class DnaSegment_PropertyManager(DnaOrCnt_PropertyManager):
"""
The DnaSegmenta_PropertyManager class provides a Property Manager
for the DnaSegment_EditCommand.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "DnaSegment Properties"
iconPath = "ui/actions/Tools/Build Structures/DNA.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_CANCEL_BUTTON | \
PM_PREVIEW_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Use resize handles to resize the segment. Drag any axis or sugar"\
" atom for translation or rotation about axis respectively. Dragging"\
" any bond will freely move the whole segment."
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.numberOfBasePairsSpinBox,
SIGNAL("valueChanged(int)"), self.numberOfBasesChanged)
change_connect(self.basesPerTurnDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.basesPerTurnChanged)
change_connect(self.duplexRiseDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.duplexRiseChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.command_update_UI()
@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
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:
#disable all widgets
if self._pmGroupBox1.isEnabled():
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 segment. Drag any axis or sugar"\
" atom for translation or rotation about axis respectively. Dragging"\
" any bond will freely move the whole segment."
self.updateMessage(msg)
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:
isStructResizable, why_not = self.command.hasResizableStructure()
params = (isStructResizable, why_not)
return params
def show(self):
"""
Show this property manager. Overrides EditCommand_PM.show()
This method also retrives the name information from the
command's structure for its name line edit field.
@see: DnaSegment_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
if self.command is not None:
name = self.command.getStructureName()
if name is not None:
self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
_superclass.close(self)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
numberOfBasePairs, \
dnaForm, \
dnaModel,\
basesPerTurn, \
duplexRise, \
endPoint1, \
endPoint2 , \
color = params
if numberOfBasePairs is not None:
self.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if duplexRise is not None:
self.duplexRiseDoubleSpinBox.setValue(duplexRise)
if basesPerTurn is not None:
self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn)
if endPoint1 is not None:
self.endPoint1 = endPoint1
if endPoint2 is not None:
self.endPoint2 = endPoint2
if color is not None:
self._colorChooser.setColor(color)
def getParameters(self):
"""
"""
#See bug 2802 for details about the parameter
#'number_of_basePairs_from_struct'. Basically it is used to check
#if the structure got modified (e.g. because of undo)
#The numberOfBases parameter obtained from the propMgr is given as a
#separate parameter for the reasons mentioned in bug 2802
#-- Ninad 2008-04-12
number_of_basePairs_from_struct = None
if self.command.hasValidStructure():
number_of_basePairs_from_struct = self.command.struct.getNumberOfBasePairs(
)
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
basesPerTurn = self.basesPerTurn
duplexRise = self.duplexRise
color = self._colorChooser.getColor()
return (number_of_basePairs_from_struct, numberOfBases, dnaForm,
dnaModel, basesPerTurn, duplexRise, self.endPoint1,
self.endPoint2, color)
def numberOfBasesChanged(self, numberOfBases):
"""
Slot for the B{Number of Bases} spinbox.
"""
duplexRise = self.duplexRiseDoubleSpinBox.value()
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation,
numberOfBases,
duplexRise = duplexRise)) \
+ " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged(self, basesPerTurn):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.basesPerTurn = basesPerTurn
def duplexRiseChanged(self, rise):
"""
Slot for the B{Rise} spinbox.
"""
self.duplexRise = rise
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Segment name:",
text="",
setAsDefault=False)
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = self.basesPerTurn,
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.basesPerTurnDoubleSpinBox.setDisabled(True)
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.duplexRise,
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.duplexRiseDoubleSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaSegmentEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaSegmentEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Duplex length",
dnaSegmentEditCommand_cursorTextCheckBox_length_prefs_key),
("Number of basepairs to be changed",
dnaSegmentEditCommand_cursorTextCheckBox_changedBasePairs_prefs_key)
]
return params
def _addWhatsThisText(self):
"""
Add what's this text.
"""
pass
def _addToolTipText(self):
"""
Add Tooltip text
"""
pass
class DnaSegment_PropertyManager(DnaOrCnt_PropertyManager):
"""
The DnaSegmenta_PropertyManager class provides a Property Manager
for the DnaSegment_EditCommand.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "DnaSegment Properties"
iconPath = "ui/actions/Tools/Build Structures/DNA.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_CANCEL_BUTTON | PM_PREVIEW_BUTTON | PM_WHATS_THIS_BUTTON)
msg = (
"Use resize handles to resize the segment. Drag any axis or sugar"
" atom for translation or rotation about axis respectively. Dragging"
" any bond will freely move the whole segment."
