self.editCommand.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.editCommand is not None and self.editCommand.hasValidStructure():
selectedSegments = self.editCommand.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides EditCommand_PM._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.editcCommand.struct)
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show
"""
self.updateListWidgets()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dan data model yet. Until thats implemented ,we
#will do an isinstance(node, Chunk) check . Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.editCommand and self.editCommand.hasValidStructure():
strandChunkList = self.editCommand.struct.getStrands()
self.strandListWidget.insertItems(
row = 0,
items = strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.editCommand and self.editCommand.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.editCommand.struct.apply2all(func)
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "Strands" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Segments" )
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
color = pmReferencesListWidgetColor,
heightByRows = 2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 9 )
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 4 )
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Search For Crossovers..." )
self.searchForCrossoversButton.setEnabled(False)
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
class BuildDna_PropertyManager(EditCommand_PM):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
sponsor_keyword = None # Nanorex is the sponsor. Change to 'DNA' to the
# the NUPACK logo.
def __init__(self, command):
"""
Constructor for the Build DNA property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__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
"""
#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.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton, SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton, SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton, SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
self._baseNumberLabelGroupBox.connect_or_disconnect_signals(isConnect)
def enable_or_disable_gui_actions(self, bool_enable=False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the list widgets *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateListWidgets()
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..." % len(
selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
return
# Calling updateListWidgets() here fixes bug 2950 without undoing the
# fix to bug 2940. --Mark 2008-12-13.
self.updateListWidgets()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_DNA command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current scommand stack change indicator and
the name of the command 'BUILD_DNA'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_DNA to the tuple to be returned. This is just to remind
#us that this method is meant for BUIL_DNA command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_DNA')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.command is not None and self.command.hasValidStructure():
selectedStrands = self.command.struct.getSelectedStrands()
selectedSegments = self.command.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None). This is a good enough check (and no need to compare
each and every strand within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.command and self.command.hasValidStructure():
strandList = []
strandList = self.command.struct.getStrands()
params = len(strandList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
"""
EditCommand_PM.show(self)
self.updateMessage("Use appropriate command in the command "\
"toolbar to create or modify a DNA Object"\
"<br>" )
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.command.hasValidStructure():
return
selectedStrandList = self.command.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.command is not None and self.command.hasValidStructure():
selectedSegments = self.command.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dna data model yet. Until that's implemented, we
#will do an isinstance(node, Chunk) check. Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.command.hasValidStructure():
strandChunkList = self.command.struct.getStrands()
self.strandListWidget.insertItems(row=0, items=strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.command.isCurrentCommand():
if self.command.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.command.struct.apply2all(func)
self.segmentListWidget.insertItems(row=0, items=segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox(self, title="Strands")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Segments")
self._loadGroupBox3(self._pmGroupBox3)
self._loadBaseNumberLabelGroupBox(self)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label="",
color=pmReferencesListWidgetColor,
heightByRows=2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=9)
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=4)
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox, label="", text="Search For Crossovers...")
self.searchForCrossoversButton.setEnabled(False)
def _loadBaseNumberLabelGroupBox(self, pmGroupBox):
"""
"""
self._baseNumberLabelGroupBox = PM_DnaBaseNumberLabelsGroupBox(
pmGroupBox, self.command)
def _addWhatsThisText(self):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
class BuildNanotube_PropertyManager(EditCommand_PM):
"""
The BuildNanotube_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Nanotube"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/BuildNanotube.png"
def __init__( self, command ):
"""
Constructor for the Build Nanotube property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
#TODO: This is a temporary fix for a bug. When you invoke a temporary
#mode, entering such a temporary mode keeps the signals of PM from the
#previous mode connected (but while exiting that temporary mode and
#reentering the previous mode, it actually reconnects the signal!
#This gives rise to lots of bugs. This needs a more general fix in
#the Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
if isConnect and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self.nanotubeListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editNanotubePropertiesButton,
SIGNAL("clicked()"),
self._editNanotube)
return
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and \
structure_params_unchanged and \
command_stack_params_unchanged:
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the nanotube list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateNanotubesListWidget()
selectedNanotubeSegments = newSelectionParams
self.nanotubeListWidget.updateSelection(selectedNanotubeSegments)
self.updateNanotubePropertiesButton()
return
self.updateNanotubesListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_NANOTUBE command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_NANOTUBE'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_NANOTUBE to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_NANOTUBE command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_NANOTUBE')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected nanotubes.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedNanotubeSegments = []
if self.command is not None: # and self.command.hasValidStructure():
selectedNanotubeSegments = self.win.assy.getSelectedNanotubeSegments()
return (selectedNanotubeSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of nanotubes within the structure
(or None). This is a good enough check (and no need to compare
each and every nanotube within the structure with a previously stored
set of strands).
