class InsertNanotube_PropertyManager(DnaOrCnt_PropertyManager):
    """
    The InsertNanotube_PropertyManager class provides a Property Manager
    for the B{Build > Nanotube > CNT} command.

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title = "Insert Nanotube"
    pmName = title
    iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png"

    def __init__(self, win, editCommand):
        """
        Constructor for the Nanotube property manager.
        """
        self.endPoint1 = None
        self.endPoint2 = None

        self.nanotube = Nanotube()  # A 5x5 CNT.

        _superclass.__init__(self, win, editCommand)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.ntTypeComboBox,
                       SIGNAL("currentIndexChanged(const QString&)"),
                       self._ntTypeComboBoxChanged)

        change_connect(self.chiralityNSpinBox, SIGNAL("valueChanged(int)"),
                       self._chiralityFixup)

        change_connect(self.chiralityMSpinBox, SIGNAL("valueChanged(int)"),
                       self._chiralityFixup)

        change_connect(self.endingsComboBox,
                       SIGNAL("currentIndexChanged(const QString&)"),
                       self._endingsComboBoxChanged)

        # This spin box is currently hidden.
        change_connect(self.bondLengthDoubleSpinBox,
                       SIGNAL("valueChanged(double)"), self._bondLengthChanged)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

    def ok_btn_clicked(self):
        """
        Slot for the OK button
        """
        if self.editCommand:
            self.editCommand.preview_or_finalize_structure(previewing=False)
            ##env.history.message(self.editCommand.logMessage)
        self.win.toolsDone()

    def cancel_btn_clicked(self):
        """
        Slot for the Cancel button.
        """
        if self.editCommand:
            self.editCommand.cancelStructure()
        self.win.toolsCancel()

    def _update_widgets_in_PM_before_show(self):
        """
        Update various widgets in this Property manager.
        Overrides MotorPropertyManager._update_widgets_in_PM_before_show.
        The various  widgets , (e.g. spinboxes) will get values from the
        structure for which this propMgr is constructed for
        (self.editcCntroller.struct)

        @see: MotorPropertyManager._update_widgets_in_PM_before_show
        @see: self.show where it is called.
        """
        pass

    def getFlyoutActionList(self):
        """
        Returns custom actionlist that will be used in a specific mode
        or editing a feature etc Example: while in movie mode,
        the _createFlyoutToolBar method calls this.
        """
        #'allActionsList' returns all actions in the flyout toolbar
        #including the subcontrolArea actions
        allActionsList = []

        #Action List for  subcontrol Area buttons.
        #In this mode there is really no subcontrol area.
        #We will treat subcontrol area same as 'command area'
        #(subcontrol area buttons will have an empty list as their command area
        #list). We will set  the Comamnd Area palette background color to the
        #subcontrol area.

        subControlAreaActionList = []

        self.exitEditCommandAction.setChecked(True)
        subControlAreaActionList.append(self.exitEditCommandAction)

        separator = QAction(self.w)
        separator.setSeparator(True)
        subControlAreaActionList.append(separator)

        allActionsList.extend(subControlAreaActionList)

        #Empty actionlist for the 'Command Area'
        commandActionLists = []

        #Append empty 'lists' in 'commandActionLists equal to the
        #number of actions in subControlArea
        for i in range(len(subControlAreaActionList)):
            lst = []
            commandActionLists.append(lst)

        params = (subControlAreaActionList, commandActionLists, allActionsList)

        return params

    def _addGroupBoxes(self):
        """
        Add the Insert Nanotube Property Manager group boxes.
        """

        self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
        self._loadGroupBox1(self._pmGroupBox1)
        self._pmGroupBox1.hide()

        self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
        self._loadGroupBox2(self._pmGroupBox2)

        self._displayOptionsGroupBox = PM_GroupBox(self,
                                                   title="Display Options")
        self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)

        self._pmGroupBox3 = PM_GroupBox(self, title="Nanotube Distortion")
        self._loadGroupBox3(self._pmGroupBox3)
        self._pmGroupBox3.hide()  #@ Temporary.

        self._pmGroupBox4 = PM_GroupBox(self, title="Multi-Walled CNTs")
        self._loadGroupBox4(self._pmGroupBox4)
        self._pmGroupBox4.hide()  #@ Temporary.

        self._pmGroupBox5 = PM_GroupBox(self, title="Advanced Options")
        self._loadGroupBox5(self._pmGroupBox5)
        self._pmGroupBox5.hide()  #@ Temporary.

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 1.
        """
        #Following toolbutton facilitates entering a temporary NanotubeLineMode
        #to create a CNT using endpoints of the specified line.
        self.specifyCntLineButton = PM_ToolButton(
            pmGroupBox,
            text="Specify Endpoints",
            iconPath="ui/actions/Properties Manager/Pencil.png",
            spanWidth=True)
        self.specifyCntLineButton.setCheckable(True)
        self.specifyCntLineButton.setAutoRaise(True)
        self.specifyCntLineButton.setToolButtonStyle(
            Qt.ToolButtonTextBesideIcon)

        #EndPoint1 and endPoint2 coordinates. These widgets are hidden
        # as of 2007- 12 - 05
        self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label="End Point 1")
        self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
        self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
        self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox

        self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label="End Point 2")
        self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
        self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
        self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox

        self._endPoint1SpinBoxes.hide()
        self._endPoint2SpinBoxes.hide()

    def _loadGroupBox2(self, pmGroupBox):
        """
        Load widgets in group box 2.
        """

        _ntTypeChoices = ['Carbon', 'Boron Nitride']
        self.ntTypeComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Type:",
                         choices       =  _ntTypeChoices,
                         setAsDefault  =  True)

        self.ntRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  self.nanotube.getRise(),
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )

        self.ntRiseDoubleSpinBox.hide()

        # Nanotube Length
        self.ntLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Nanotube Length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.ntLengthLineEdit.setDisabled(True)
        self.ntLengthLineEdit.hide()

        # Nanotube diameter
        self.ntDiameterLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Diameter: ",
                         setAsDefault  =  False)

        self.ntDiameterLineEdit.setDisabled(True)
        self.updateNanotubeDiameter()

        self.chiralityNSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (n):",
                        value        = self.nanotube.getChiralityN(),
                        minimum      =  2,
                        maximum      =  100,
                        setAsDefault = True )

        self.chiralityMSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (m):",
                        value        = self.nanotube.getChiralityM(),
                        minimum      =  0,
                        maximum      =  100,
                        setAsDefault = True )

        # How about having user prefs for CNT and BNNT bond lengths?
        # I'm guessing that if the user wants to set these values, they will
        # do it once and would like those bond length values persist forever.
        # Need to discuss with others to determine if this spinbox comes out.
        # --Mark 2008-03-29
        self.bondLengthDoubleSpinBox = \
            PM_DoubleSpinBox( pmGroupBox,
                              label        = "Bond length:",
                              value        = self.nanotube.getBondLength(),
                              setAsDefault = True,
                              minimum      = 1.0,
                              maximum      = 3.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        #self.bondLengthDoubleSpinBox.hide()

        endingChoices = ["Hydrogen", "None"]  # Removed:, "Nitrogen"]

        self.endingsComboBox= \
            PM_ComboBox( pmGroupBox,
                         label        = "Endings:",
                         choices      = endingChoices,
                         index        = 0,
                         setAsDefault = True,
                         spanWidth    = False )

    def _loadGroupBox3(self, inPmGroupBox):
        """
        Load widgets in group box 3.
        """

        self.zDistortionDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "Z-distortion:",
                              value        = 0.0,
                              setAsDefault = True,
                              minimum      = 0.0,
                              maximum      = 10.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        self.xyDistortionDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "XY-distortion:",
                              value        = 0.0,
                              setAsDefault = True,
                              minimum      = 0.0,
                              maximum      = 2.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        self.twistSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Twist:",
                        value        = 0,
                        setAsDefault = True,
                        minimum      = 0,
                        maximum      = 100, # What should maximum be?
                        suffix       = " deg/A" )

        self.bendSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Bend:",
                        value        = 0,
                        setAsDefault = True,
                        minimum      = 0,
                        maximum      = 360,
                        suffix       = " deg" )

    def _loadGroupBox4(self, inPmGroupBox):
        """
        Load widgets in group box 4.
        """