)
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.numberOfBasePairsSpinBox, SIGNAL("valueChanged(int)"), self.numberOfBasesChanged)
change_connect(self.basesPerTurnDoubleSpinBox, SIGNAL("valueChanged(double)"), self.basesPerTurnChanged)
change_connect(self.duplexRiseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.duplexRiseChanged)
change_connect(
self.showCursorTextCheckBox, SIGNAL("stateChanged(int)"), self._update_state_of_cursorTextGroupBox
)
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.command_update_UI()
@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
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:
# disable all widgets
if self._pmGroupBox1.isEnabled():
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 segment. Drag any axis or sugar"
" atom for translation or rotation about axis respectively. Dragging"
" any bond will freely move the whole segment."
)
self.updateMessage(msg)
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:
isStructResizable, why_not = self.command.hasResizableStructure()
params = (isStructResizable, why_not)
return params
def show(self):
"""
Show this property manager. Overrides EditCommand_PM.show()
This method also retrives the name information from the
command's structure for its name line edit field.
@see: DnaSegment_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
if self.command is not None:
name = self.command.getStructureName()
if name is not None:
self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
_superclass.close(self)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
Some property manager ui elements then display the information
obtained from the object being edited.
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
numberOfBasePairs, dnaForm, dnaModel, basesPerTurn, duplexRise, endPoint1, endPoint2, color = params
if numberOfBasePairs is not None:
self.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if duplexRise is not None:
self.duplexRiseDoubleSpinBox.setValue(duplexRise)
if basesPerTurn is not None:
self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn)
if endPoint1 is not None:
self.endPoint1 = endPoint1
if endPoint2 is not None:
self.endPoint2 = endPoint2
if color is not None:
self._colorChooser.setColor(color)
def getParameters(self):
"""
"""
# See bug 2802 for details about the parameter
#'number_of_basePairs_from_struct'. Basically it is used to check
# if the structure got modified (e.g. because of undo)
# The numberOfBases parameter obtained from the propMgr is given as a
# separate parameter for the reasons mentioned in bug 2802
# -- Ninad 2008-04-12
number_of_basePairs_from_struct = None
if self.command.hasValidStructure():
number_of_basePairs_from_struct = self.command.struct.getNumberOfBasePairs()
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
basesPerTurn = self.basesPerTurn
duplexRise = self.duplexRise
color = self._colorChooser.getColor()
return (
number_of_basePairs_from_struct,
numberOfBases,
dnaForm,
dnaModel,
basesPerTurn,
duplexRise,
self.endPoint1,
self.endPoint2,
color,
)
def numberOfBasesChanged(self, numberOfBases):
"""
Slot for the B{Number of Bases} spinbox.
"""
duplexRise = self.duplexRiseDoubleSpinBox.value()
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation, numberOfBases, duplexRise=duplexRise)) + " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged(self, basesPerTurn):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.basesPerTurn = basesPerTurn
def duplexRiseChanged(self, rise):
"""
Slot for the B{Rise} spinbox.
"""
self.duplexRise = rise
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox, label="Segment name:", text="", setAsDefault=False)
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = PM_SpinBox(
pmGroupBox, label="Base pairs:", value=self._numberOfBases, setAsDefault=False, minimum=2, maximum=10000
)
self.basesPerTurnDoubleSpinBox = PM_DoubleSpinBox(
pmGroupBox,
label="Bases per turn:",
value=self.basesPerTurn,
setAsDefault=True,
minimum=8.0,
maximum=20.0,
decimals=2,
singleStep=0.1,
)
self.basesPerTurnDoubleSpinBox.setDisabled(True)
self.duplexRiseDoubleSpinBox = PM_DoubleSpinBox(
pmGroupBox,
label="Rise:",
value=self.duplexRise,
setAsDefault=True,
minimum=2.0,
maximum=4.0,
decimals=3,
singleStep=0.01,
)
self.duplexRiseDoubleSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = PM_LineEdit(
pmGroupBox, label="Duplex length: ", text="0.0 Angstroms", setAsDefault=False
)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox, dnaSegmentEditCommand_showCursorTextCheckBox_prefs_key
)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = [ # Format: (" checkbox text", prefs_key)
("Number of base pairs", dnaSegmentEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Duplex length", dnaSegmentEditCommand_cursorTextCheckBox_length_prefs_key),
("Number of basepairs to be changed", dnaSegmentEditCommand_cursorTextCheckBox_changedBasePairs_prefs_key),
]
return params
def _addWhatsThisText(self):
"""
Add what's this text.
"""
pass
def _addToolTipText(self):
"""
Add Tooltip text
"""
pass