"""
params = None
if self.command: # and self.command.hasValidStructure():
nanotubeSegmentList = []
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
params = len(nanotubeSegmentList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.nanotubeListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Nanotube</b> to create a nanotube or "\
"select an existing nantube to modify it."
self.updateMessage(msg)
return
def _editNanotube(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
nanotubeSegment = self.win.assy.getSelectedNanotubeSegment()
if nanotubeSegment:
nanotubeSegment.edit()
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the CNT Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the CNT Property Manager.
"""
pass
def _addGroupBoxes( self ):
"""
Add the Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Nanotubes" )
self._loadGroupBox1( self._pmGroupBox1 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.nanotubeListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.nanotubeListWidget.setObjectName('nanotubeListWidget')
self.nanotubeListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editNanotubePropertiesButton = PM_PushButton(pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editNanotubePropertiesButton.setEnabled(False)
return
def updateNanotubesListWidget(self):
"""
Updates the nanotubes (selection) groupbox. This includes both the
nanotube selection list widget (showing all nanotubes in the part)
and the B{Edit Properties} button just below it (enabled if only
one of the nanotubes is selected).
"""
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
if nanotubeSegmentList:
self.nanotubeListWidget.insertItems(
row = 0,
items = nanotubeSegmentList)
else:
self.nanotubeListWidget.clear()
self.updateNanotubePropertiesButton()
return
def updateNanotubePropertiesButton(self):
"""
Enables the B{Edit Properties} button if a single nanotube is currently
selected. Otherwise, the button is disabled.
"""
self.editNanotubePropertiesButton.setEnabled(
bool(self.win.assy.getSelectedNanotubeSegment()))
return
class DnaOrCnt_PropertyManager(EditCommand_PM):
"""
DnaOrCnt_PropertyManager class provides common functionality
(e.g. groupboxes etc) to the subclasses that define various Dna and Cnt
(Carbon nanotube) Property Managers.
@see: DnaSegment_PropertyManager (subclass)
@see: InsertDna_PropertyManager (subclass)
"""
def __init__(self, command):
"""
Constructor for the DNA Duplex property manager.
"""
self._cursorTextGroupBox = None
self._colorChooser = None
self.showCursorTextCheckBox = None
self.referencePlaneListWidget = None
#For model changed signal
#@see: self.model_changed() and self._current_model_changed_params
#for example use
self._previous_model_changed_params = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__(self, command)
def show(self):
"""
Show this PM
"""
_superclass.show(self)
if isinstance(self.showCursorTextCheckBox, PM_CheckBox):
self._update_state_of_cursorTextGroupBox(
self.showCursorTextCheckBox.isChecked())
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
"""
self._loadCursorTextGroupBox(pmGroupBox)
def _loadColorChooser(self, pmGroupBox):
self._colorChooser = PM_ColorComboBox(pmGroupBox)
def _loadCursorTextGroupBox(self, pmGroupBox):
"""
Load various checkboxes within the cursor text groupbox.
@see: self. _loadDisplayOptionsGroupBox()
@see: self._connect_showCursorTextCheckBox()
@see: self._params_for_creating_cursorTextCheckBoxes()
"""
self.showCursorTextCheckBox = \
PM_CheckBox(
pmGroupBox,
text = "Show cursor text",
widgetColumn = 0,
state = Qt.Checked)
self._connect_showCursorTextCheckBox()
paramsForCheckBoxes = self._params_for_creating_cursorTextCheckBoxes()
self._cursorTextGroupBox = PM_PrefsCheckBoxes(
pmGroupBox,
paramsForCheckBoxes=paramsForCheckBoxes,
title='Cursor text options:')
def connect_or_disconnect_signals(self, isConnect):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
if self._colorChooser:
change_connect(self._colorChooser, SIGNAL("editingFinished()"),
self._changeStructureColor)
pass
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Subclasses should override this method. The default implementation
does nothing.
"""
pass
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Subclasses should override this method. The default implementation
returns an empty list.