        # "Number of Nanotubes" SpinBox
        self.mwntCountSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Number:",
                        value        = 1,
                        setAsDefault = True,
                        minimum      = 1,
                        maximum      = 10,
                        suffix       = " nanotubes" )

        self.mwntCountSpinBox.setSpecialValueText("SWNT")

        # "Spacing" lineedit.
        self.mwntSpacingDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "Spacing:",
                              value        = 2.46,
                              setAsDefault = True,
                              minimum      = 1.0,
                              maximum      = 10.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

    def _loadGroupBox5(self, pmGroupBox):
        """
        Load widgets in group box 5.
        """
        self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
                                                   title='Rubber band Line:')

        ntLineChoices = ['Ladder']
        self.ntRubberBandLineDisplayComboBox = \
            PM_ComboBox( self._rubberbandLineGroupBox ,
                         label         =  " Display as:",
                         choices       =  ntLineChoices,
                         setAsDefault  =  True)

        self.lineSnapCheckBox = \
            PM_CheckBox(self._rubberbandLineGroupBox ,
                        text         = 'Enable line snap' ,
                        widgetColumn = 1,
                        state        = Qt.Checked
                        )

    def _connect_showCursorTextCheckBox(self):
        """
        Connect the show cursor text checkbox with user prefs_key.
        Overrides
        DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
        """
        connect_checkbox_with_boolean_pref(
            self.showCursorTextCheckBox,
            insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key)

    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
               [  #Format: (" checkbox text", prefs_key)

                   ("Nanotube length",
                    insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ),

                    ("Angle",
                     insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key )
                 ]

        return params

    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the Insert Nanotube Property Manager.
        """
        pass

    def _setEndPoints(self):
        """
        Set the two endpoints of the nanotube using the values from the
        X, Y, Z coordinate spinboxes in the property manager.

        @note: The group box containing the 2 sets of XYZ spin boxes are
        currently hidden.
        """
        # First endpoint (origin) of nanotube
        x1 = self.x1SpinBox.value()
        y1 = self.y1SpinBox.value()
        z1 = self.z1SpinBox.value()

        # Second endpoint (direction vector/axis) of nanotube.
        x2 = self.x2SpinBox.value()
        y2 = self.y2SpinBox.value()
        z2 = self.z2SpinBox.value()

        if not self.endPoint1:
            self.endPoint1 = V(x1, y1, z1)
        if not self.endPoint2:
            self.endPoint2 = V(x2, y2, z2)

        self.nanotube.setEndPoints(self.endPoint1, self.endPoint2)
        # Need arg "recompute=True", which will recompute the second
        # endpoint (endPoint2) using the nanotube rise.

    def getParameters(self):
        """
        Return the parameters from this property manager to be used to create
        the nanotube.

        @return: A nanotube instance with its attrs set to the current
                 parameters in the property manager.
        @rtype: L{Nanotube}

        @see: L{InsertNanotube_EditCommand._gatherParameters} where this is used
        """
        self._setEndPoints()
        return (self.nanotube)

    def _ntTypeComboBoxChanged(self, type):
        """
        Slot for the Type combobox. It is called whenever the
        Type choice is changed.

        @param inIndex: The new index.
        @type  inIndex: int
        """
        self.nanotube.setType(str(type))
        print "Bond Length =", self.nanotube.getBondLength()
        self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength())
        #self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex])

    def _bondLengthChanged(self, bondLength):
        """
        Slot for the B{Bond Length} spinbox.
        """
        self.nanotube.setBondLength(bondLength)
        self.updateNanotubeDiameter()
        return

    def _chiralityFixup(self, spinBoxValueJunk=None):
        """
        Slot for several validators for different parameters.
        This gets called whenever the user changes the n, m chirality values.

        @param spinBoxValueJunk: This is the Spinbox value from the valueChanged
                                 signal. It is not used. We just want to know
                                 that the spinbox value has changed.
        @type  spinBoxValueJunk: double or None
        """
        _n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(),
                                            self.chiralityMSpinBox.value())

        #self.n, self.m = self.nanotube.getChirality()

        self.connect_or_disconnect_signals(isConnect=False)
        self.chiralityNSpinBox.setValue(_n)
        self.chiralityMSpinBox.setValue(_m)
        self.connect_or_disconnect_signals(isConnect=True)

        self.updateNanotubeDiameter()

    def updateNanotubeDiameter(self):
        """
        Update the nanotube Diameter lineEdit widget.
        """
        diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
        self.ntDiameterLineEdit.setText(diameterText)

        # ntRiseDoubleSpinBox is currently hidden.
        self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise())

    def _endingsComboBoxChanged(self, endings):
        """
        Slot for the B{Ending} combobox.

        @param endings: The option's text.
        @type  endings: string
        """
        self.nanotube.setEndings(str(endings))
        return

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_InsertNanotube_PropertyManager(self)
        return
class OrderDna_PropertyManager(Command_PropertyManager):
    """
    The OrderDna_PropertyManager class provides a Property Manager 
    for the B{Order Dna} command on the flyout toolbar in the 
    Build > Dna mode. 

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title = "Order DNA"
    pmName = title
    iconPath = "ui/actions/Command Toolbar/BuildDna/OrderDna.png"

    def __init__(self, command):
        """
        Constructor for the property manager.
        """

        _superclass.__init__(self, command)

        self.assy = self.win.assy

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

        self.update_includeStrands()  # Updates the message box.
        return

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot 
                          method. 
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.viewDnaOrderFileButton, SIGNAL("clicked()"),
                       self.viewDnaOrderFile)

        change_connect(self.includeStrandsComboBox, SIGNAL("activated(int)"),
                       self.update_includeStrands)
        return

    def _addGroupBoxes(self):
        """
        Add the Property Manager group boxes.
        """
        self._pmGroupBox1 = PM_GroupBox(self, title="Options")
        self._loadGroupBox1(self._pmGroupBox1)

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        """

        includeStrandsChoices = [
            "All strands in model", "Selected strands only"
        ]

        self.includeStrandsComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Include strands:",
                         choices       =  includeStrandsChoices,
                         setAsDefault  =  True)

        self.numberOfBasesLineEdit  = \
            PM_LineEdit( pmGroupBox,
                         label  =  "Total nucleotides:",
                         text   = str(self.getNumberOfBases()))
        self.numberOfBasesLineEdit.setEnabled(False)

        self.numberOfXBasesLineEdit  = \
            PM_LineEdit( pmGroupBox,
                         label  =  "Unassigned:",
                         text   = str(self.getNumberOfBases(unassignedOnly = True)))
        self.numberOfXBasesLineEdit.setEnabled(False)

        self.viewDnaOrderFileButton = \
            PM_PushButton( pmGroupBox,
                           label     = "",
                           text      = "View DNA Order File...",
                           spanWidth = True)
        return

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_OrderDna_PropertyManager(self)
        return

    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the DNA Property Manager.  
        """
        pass

    # Ask Bruce where this should live (i.e. class Part?) --Mark
    def getAllDnaStrands(self, selectedOnly=False):
        """
        Returns a list of all the DNA strands in the current part, or only
        the selected strands if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the selected DNA strands.
        @type  selectedOnly: bool
        """

        dnaStrandList = []

        def func(node):
            if isinstance(node, DnaStrand):
                if selectedOnly:
                    if node.picked:
                        dnaStrandList.append(node)
                else:
                    dnaStrandList.append(node)

        self.win.assy.part.topnode.apply2all(func)

        return dnaStrandList

    def getNumberOfBases(self, selectedOnly=False, unassignedOnly=False):
        """
        Returns the number of bases count for all the DNA strands in the 
        current part, or only the selected strand if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the number of bases in the
                             selected DNA strands.
        @type  selectedOnly: bool
        
        @param unassignedOnly: If True, return only the number of unassigned
                               bases (i.e. base letters = X).
        @type  unassignedOnly: bool
        """
        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)

        for strand in strandList:
            strandSequenceString = str(strand.getStrandSequence())
            dnaSequenceString += strandSequenceString

        if unassignedOnly:
            return dnaSequenceString.count("X")

        return len(dnaSequenceString)

    def _update_UI_do_updates(self):
        """
        Overrides superclass method.
        """
        self.update_includeStrands()
        return

    def getDnaSequence(self, format='CSV'):
        """
        Return the complete Dna sequence information string (i.e. all strand 
        sequences) in the specified format. 
        
        @return: The Dna sequence string
        @rtype: string
        
        """
        if format == 'CSV':  #comma separated values.
            separator = ','

        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)

        for strand in strandList:
            dnaSequenceString = dnaSequenceString + strand.name + separator
            strandSequenceString = str(strand.getStrandSequence())
            if strandSequenceString:
                strandSequenceString = strandSequenceString.upper()
                strandLength = str(len(strandSequenceString)) + separator
                dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString

            dnaSequenceString = dnaSequenceString + "\n"

        return dnaSequenceString

    def viewDnaOrderFile(self, openFileInEditor=True):
        """
        Writes a DNA Order file in comma-separated values (CSV) format 
        and opens it in a text editor.

        The user must save the file to a permanent location using the 
        text editor.

        @see: Ui_DnaFlyout.orderDnaCommand
        @see: writeDnaOrderFile()
        @TODO: assy.getAllDnaObjects(). 
        """
        dnaSequence = self.getDnaSequence(format='CSV')

        if dnaSequence:
            tmpdir = find_or_make_Nanorex_subdir('temp')
            fileBaseName = 'DnaOrder'
            temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
            writeDnaOrderFile(temporaryFile, self.assy,
                              self.getNumberOfBases(),
                              self.getNumberOfBases(unassignedOnly=True),
                              dnaSequence)

            if openFileInEditor:
                open_file_in_editor(temporaryFile)

        return

    def update_includeStrands(self, ignoreVal=0):
        """
        Slot method for "Include (strands)" combobox.
        """

        idx = self.includeStrandsComboBox.currentIndex()

        includeType = ["model", "selection"]

        _numberOfBases = self.getNumberOfBases()
        self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases")

        _numberOfXBases = self.getNumberOfBases(unassignedOnly=True)
        self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases")

        # Make the background color red if there are any unassigned bases.
        if _numberOfXBases:
            self.numberOfXBasesLineEdit.setStyleSheet(\
                "QLineEdit {"\
                "background-color: rgb(255, 0, 0)"\
                "}")
        else:
            self.numberOfXBasesLineEdit.setStyleSheet(\
                "QLineEdit {"\
                "background-color: rgb(255, 255, 255)"\
                "}")

        if _numberOfBases > 0:
            self.viewDnaOrderFileButton.setEnabled(True)
            msg = "Click on <b>View DNA Order File...</b> to preview a " \
                "DNA order for all DNA strands in the current %s." \
                % includeType[idx]
        else:
            self.viewDnaOrderFileButton.setEnabled(False)
            msg = "<font color=red>" \
                "There are no DNA strands in the current %s." \
                % includeType[idx]

        self.updateMessage(msg)
        return
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager):
    """
    The DnaStrand_PropertyManager class provides a Property Manager
    for the DnaStrand_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         =  "DnaStrand Properties"
    iconPath      =  "ui/actions/Properties Manager/Strand.png"

    def __init__( self, command ):
        """
        Constructor for the Build DNA property manager.
        """

        self.sequenceEditor = None

        self._numberOfBases = 0
        self._conformation = 'B-DNA'
        self.dnaModel = 'PAM3'

        _superclass.__init__( self, command)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        return

    def _addGroupBoxes( self ):
        """
        Add group boxes to this PM.
        """

        self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" )
        self._loadGroupBox1( self._pmGroupBox1 )
        self._displayOptionsGroupBox = PM_GroupBox( self,
                                                    title = "Display Options" )
        self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )

        #Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here
        #so that the sequence editor gets connected! Perhaps
        #superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03
        self._loadSequenceEditor()
        return

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 1.
        """

        self.nameLineEdit = PM_LineEdit( pmGroupBox,
                         label         =  "Name:",
                         text          =  "",
                         setAsDefault  =  False)

        self.numberOfBasesSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label         =  "Number of bases:",
                        value         =  self._numberOfBases,
                        setAsDefault  =  False,
                        minimum       =  2,
                        maximum       =  10000 )

        self.disableStructHighlightingCheckbox = \
            PM_CheckBox( pmGroupBox,
                         text         = "Don't highlight while editing DNA",
                         widgetColumn  = 0,
                         state        = Qt.Unchecked,
                         setAsDefault = True,
                         spanWidth = True
                         )

        #As of 2008-03-31, the properties such as number of bases will be
        #editable only by using the resize handles.
        self.numberOfBasesSpinBox.setEnabled(False)
        return

    def _loadSequenceEditor(self):
        """
        Temporary code  that shows the Sequence editor ..a doc widget docked
        at the bottom of the mainwindow. The implementation is going to change
        before 'rattleSnake' product release.
        As of 2007-11-20: This feature (sequence editor) is waiting
        for the ongoing dna model work to complete.
        """
        self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
        self.sequenceEditor.hide()
        return

    def _loadDisplayOptionsGroupBox(self, pmGroupBox):
        """
        Overrides superclass method.
        Also loads the color chooser widget.
        """
        self._loadColorChooser(pmGroupBox)
        _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
        return

    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 ,
            dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
        return


    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 bases",
                   dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),

                  ("Number of bases to be changed",
                   dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
                 ]

        return params


    def getParameters(self):
        name = self.nameLineEdit.text()
        numberOfBases = self.numberOfBasesSpinBox.value()
        dnaForm  = self._conformation
        dnaModel = self.dnaModel
        color = self._colorChooser.getColor()

        return (numberOfBases,
                dnaForm,
                dnaModel,
                color,
                name
                )

    def setParameters(self, params):
        """
        This is usually called when you are editing an existing structure.
        It also gets called when selecting a new strand (within this command).
        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?
        """
        numberOfBases, \
            dnaForm, \
            dnaModel, \
            color, \
            name = params

        if numberOfBases is not None:
            self.numberOfBasesSpinBox.setValue(numberOfBases)
        if dnaForm is not None:
            self._conformation = dnaForm
        if dnaModel is not None:
            self.dnaModel = dnaModel

        if color is not None:
            self._colorChooser.setColor(color)

        if name:  # Minimal test. Should add a validator. --Mark 2008-12-16
            self.nameLineEdit.setText(name)

        # This gets called when we enter the command *and* when selecting a new
        # strand. In either case, we must update the sequence in the sequenece
        # editor. Fixes bug 2951. --Mark 2008-12-16
        if self.command and self.command.hasValidStructure():
            #print "setParameters(): loading sequence in sequence editor for ", name
            self.updateSequence(strand = self.command.struct)
        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 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


        if self.sequenceEditor:
            self.sequenceEditor.connect_or_disconnect_signals(isConnect)