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: self._loadCursorTextGroupBox()
@see: subclass method:
DnaSegment_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = [] #Format: (" checkbox text", prefs_key)
return params
def _update_state_of_cursorTextGroupBox(self, enable):
"""
"""
if not isinstance(self._cursorTextGroupBox, PM_PrefsCheckBoxes):
return
if enable:
self._cursorTextGroupBox.setEnabled(True)
else:
self._cursorTextGroupBox.setEnabled(False)
def _loadReferencePlaneGroupBox(self, pmGroupBox):
"""
Load widgets in reference plane groupbox
@see: InsertDna_PropertyManager._addGroupBoxes where this groupbox
is added.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen (default)", "Parallel to screen" ),
( 1, "On the specified plane:", "On specified plane" )]
self._placementOptions = \
PM_RadioButtonList( pmGroupBox,
##label = "Duplex Placement Options:",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 0,
spanWidth = True,
borders = False)
self._specifyReferencePlane_radioButton = self._placementOptions.getButtonById(
1)
self.referencePlaneListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=2)
def useSpecifiedDrawingPlane(self):
"""
Tells if the the command (rather the graphicsmode) should use the user
specified drawing plane on which the structure (such as dna duplex or
CNT) will be created.
Returns True if a Palne is specified by the user AND 'use specified
plane' radio button in the Property manager is checked.
@see: InsertDna_GraphicsMode.getDrawingPlane()
"""
if self.referencePlaneListWidget is None:
return False
if self._specifyReferencePlane_radioButton.isChecked():
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 1:
return True
return False
def activateSpecifyReferencePlaneTool(self, index):
"""
Slot method that changes the appearance of some ui elements, suggesting
that the Specify reference plane tool is active.
@see: self.isSpecifyPlaneToolActive()
"""
if self.referencePlaneListWidget is None:
return
if index == 0:
self.referencePlaneListWidget.resetColor()
else:
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 0:
self.referencePlaneListWidget.setColor(lightgreen_2)
else:
self.referencePlaneListWidget.resetColor()
def isSpecifyPlaneToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments) is active
@see: InsertDna_EditCommand.isSpecifyPlaneToolActive()
@see: InsertDna_GraphicsMode.isSpecifyPlaneToolActive()
@see: InsertDna_GraphicsMode.jigLeftUp()
"""
if self.referencePlaneListWidget is None:
return False
if self._specifyReferencePlane_radioButton.isChecked():
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 1:
return False
else:
return True
return False
def removeListWidgetItems(self):
"""
Removes all the items in the list widget
@TODO: At the moment the list widget means 'self.referencePlaneListWidget'
the method name needs renaming if there are some more list widgets
in the Property manager.
"""
if self.referencePlaneListWidget is None:
return
self.referencePlaneListWidget.insertItems(row=0, items=())
self.referencePlaneListWidget.setColor(lightgreen_2)
def updateReferencePlaneListWidget(self, plane=None):
"""
Update the reference plane list widget by replacing the
current item (if any) with the specified <plane >. This plane object
(if not None) will be used as a referecne plane on which the structure
will be constructed.
@param plane: Plane object to be
"""
if self.referencePlaneListWidget is None:
return
planeList = []
if plane is not None:
planeList = [plane]
self.referencePlaneListWidget.insertItems(row=0, items=planeList)
def listWidgetHasFocus(self):
"""
Checks if the list widget that lists the referecne plane, on which
the dna will be created, has the Qt focus. This is used to just remove
items from the list widget (without actually 'deleting' the
corresponding Plane in the GLPane)
@see: InsertDna_GraphicsMode.keyPressEvent() where this is called
"""
if self.referencePlaneListWidget and \
self.referencePlaneListWidget.hasFocus():
return True
return False
def _changeStructureColor(self):
"""
"""
if self._colorChooser is None:
return
if self.command and self.command.hasValidStructure():
color = self._colorChooser.getColor()
if hasattr(self.command.struct, 'setColor'):
self.command.struct.setColor(color)
self.win.glpane.gl_update()
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()
class BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildProtein_PropertyManager class provides a Property Manager
for the B{Build Protein} 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 = "Build Protein"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/BuildProtein.png"
current_protein = "" # name of the single selected peptide. To be deprecated soon. --Mark 2008-12-14
def __init__(self, command):
"""
Constructor for the Build Protein property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
self.proteinListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editPeptidePropertiesButton, SIGNAL("clicked()"),
self._editPeptide)
change_connect(self.compareProteinsButton, SIGNAL("clicked()"),
self._compareProteins)
return
def enable_or_disable_gui_actions(self, bool_enable=False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
if 0:
print "Build Protein: _update_UI_do_updates() - DO NOTHING"
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the protein list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateProteinListWidget()
selectedProteins = newSelectionParams
self.proteinListWidget.updateSelection(selectedProteins)