        _superclass.connect_or_disconnect_signals(self, isConnect)


        change_connect(self.disableStructHighlightingCheckbox,
                       SIGNAL('stateChanged(int)'),
                       self.change_struct_highlightPolicy)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

        change_connect(self.nameLineEdit,
                       SIGNAL("editingFinished()"),
                       self._nameChanged)
        return

    def _update_UI_do_updates(self):
        """
        @see: Command_PropertyManager. _update_UI_do_updates()
        @see: DnaStrand_EditCommand.command_update_UI()
        @see: DnaStrand_EditCommand.hasResizableStructure()
        """
        if not self.command.hasValidStructure():
            print "DnaStrand not a valid structure."
            self._pmGroupBox1.setEnabled(False)
            self._displayOptionsGroupBox.setEnabled(False)
            self.sequenceEditor.updateSequence(strand = " ")
            self.sequenceEditor.setEnabled(False)
            self.nameLineEdit.setText("")
            self.numberOfBasesSpinBox.setValue(0)
            return
        else:
            self._pmGroupBox1.setEnabled(True)
            self._displayOptionsGroupBox.setEnabled(True)
            self.sequenceEditor.setEnabled(True)

        isStructResizable, why_not = self.command.hasResizableStructure()
        if not isStructResizable:
            #disable all widgets
            if self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(False)
                msg1 = ("Attention: ") % (self.command.struct.name)
                msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \
                              (self.command.struct.name, why_not))
                self.updateMessage(msg1 + msg2)
        else:
            if not self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(True)
            msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name)
            msg2 = "Use resize handles to resize the strand. "\
                 "Use the <i>Sequence Editor</i> to edit the sequence."
            self.updateMessage(msg1 + msg2)
        return

    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)

        if self.sequenceEditor:
            self.sequenceEditor.close()

        _superclass.close(self)
        return

    def updateSequence(self, strand = None):
        """
        Public method provided for convenience. If any callers outside of this
        command need to update the sequence in the sequence editor, they can simply
        do DnaStrand_ProprtyManager.updateSequence() rather than
        DnaStrand_ProprtyManager.sequenceEditor.updateSequence()
        @see: Ui_DnaSequenceEditor.updateSequence()
        """
        if self.sequenceEditor:
            self.sequenceEditor.updateSequence(strand = strand)
        return

    def change_struct_highlightPolicy(self,checkedState = False):
        """
        Change the 'highlight policy' of the structure being edited
        (i.e. self.command.struct) .
        @param checkedState: The checked state of the checkbox that says
                             'Don't highlight while editing DNA'. So, it
                             its True, the structure being edited won't get
                             highlighted.
        @see: DnaStrand.setHighlightPolicy for more comments
        """
        if self.command and self.command.hasValidStructure():
            highlight = not checkedState
            self.command.struct.setHighlightPolicy(highlight = highlight)
        return

    def _addWhatsThisText(self):
        """
        Add what's this text.
        Abstract method.
        """
        pass

    def _nameChanged(self): # Added by Mark. 2008-12-16
        """
        Slot for "Name" field. Changes the name of the strand if the user types
        in a new name.

        @warning: this lacks a validator. User can type in a name with invalid
                  characters.
        """
        if not self.command.hasValidStructure():
            return

        name = str(self.nameLineEdit.text())

        if not name: # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16
            if self.command.hasValidStructure():
                self.nameLineEdit.setText(self.command.getStructureName())

            return

        self.command.setStructureName(name)

        self._update_UI_do_updates() # Updates the message box.

        return
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager):
    """
    The DnaStrand_PropertyManager class provides a Property Manager 
    for the DnaStrand_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         =  "DnaStrand Properties"
    pmName        =  title
    iconPath      =  "ui/actions/Properties Manager/Strand.png"

    def __init__( self, win, editCommand ):
        """
        Constructor for the Build DNA property manager.
        """
        
        #For model changed signal
        self.previousSelectionParams = None
        
        #see self.connect_or_disconnect_signals for comment about this flag
        self.isAlreadyConnected = False
        self.isAlreadyDisconnected = False
        
        self.sequenceEditor = None      
        
        self._numberOfBases = 0 
        self._conformation = 'B-DNA'
        self.duplexRise = 3.18
        self.basesPerTurn = 10
        self.dnaModel = 'PAM3'
        
        
        _superclass.__init__( self, 
                                    win,
                                    editCommand)


        
        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        
        self._loadSequenceEditor()
        
        msg = "Use resize handles to resize the strand. Use sequence editor"\
                   "to assign a new sequence or the current one to a file."
        self.updateMessage(msg)
        
               
    
    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         =  "Strand name:",
                         text          =  "",
                         setAsDefault  =  False)
        
        self.numberOfBasesSpinBox = \
            PM_SpinBox( pmGroupBox, 
                        label         =  "Number of bases:", 
                        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.duplexRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  self.duplexRise,
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )
        
        self.disableStructHighlightingCheckbox = \
            PM_CheckBox( pmGroupBox,
                         text         = "Don't highlight while editing DNA",
                         widgetColumn  = 0,
                         state        = Qt.Unchecked,
                         setAsDefault = True,
                         spanWidth = True
                         )
        
        #As of 2008-03-31, the properties such as number of bases will be 
        #editable only by using the resize handles. post FNANO we will support 
        #the 
        self.numberOfBasesSpinBox.setEnabled(False)
        self.basesPerTurnDoubleSpinBox.setEnabled(False)
        self.duplexRiseDoubleSpinBox.setEnabled(False)
        
    
            
    def _loadSequenceEditor(self):
        """
        Temporary code  that shows the Sequence editor ..a doc widget docked
        at the bottom of the mainwindow. The implementation is going to change
        before 'rattleSnake' product release.
        As of 2007-11-20: This feature (sequence editor) is waiting 
        for the ongoing dna model work to complete.
        """
        self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded() 
        self.sequenceEditor.hide()
        
        
    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 , 
            dnaStrandEditCommand_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 bases", 
                   dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),

                  ("Number of bases to be changed",
                   dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key) 
                 ]

        return params
    
        
    def getParameters(self):
        numberOfBases = self.numberOfBasesSpinBox.value()
        dnaForm  = self._conformation
        dnaModel = self.dnaModel
        basesPerTurn = self.basesPerTurn
        duplexRise = self.duplexRise
        color = self._colorChooser.getColor()
              
        return (numberOfBases, 
                dnaForm,
                dnaModel,
                basesPerTurn,
                duplexRise, 
                color
                )
    
    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?  
        """
        #Set the duplex rise and bases per turn spinbox values. 
        
        numberOfBases, \
                     dnaForm, \
                     dnaModel, \
                     basesPerTurn, \
                     duplexRise, \
                     color  = params 
        
        if numberOfBases is not None:
            self.numberOfBasesSpinBox.setValue(numberOfBases)
        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 color is not None:
            self._colorChooser.setColor(color)
    
    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 
          
                
        if self.sequenceEditor:
            self.sequenceEditor.connect_or_disconnect_signals(isConnect)
            
        _superclass.connect_or_disconnect_signals(self, isConnect)
            
        
        change_connect(self.disableStructHighlightingCheckbox, 
                       SIGNAL('stateChanged(int)'), 
                       self.change_struct_highlightPolicy)
        
        change_connect(self.showCursorTextCheckBox, 
                       SIGNAL('stateChanged(int)'), 
                       self._update_state_of_cursorTextGroupBox)
        
    def model_changed(self): 
        """
        @see: DnaStrand_EditCommand.model_changed()
        @see: DnaStrand_EditCommand.hasResizableStructure()
        """
        isStructResizable, why_not = self.editCommand.hasResizableStructure()
        if not isStructResizable:
            #disable all widgets
            if self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(False)
                msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name) 
                msg2 = redmsg("DnaStrand is not resizable. Reason: %s"%(why_not))                    
                self.updateMessage(msg1 + msg2)
        else:
            if not self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(True)
                msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name) 
                msg2 = "Use resize handles to resize the strand. Use sequence editor"\
                    "to assign a new sequence or the current one to a file."
                self.updateMessage(msg1 + msg2)
        
    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
        This method also retrives the name information from the 
        editCommand's structure for its name line edit field. 
        @see: DnaStrand_EditCommand.getStructureName()
        @see: self.close()
        """
        _superclass.show(self) 
        self._showSequenceEditor()
    
        if self.editCommand is not None:
            name = self.editCommand.getStructureName()
            if name is not None:
                self.nameLineEdit.setText(name)     
           
    def close(self):
        """
        Close this property manager. 
        Also sets the name of the self.editCommand's structure to the one 
        displayed in the line edit field.
        @see self.show()
        @see: DnaSegment_EditCommand.setStructureName
        """
        if self.editCommand is not None:
            name = str(self.nameLineEdit.text())
            self.editCommand.setStructureName(name)
            
        if self.sequenceEditor:
            self.sequenceEditor.close()
                            