# Enable/disable "Edit Sequence" button.
if len(selectedProteins) == 1:
self.editPeptidePropertiesButton.setEnabled(True)
else:
self.editPeptidePropertiesButton.setEnabled(False)
# Enable/disable "Compare Proteins" button.
if len(selectedProteins) == 2:
self.compareProteinsButton.setEnabled(True)
else:
self.compareProteinsButton.setEnabled(False)
return
self.updateProteinListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_PROTEIN command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_PROTEIN'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_PROTEIN to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_PROTEIN command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_PROTEIN')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected peptides.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedProteins = []
if self.command is not None: # and self.command.hasValidStructure():
selectedProteins = self.win.assy.getSelectedProteinChunks()
return (selectedProteins)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of peptides within the structure
(or None). This is a good enough check (and no need to compare
each and every peptide within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of peptides remains the same even
#after some alterations to the peptides? Unlikely. (Example: a single
#(future) Break peptide operation will increase the number of peptides
#by one. Or Join peptides decrease it by 1)
params = None
if self.command: # and self.command.hasValidStructure():
proteinList = []
proteinList = getAllProteinChunksInPart(self.win.assy)
params = len(proteinList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.proteinListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Peptide</b> to create a peptide chain or "\
"select another modeling tool to modify an existing protein."
self.updateMessage(msg)
return
def _editPeptide(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
proteinChunk = self.win.assy.getSelectedProteinChunk()
if proteinChunk:
proteinChunk.protein.edit(self.win)
return
def _compareProteins(self):
"""
Slot for the "Compare Proteins" button.
"""
self.win.commandSequencer.userEnterCommand('COMPARE_PROTEINS')
return
def _addWhatsThisText(self):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
def _addGroupBoxes(self):
"""
Add the Build Protein Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Peptides")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=6)
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label="",
text="Compare Proteins...")
self.compareProteinsButton.setEnabled(False)
return
def updateProteinListWidget(self):
"""
Update the peptide list widget. It shows all peptides in the part.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
if proteinChunkList:
self.proteinListWidget.insertItems(row=0, items=proteinChunkList)
else:
self.proteinListWidget.clear()
return
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 DnaOrCnt_PropertyManager(EditCommand_PM):
"""
DnaOrCnt_PropertyManager class provides common functionality
(e.g. groupboxes etc) to the subclasses that define various Dna and Cnt
(Carbon nanotube) Property Managers.
@see: DnaSegment_PropertyManager (subclass)
@see: InsertDna_PropertyManager (subclass)
"""
def __init__( self, command ):
"""
Constructor for the DNA Duplex property manager.
"""
self._cursorTextGroupBox = None
self._colorChooser = None
self.showCursorTextCheckBox = None
self.referencePlaneListWidget = None
#For model changed signal
#@see: self.model_changed() and self._current_model_changed_params
#for example use
self._previous_model_changed_params = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
_superclass.__init__( self, command)
def show(self):
"""
Show this PM
"""
_superclass.show(self)
if isinstance(self.showCursorTextCheckBox, PM_CheckBox):
self._update_state_of_cursorTextGroupBox(
self.showCursorTextCheckBox.isChecked())
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
"""
self._loadCursorTextGroupBox(pmGroupBox)
def _loadColorChooser(self, pmGroupBox):
self._colorChooser = PM_ColorComboBox(pmGroupBox)
def _loadCursorTextGroupBox(self, pmGroupBox):
"""
Load various checkboxes within the cursor text groupbox.
@see: self. _loadDisplayOptionsGroupBox()
@see: self._connect_showCursorTextCheckBox()
@see: self._params_for_creating_cursorTextCheckBoxes()
"""
self.showCursorTextCheckBox = \
PM_CheckBox(
pmGroupBox,
text = "Show cursor text",
widgetColumn = 0,
state = Qt.Checked)
self._connect_showCursorTextCheckBox()
paramsForCheckBoxes = self._params_for_creating_cursorTextCheckBoxes()
self._cursorTextGroupBox = PM_PrefsCheckBoxes(
pmGroupBox,
paramsForCheckBoxes = paramsForCheckBoxes,
title = 'Cursor text options:')
def connect_or_disconnect_signals(self, isConnect):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
if self._colorChooser:
change_connect(self._colorChooser,
SIGNAL("editingFinished()"),
self._changeStructureColor)
pass
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Subclasses should override this method. The default implementation
does nothing.