        _superclass.close(self)
            
    def _showSequenceEditor(self):
        if self.sequenceEditor:
            if not self.sequenceEditor.isVisible():
                #Show the sequence editor
                #ATTENTION: the sequence editor also closes (temporarily) the
                #reports dockwidget (if visible) Its state is later restored when
                #the sequuence Editor is closed. 
                self.sequenceEditor.show()     
                                              
            self.updateSequence()

        
    def updateSequence(self):
        """
        Update the sequence string in the sequence editor
        @see: DnaSequenceEditor.setSequence()
        @see DnaSequenceEditor._determine_complementSequence()
        @see: DnaSequenceEditor.setComplementSequence()
        @see: DnaStrand.getStrandSequenceAndItsComplement()
        """
        #Read in the strand sequence of the selected strand and 
        #show it in the text edit in the sequence editor.
        ##strand = self.strandListWidget.getPickedItem()
        
        if not self.editCommand.hasValidStructure():
            return
        
        strand = self.editCommand.struct
        
        titleString = 'Sequence Editor for ' + strand.name
                           
        self.sequenceEditor.setWindowTitle(titleString)
        sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement()
        if sequenceString:
            sequenceString = QString(sequenceString) 
            sequenceString = sequenceString.toUpper()
            #Set the initial sequence (read in from the file)
            self.sequenceEditor.setSequence(sequenceString)
            
            #Set the initial complement sequence for DnaSequence editor. 
            #do this independently because 'complementSequenceString' may have
            #some characters (such as * ) that denote a missing base on the 
            #complementary strand. this information is used by the sequence
            #editor. See DnaSequenceEditor._determine_complementSequence() 
            #for more details. See also bug 2787
            self.sequenceEditor.setComplementSequence(complementSequenceString)

            
    def change_struct_highlightPolicy(self,checkedState = False):
        """
        Change the 'highlight policy' of the structure being edited 
        (i.e. self.editCommand.struct) . 
        @param checkedState: The checked state of the checkbox that says 
                             'Don't highlight while editing DNA'. So, it 
                             its True, the structure being edited won't get
                             highlighted. 
        @see: DnaStrand.setHighlightPolicy for more comments        
        """        
        if self.editCommand and self.editCommand.hasValidStructure():
            highlight = not checkedState
            self.editCommand.struct.setHighlightPolicy(highlight = highlight)

    def _addWhatsThisText(self):
        """
        Add what's this text. 
        Abstract method.
        """
        pass
class EditNanotube_PropertyManager( DnaOrCnt_PropertyManager ):
    """
    The NanotubeSegmenta_PropertyManager class provides a Property Manager
    for the EditNanotube_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         =  "Nanotube Properties"
    pmName        =  title
    iconPath      =  "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png"

    def __init__( self,  command ):
        """
        Constructor for the Cnt Segment Properties property manager.
        """

        #For model changed signal
        self.previousSelectionParams = None

        #see self.connect_or_disconnect_signals for comment about this flag
        self.isAlreadyConnected = False
        self.isAlreadyDisconnected = False

        # Initialized here. Their values will be set in
        # _update_widgets_in_PM_before_show()
        self.endPoint1 = V(0, 0, 0)
        self.endPoint2 = V(0, 0, 0)

        _superclass.__init__( self, command)


        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.nameLineEdit,
                       SIGNAL("editingFinished()"),
                       self._nameChanged)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)
        return

    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: EditNanotube_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: EditNanotube_EditCommand.setStructureName
        """
        if self.command is not None:
            name = str(self.nameLineEdit.text())
            self.command.setStructureName(name)
        _superclass.close(self)

    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 ,
            editNanotubeEditCommand_showCursorTextCheckBox_prefs_key)


    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
               [  #Format: (" checkbox text", prefs_key)

                  ("Nanotube length",
                   editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key)
                 ]

        return params

    def setParameters(self, params):
        """
        This is called when entering "Nanotube Segment Properties
        (i.e. "Edit properties...") to retrieve and set parameters of the
        nanotube segment that might be modified during this command and
        are needed to regenerate the nanotube segment.

        @param params: The parameters of the nanotube segment.
                       These parameters are retreived via
                       L{NanotubeSegment.getProps()}, called from
                       L{EditNanotube_EditCommand.editStructure()}.

                       Parameters:
                       - n, m (chirality)
                       - type (i.e. carbon or boron nitride)
                       - endings (none, hydrogen, nitrogen)
                       - endpoints (endPoint1, endPoint2)
        @type params: list (n, m), type, endings, (endPoint1, endPoint2)

        @note: Any widgets in the property manager that display these
        parameters should be updated here.

        @see: L{NanotubeSegment.getProps()}

        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?
        """
        (self.n, self.m), self.type, self.endings,\
            (self.endPoint1, self.endPoint2) = params

        # This is needed to update the endpoints since the Nanotube segment
        # may have been moved (i.e. translated or rotated). In that case,
        # the endpoints are not updated, so we recompute them here.
        nanotubeChunk = self.command.struct.members[0]
        self.endPoint1, self.endPoint2, radius = \
            self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk)

        if 0:
            print "\n--------------"
            print "setParameters():"
            print "Struct=", self.command.struct
            print "N, M:", self.n, self.m
            print "type:", self.type
            print "endings:", self.endings
            print "pt1, pt2:", self.endPoint1, self.endPoint2

    def getParameters(self):
        """
        Get the parameters that the edit command will use to determine if
        any have changed. If any have, then the nanotube will be modified.
        """
        if 0:
            print "\n--------------"
            print "getParameters():"
            print "Struct=", self.command.struct
            print "N, M:", self.n, self.m
            print "type:", self.type
            print "endings:", self.endings
            print "pt1, pt2:", self.endPoint1, self.endPoint2

        return (self.n, self.m,
                self.type,
                self.endings,
                self.endPoint1, self.endPoint2)

    def _update_widgets_in_PM_before_show(self):
        """
        This is called only when user is editing an existing structure.
        Its different than self.update_widgets_in_pm_before_show. (that method
        is called just before showing the property manager)
        @see: EditNanotube_EditCommand.editStructure()

        """
        if self.command and self.command.hasValidStructure():

            self.nanotube = self.command.struct.nanotube

            self.n, self.m = self.nanotube.getChirality()
            self.type = self.nanotube.getType()
            self.endings = self.nanotube.getEndings()
            self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints()
            pass

        # Note that _update_widgets_in_PM_before_show() is called in
        # self.show, before you connect the signals. So, for the
        # 'first show' we will need to manually set the value of any
        # widgets that need updated. But later, when a different
        # NanotubeSegment is clicked, (while still in
        # EditNanotube_EditCommand, the propMgr will already be connected
        # so any calls in that case is redundant.
        self.updateNameField()
        self.updateLength()
        self.updateNanotubeDiameter()
        self.updateChirality()

        return

    def _update_UI_do_updates(self):
        """
        Overrides superclass method.

        @see: Command_PropertyManager._update_UI_do_updates()
        """
        self._update_widgets_in_PM_before_show()

        if self.command.struct:
            msg = "Editing structure <b>%s</b>." % \
                self.command.getStructureName()
        else:
            msg = "Select a nanotube to edit."
        self.updateMessage(msg)
        return

    def _addGroupBoxes( self ):
        """
        Add the 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         =  "Name:",
                         text          =  "",
                         setAsDefault  =  False)

        # Nanotube Length
        self.ntLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.ntLengthLineEdit.setDisabled(True)

        # Nanotube Radius
        self.ntDiameterLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Nanotube Diameter: ",
                         setAsDefault  =  False)

        self.ntDiameterLineEdit.setDisabled(True)

        # Nanotube chirality. These are disabled (read-only) for now. --Mark
        self.chiralityNSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (n) :",
                        minimum      =  2,
                        maximum      =  100,
                        setAsDefault = True )
        self.chiralityNSpinBox.setDisabled(True)

        self.chiralityMSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (m) :",
                        minimum      =  0,
                        maximum      =  100,
                        setAsDefault = True )
        self.chiralityMSpinBox.setDisabled(True)

    def _addWhatsThisText(self):
        """
        Add what's this text.
        """
        pass

    def _addToolTipText(self):
        """
        Add Tooltip text
        """
        pass

    def _nameChanged(self):
        """
        Slot for "Name" field.

        @TODO: Include a validator for the name field.
        """

        _name = str(self.nameLineEdit.text())

        if not _name: # Minimal test. Need to implement a validator.
            self.updateNameField()
            return

        self.command.setStructureName(_name)
        msg = "Editing structure <b>%s</b>." % _name
        self.updateMessage(msg)

        return

    def updateNameField(self):
        """
        Update the name field showing the name of the currently selected protein.
        clear the combobox list.
        """

        if self.command.hasValidStructure():
            self.nameLineEdit.setEnabled(True)
            self.nameLineEdit.setText(self.command.getStructureName())
        else:
            self.nameLineEdit.setDisabled(True)
            self.nameLineEdit.setText("")
        return

    def updateLength( self ):
        """
        Update the nanotube Length lineEdit widget.
        """
        if self.command.hasValidStructure():
            _nanotubeLength = vlen(self.endPoint1 - self.endPoint2)
            _lengthText = "%-7.4f Angstroms" % (_nanotubeLength)
        else:
            _lengthText = ""
        self.ntLengthLineEdit.setText(_lengthText)
        return

    def updateNanotubeDiameter(self):
        """
        Update the nanotube Diameter lineEdit widget.
        """
        if self.command.hasValidStructure():
            _diameterText = "%-7.4f Angstroms" %  (self.nanotube.getDiameter())
        else:
            _diameterText = ""
        self.ntDiameterLineEdit.setText(_diameterText)
        return

    def updateChirality( self ):
        """
        Update the nanotube chirality spinboxes (read-only).
        """
        if self.command.hasValidStructure():
            n, m = self.nanotube.getChirality()
        else:
            n = 0
            m = 0
        self.chiralityNSpinBox.setValue(n)
        self.chiralityMSpinBox.setValue(m)
        return

    pass # End of EditNanotube_PropertyManager class
Exemplo n.º 6
0
class InsertDna_PropertyManager(DnaOrCnt_PropertyManager):
    """
    The InsertDna_PropertyManager class provides a Property Manager
    for the B{Insert Dna} command.

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title = "Insert DNA"
    pmName = title
    iconPath = "ui/actions/Command Toolbar/BuildDna/InsertDna.png"

    def __init__(self, command):
        """
        Constructor for the DNA Duplex property manager.
        """
        self.endPoint1 = None
        self.endPoint2 = None

        self._conformation = "B-DNA"
        self._numberOfBases = 0
        self._basesPerTurn = getDuplexBasesPerTurn(self._conformation)
        self._duplexRise = getDuplexRise(self._conformation)
        self._duplexLength = getDuplexLength(self._conformation,
                                             self._numberOfBases)

        _superclass.__init__(self, command)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self._placementOptions.buttonGroup,
                       SIGNAL("buttonClicked(int)"),
                       self.activateSpecifyReferencePlaneTool)

        change_connect(self.conformationComboBox,
                       SIGNAL("currentIndexChanged(int)"),
                       self.conformationComboBoxChanged)

        change_connect(self.numberOfBasePairsSpinBox,
                       SIGNAL("valueChanged(int)"), self.numberOfBasesChanged)

        change_connect(self.basesPerTurnDoubleSpinBox,
                       SIGNAL("valueChanged(double)"),
                       self.basesPerTurnChanged)

        change_connect(self.duplexRiseDoubleSpinBox,
                       SIGNAL("valueChanged(double)"), self.duplexRiseChanged)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

        self.duplexRiseDoubleSpinBox.connectWithState(
            Preferences_StateRef_double(bdnaRise_prefs_key,
                                        env.prefs[bdnaRise_prefs_key]))

        self.basesPerTurnDoubleSpinBox.connectWithState(
            Preferences_StateRef_double(bdnaBasesPerTurn_prefs_key,
                                        env.prefs[bdnaBasesPerTurn_prefs_key]))

    def show(self):
        _superclass.show(self)
        self.updateMessage("Specify the DNA parameters below, then click "\
                           "two endpoints in the graphics area to insert a DNA duplex.")

    def _addGroupBoxes(self):
        """
        Add the DNA Property Manager group boxes.
        """
        self._pmReferencePlaneGroupBox = PM_GroupBox(self,
                                                     title="Placement Options")
        self._loadReferencePlaneGroupBox(self._pmReferencePlaneGroupBox)

        self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
        self._loadGroupBox1(self._pmGroupBox1)

        self._pmGroupBox1.hide()

        self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
        self._loadGroupBox2(self._pmGroupBox2)

        self._displayOptionsGroupBox = PM_GroupBox(self,
                                                   title="Display Options")
        self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 3.
        """
        #Folllowing toolbutton facilitates entering a temporary DnaLineMode
        #to create a DNA using endpoints of the specified line.
        self.specifyDnaLineButton = PM_ToolButton(
            pmGroupBox,
            text="Specify Endpoints",
            iconPath="ui/actions/Properties Manager/Pencil.png",
            spanWidth=True)
        self.specifyDnaLineButton.setCheckable(True)
        self.specifyDnaLineButton.setAutoRaise(True)
        self.specifyDnaLineButton.setToolButtonStyle(
            Qt.ToolButtonTextBesideIcon)

        #EndPoint1 and endPoint2 coordinates. These widgets are hidden
        # as of 2007- 12 - 05
        self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label="End Point 1")
        self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
        self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
        self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox

        self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label="End Point 2")
        self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
        self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
        self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox

        self._endPoint1SpinBoxes.hide()
        self._endPoint2SpinBoxes.hide()

    def _loadGroupBox2(self, pmGroupBox):
        """
        Load widgets in group box 4.
        """

        self.conformationComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Conformation:",
                         choices       =  ["B-DNA"],
                         setAsDefault  =  True)

        dnaModelChoices = ['PAM3', 'PAM5']
        self.dnaModelComboBox = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Model:",
                         choices       =  dnaModelChoices,
                         setAsDefault  =  True)


        self.basesPerTurnDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Bases per turn:",
                              value         =  env.prefs[bdnaBasesPerTurn_prefs_key],
                              setAsDefault  =  True,
                              minimum       =  8.0,
                              maximum       =  20.0,
                              decimals      =  2,
                              singleStep    =  0.1 )


        self.duplexRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  env.prefs[bdnaRise_prefs_key],
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )

        # Strand Length (i.e. the number of bases)
        self.numberOfBasePairsSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label         =  "Base pairs:",
                        value         =  self._numberOfBases,
                        setAsDefault  =  False,
                        minimum       =  0,
                        maximum       =  10000 )

        self.numberOfBasePairsSpinBox.setDisabled(True)

        # Duplex Length
        self.duplexLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Duplex length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.duplexLengthLineEdit.setDisabled(True)

    def _loadDisplayOptionsGroupBox(self, pmGroupBox):
        """
        Load widgets in the Display Options GroupBox
        @see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
        """
        #Call the superclass method that loads the cursor text checkboxes.
        #Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
        #only loads the cursor text groupboxes. Subclasses like this can
        #call custom methods like self._loadCursorTextCheckBoxes etc if they
        #don't need all groupboxes that the superclass loads.
        _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)

        self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
                                                   title='Rubber band line:')

        dnaLineChoices = ['Ribbons', 'Ladder']
        self.dnaRubberBandLineDisplayComboBox = \
            PM_ComboBox( self._rubberbandLineGroupBox ,
                         label         =  " Display as:",
                         choices       =  dnaLineChoices,
                         setAsDefault  =  True)

        self.lineSnapCheckBox = \
            PM_CheckBox(self._rubberbandLineGroupBox ,
                        text         = 'Enable line snap' ,
                        widgetColumn = 1,
                        state        = Qt.Checked
                    )

    def _connect_showCursorTextCheckBox(self):
        """
        Connect the show cursor text checkbox with user prefs_key.
        Overrides
        DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
        """
        connect_checkbox_with_boolean_pref(
            self.showCursorTextCheckBox,
            dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)

    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
        [  #Format: (" checkbox text", prefs_key)
            ("Number of base pairs",
             dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),

            ("Number of turns",
             dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),

            ("Duplex length",
             dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),

            ("Angle",
             dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]

        return params

    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the DNA Property Manager.
        """
        pass

    def conformationComboBoxChanged(self, inIndex):
        """
        Slot for the Conformation combobox. It is called whenever the
        Conformation choice is changed.