"""
pass
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Subclasses should override this method. The default implementation
returns an empty list.
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: self._loadCursorTextGroupBox()
@see: subclass method:
DnaSegment_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = [] #Format: (" checkbox text", prefs_key)
return params
def _update_state_of_cursorTextGroupBox(self, enable):
"""
"""
if not isinstance(self._cursorTextGroupBox, PM_PrefsCheckBoxes):
return
if enable:
self._cursorTextGroupBox.setEnabled(True)
else:
self._cursorTextGroupBox.setEnabled(False)
def _loadReferencePlaneGroupBox(self, pmGroupBox):
"""
Load widgets in reference plane groupbox
@see: InsertDna_PropertyManager._addGroupBoxes where this groupbox
is added.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen (default)", "Parallel to screen" ),
( 1, "On the specified plane:", "On specified plane" )]
self._placementOptions = \
PM_RadioButtonList( pmGroupBox,
##label = "Duplex Placement Options:",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 0,
spanWidth = True,
borders = False)
self._specifyReferencePlane_radioButton = self._placementOptions.getButtonById(1)
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
heightByRows = 2)
def useSpecifiedDrawingPlane(self):
"""
Tells if the the command (rather the graphicsmode) should use the user
specified drawing plane on which the structure (such as dna duplex or
CNT) will be created.
Returns True if a Palne is specified by the user AND 'use specified
plane' radio button in the Property manager is checked.
@see: InsertDna_GraphicsMode.getDrawingPlane()
"""
if self.referencePlaneListWidget is None:
return False
if self._specifyReferencePlane_radioButton.isChecked():
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 1:
return True
return False
def activateSpecifyReferencePlaneTool(self, index):
"""
Slot method that changes the appearance of some ui elements, suggesting
that the Specify reference plane tool is active.
@see: self.isSpecifyPlaneToolActive()
"""
if self.referencePlaneListWidget is None:
return
if index == 0:
self.referencePlaneListWidget.resetColor()
else:
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 0:
self.referencePlaneListWidget.setColor(lightgreen_2)
else:
self.referencePlaneListWidget.resetColor()
def isSpecifyPlaneToolActive(self):
"""
Returns True if the add segments tool (which adds the segments to the
list of segments) is active
@see: InsertDna_EditCommand.isSpecifyPlaneToolActive()
@see: InsertDna_GraphicsMode.isSpecifyPlaneToolActive()
@see: InsertDna_GraphicsMode.jigLeftUp()
"""
if self.referencePlaneListWidget is None:
return False
if self._specifyReferencePlane_radioButton.isChecked():
itemDict = self.referencePlaneListWidget.getItemDictonary()
planeList = itemDict.values()
if len(planeList) == 1:
return False
else:
return True
return False
def removeListWidgetItems(self):
"""
Removes all the items in the list widget
@TODO: At the moment the list widget means 'self.referencePlaneListWidget'
the method name needs renaming if there are some more list widgets
in the Property manager.
"""
if self.referencePlaneListWidget is None:
return
self.referencePlaneListWidget.insertItems(
row = 0,
items = ())
self.referencePlaneListWidget.setColor(lightgreen_2)
def updateReferencePlaneListWidget(self, plane = None):
"""
Update the reference plane list widget by replacing the
current item (if any) with the specified <plane >. This plane object
(if not None) will be used as a referecne plane on which the structure
will be constructed.
@param plane: Plane object to be
"""
if self.referencePlaneListWidget is None:
return
planeList = [ ]
if plane is not None:
planeList = [plane]
self.referencePlaneListWidget.insertItems(
row = 0,
items = planeList)
def listWidgetHasFocus(self):
"""
Checks if the list widget that lists the referecne plane, on which
the dna will be created, has the Qt focus. This is used to just remove
items from the list widget (without actually 'deleting' the
corresponding Plane in the GLPane)
@see: InsertDna_GraphicsMode.keyPressEvent() where this is called
"""
if self.referencePlaneListWidget and \
self.referencePlaneListWidget.hasFocus():
return True
return False
def _changeStructureColor(self):
"""
"""
if self._colorChooser is None:
return
if self.command and self.command.hasValidStructure():
color = self._colorChooser.getColor()
if hasattr(self.command.struct, 'setColor'):
self.command.struct.setColor(color)
self.win.glpane.gl_update()