        @param inIndex: The new index.
        @type  inIndex: int
        """
        conformation = self.conformationComboBox.currentText()

        if conformation == "B-DNA":
            self.basesPerTurnDoubleSpinBox.setValue("10.0")

        elif conformation == "Z-DNA":
            self.basesPerTurnDoubleSpinBox.setValue("12.0")

        else:
            msg = redmsg("conformationComboBoxChanged(): \
                         Error - unknown DNA conformation. Index = " + inIndex)
            env.history.message(msg)

        self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))

    def numberOfBasesChanged(self, numberOfBases):
        """
        Slot for the B{Number of Bases} spinbox.
        """
        # Update the Duplex Length lineEdit widget.
        text = str(getDuplexLength(self._conformation,
                                   numberOfBases,
                                   self._duplexRise)) \
             + " Angstroms"
        self.duplexLengthLineEdit.setText(text)
        return

    def basesPerTurnChanged(self, basesPerTurn):
        """
        Slot for the B{Bases per turn} spinbox.
        """
        self.command.basesPerTurn = basesPerTurn
        self._basesPerTurn = basesPerTurn
        return

    def duplexRiseChanged(self, rise):
        """
        Slot for the B{Rise} spinbox.
        """
        self.command.duplexRise = rise
        self._duplexRise = rise
        return

    def getParameters(self):
        """
        Return the parameters from this property manager
        to be used to create the DNA duplex.
        @return: A tuple containing the parameters
        @rtype: tuple
        @see: L{InsertDna_EditCommand._gatherParameters} where this is used
        """
        numberOfBases = self.numberOfBasePairsSpinBox.value()
        dnaForm = str(self.conformationComboBox.currentText())
        basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
        duplexRise = self.duplexRiseDoubleSpinBox.value()

        dnaModel = str(self.dnaModelComboBox.currentText())

        # First endpoint (origin) of DNA duplex
        x1 = self.x1SpinBox.value()
        y1 = self.y1SpinBox.value()
        z1 = self.z1SpinBox.value()

        # Second endpoint (direction vector/axis) of DNA duplex.
        x2 = self.x2SpinBox.value()
        y2 = self.y2SpinBox.value()
        z2 = self.z2SpinBox.value()

        if not self.endPoint1:
            self.endPoint1 = V(x1, y1, z1)
        if not self.endPoint2:
            self.endPoint2 = V(x2, y2, z2)

        return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise,
                self.endPoint1, self.endPoint2)

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_InsertDna_PropertyManager(self)
Exemplo n.º 7
0
class OrderDna_PropertyManager( PM_Dialog, DebugMenuMixin ):
    """
    The OrderDna_PropertyManager class provides a Property Manager 
    for the B{Order Dna} command on the flyout toolbar in the 
    Build > Dna mode. 

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title         =  "Order Dna"
    pmName        =  title
    iconPath      =  "ui/actions/Command Toolbar/Order_DNA.png"
    
    def __init__( self, parentCommand ):
        """
        Constructor for the property manager.
        """

        self.parentMode = parentCommand
        self.w = self.parentMode.w
        self.win = self.parentMode.w
        self.pw = self.parentMode.pw        
        self.o = self.win.glpane
        self.assy = self.win.assy
                    
        PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
        
        DebugMenuMixin._init1( self )

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        
        self.update_includeStrands() # Updates the message box.
        """
        if self.getNumberOfBases():
            msg = "Click on <b>View DNA Order File...</b> to preview a "\
                "DNA order for all DNA strands in the current model."
        else:
            msg = "<font color=red>There is no DNA in the current model."
        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 
        
        change_connect( self.viewDnaOrderFileButton,
                        SIGNAL("clicked()"), 
                        self.viewDnaOrderFile)
        
        change_connect( self.includeStrandsComboBox,
                      SIGNAL("activated(int)"),
                      self.update_includeStrands )
        
    def ok_btn_clicked(self):
        """
        Slot for the OK button
        """      
        self.win.toolsDone()
        
    def show(self):
        """
        Shows the Property Manager. Overrides PM_Dialog.show.
        """
        PM_Dialog.show(self)
        self.connect_or_disconnect_signals(isConnect = True)

    def close(self):
        """
        Closes the Property Manager. Overrides PM_Dialog.close.
        """
        self.connect_or_disconnect_signals(False)
        PM_Dialog.close(self)
    
    def _addGroupBoxes( self ):
        """
        Add the Property Manager group boxes.
        """        
        self._pmGroupBox1 = PM_GroupBox( self, title = "Options" )
        self._loadGroupBox1( self._pmGroupBox1 )
    
    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        """
        
        includeStrandsChoices = ["All strands in model",
                                 "Selected strands only"]
        
        self.includeStrandsComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Include strands:", 
                         choices       =  includeStrandsChoices,
                         setAsDefault  =  True)
        
        self.numberOfBasesLineEdit  = \
            PM_LineEdit( pmGroupBox,
                         label  =  "Number of bases:",
                         text   = str(self.getNumberOfBases()))
        self.numberOfBasesLineEdit.setEnabled(False)
        
        self.viewDnaOrderFileButton = \
            PM_PushButton( pmGroupBox,
                           label     = "",
                           text      = "View DNA Order File...",
                           spanWidth = True)
    
    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
    
    # Ask Bruce where this should live (i.e. class Part?) --Mark
    def getAllDnaStrands(self, selectedOnly = False):
        """
        Returns a list of all the DNA strands in the current part, or only
        the selected strands if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the selected DNA strands.
        @type  selectedOnly: bool
        """
        
        dnaStrandList = []
         
        def func(node):
            if isinstance(node, DnaStrand):
                if selectedOnly:
                    if node.picked:
                        dnaStrandList.append(node)
                else:
                    dnaStrandList.append(node)
                    
        self.win.assy.part.topnode.apply2all(func)
        
        return dnaStrandList
    
    def getNumberOfBases(self, selectedOnly = False):
        """
        Returns the number of bases count for all the DNA strands in the 
        current part, or only the selected strand if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the selected DNA strands.
        @type  selectedOnly: bool
        """
        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)
        
        for strand in strandList:
            strandSequenceString = str(strand.getStrandSequence())
            dnaSequenceString += strandSequenceString
            
        return len(dnaSequenceString)
        
    def getDnaSequence(self, format = 'CSV'):
        """
        Return the complete Dna sequence information string (i.e. all strand 
        sequences) in the specified format. 
        
        @return: The Dna sequence string
        @rtype: string
        
        """
        if format == 'CSV': #comma separated values.
            separator = ','
            
        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)
        
        for strand in strandList:
            dnaSequenceString = dnaSequenceString + strand.name + separator
            strandSequenceString = str(strand.getStrandSequence())
            if strandSequenceString: 
                strandSequenceString = strandSequenceString.upper()
                dnaSequenceString = dnaSequenceString + strandSequenceString
                
            dnaSequenceString = dnaSequenceString + "\n"
            
        return dnaSequenceString
        
    def viewDnaOrderFile(self, openFileInEditor = True):
        """
        Opens a text editor and loads a temporary text file containing all the 
        DNA strand names and their sequences in the current DNA object. It will
        look something like this: 

        Strand1,ATCAGCTACGCATCGCT
        Strand2,TAGTCGATGCGTAGCGA
        ...
        Strandn, ...

        The user can then save the file to a permanent location using the 
        text editor the file is loaded (and displayed) in.

        @see: Ui_DnaFlyout.orderDnaCommand
        @see: writeDnaOrderFile()
        @TODO: assy.getAllDnaObjects(). 
        """
        dnaSequence = self.getDnaSequence(format = 'CSV')

        if dnaSequence: 
            tmpdir = find_or_make_Nanorex_subdir('temp')
            fileBaseName = 'DnaOrder'
            temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)            
            writeDnaOrderFile(temporaryFile, 
                              self.assy,
                              dnaSequence)      

            if openFileInEditor:
                open_file_in_editor(temporaryFile)

    def update_includeStrands(self, ignoreVal = 0):
        """
        Slot method for "Include (strands)" combobox.
        """
        
        idx = self.includeStrandsComboBox.currentIndex()
        
        includeType = ["model", "selection"]
        
        _numberOfBases = self.getNumberOfBases()
        self.numberOfBasesLineEdit.setText(str(_numberOfBases))
        
        if _numberOfBases > 0:
            self.viewDnaOrderFileButton.setEnabled(True)
            msg = "Click on <b>View DNA Order File...</b> to preview a " \
                "DNA order for all DNA strands in the current %s." \
                % includeType[idx]
        else:
            self.viewDnaOrderFileButton.setEnabled(False)
            msg = "<font color=red>" \
                "There are no DNA strands in the current %s." \
                % includeType[idx]
                
        self.updateMessage(msg)
            
class CompareProteins_PropertyManager(Command_PropertyManager):
    """
    The CompareProteins_PropertyManager class provides a Property Manager
    for the B{Compare Proteins} command on the Build Protein flyout toolbar.

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str

    @ivar proteinChunk1: The first currently selected protein to be compared.
    @type proteinChunk1: protein chunk

    @ivar proteinChunk2: The second currently selected protein to be compared.
    @type proteinChunk2: protein chunk
    """

    title = "Compare Proteins"
    pmName = title
    iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png"
    proteinChunk1 = None
    proteinChunk2 = None

    def __init__(self, command):
        """
        Constructor for the property manager.
        """
        self.threshold = 10.0

        _superclass.__init__(self, command)

        self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
        return

    def connect_or_disconnect_signals(self, isConnect=True):

        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.comparePushButton, SIGNAL("clicked()"), self._compareProteins)

        change_connect(self.thresholdDoubleSpinBox, SIGNAL("valueChanged(double)"), self._thresholdChanged)

        change_connect(self.hidePushButton, SIGNAL("clicked()"), self._hideDifferences)
        return

    def close(self):
        """
        Closes the Property Manager. Overrides EditCommand_PM.close()
        """

        env.history.statusbar_msg("")
        self._resetAminoAcids()
        _superclass.close(self)

        # Restore the original global display style.
        self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
        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.
        """
        _superclass.show(self)
        env.history.statusbar_msg("")

        # Force the Global Display Style to "Protein" since this is the only way
        # to see comparisons. The global display style will be restored when leaving
        # this command (via self.close()).
        self.originalDisplayStyle = self.o.displayMode
        self.o.setGlobalDisplayStyle(diPROTEIN)
        return

    def _addGroupBoxes(self):
        """
        Add the Property Manager group boxes.
        """
        self._pmGroupBox1 = PM_GroupBox(self, title="Compare")
        self._loadGroupBox1(self._pmGroupBox1)
        return

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        pass

    def _addToolTipText(self):
        """
        Tool Tip text for widgets in this Property Manager.
        """
        pass

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        """

        self.structure1LineEdit = PM_LineEdit(pmGroupBox, label="First structure:", setAsDefault=False)
        self.structure1LineEdit.setEnabled(False)

        self.structure2LineEdit = PM_LineEdit(pmGroupBox, label="Second structure:", setAsDefault=False)
        self.structure2LineEdit.setEnabled(False)

        self.thresholdDoubleSpinBox = PM_DoubleSpinBox(
            pmGroupBox,
            label="Threshold:",
            value=self.threshold,
            setAsDefault=True,
            minimum=0.0,
            maximum=360.0,
            decimals=1,
            singleStep=30.0,
            suffix=" deg",
            spanWidth=False,
        )

        self.comparePushButton = PM_PushButton(pmGroupBox, text="Compare", setAsDefault=True)

        self.hidePushButton = PM_PushButton(pmGroupBox, text="Hide differences", setAsDefault=True)
        return

    def _compareProteins(self):
        """
        Slot for Compare button.

        Compares two selected proteins of the same length.
        Amino acids that differ greater than the "threshold"
        value are displayed in two colors (red for the first protein
        and yellow for the second protein) and are only visible when
        the two proteins are displayed in the
        reduced display style.
        """
        from utilities.constants import red, orange, green, cyan

        if not self.proteinChunk1 or not self.proteinChunk2:
            return

        protein_1 = self.proteinChunk1.protein
        protein_2 = self.proteinChunk2.protein

        if protein_1 and protein_2:
            aa_list_1 = protein_1.get_amino_acids()
            aa_list_2 = protein_2.get_amino_acids()
            protein_1.collapse_all_rotamers()
            protein_2.collapse_all_rotamers()
            if len(aa_list_1) == len(aa_list_2):
                for aa1, aa2 in zip(aa_list_1, aa_list_2):
                    aa1.color = None
                    aa2.color = None
                    # aa1.collapse()
                    # aa2.collapse()
                    if aa1.get_one_letter_code() != aa2.get_one_letter_code():
                        aa1.set_color(red)
                        aa1.expand()
                        aa2.set_color(yellow)
                        aa2.expand()
                    else:
                        max = 0.0
                        for chi in range(0, 3):
                            angle1 = aa1.get_chi_angle(chi)
                            angle2 = aa2.get_chi_angle(chi)
                            if angle1 and angle2:
                                if angle1 < 0.0:
                                    angle1 += 360.0
                                if angle2 < 0.0:
                                    angle2 += 360.0
                                diff = abs(angle1 - angle2)
                                if diff > max:
                                    max = diff
                        if max >= self.threshold:
                            # This be a parameter.
                            aa1.set_color(green)
                            aa1.expand()
                            aa2.set_color(cyan)
                            aa2.expand()

                self.win.glpane.gl_update()
            else:
                msg = "The lengths of compared proteins are not equal."
                self.updateMessage(msg)
                env.history.redmsg(msg)
        return

    def _hideDifferences(self):
        """
        Slot for the "Hide differences" button.

        Hides amino acids that differ greater than the "threshold" value.

        @warning: Untested. Code looks suspicious.
        """
        if not self.proteinChunk1 or not self.proteinChunk2:
            return

        protein_1 = self.proteinChunk1.protein
        protein_2 = self.proteinChunk2.protein

        if protein_1 and protein_2:
            aa_list_1 = protein_1.get_amino_acids()
            aa_list_2 = protein_2.get_amino_acids()
            if len(aa_list_1) == len(aa_list_2):
                protein_1.collapse_all_rotamers()  # @@@
                protein_2.collapse_all_rotamers()  # @@@
                for aa1, aa2 in zip(aa_list_1, aa_list_2):
                    aa1.color = None
                    aa2.color = None
                    aa1.collapse()
                    aa2.collapse()
            self.win.glpane.gl_update()
        return

    def _thresholdChanged(self, value):
        """
        Slot for Threshold spinbox.
        """
        self.threshold = value
        self._compareProteins()
        return

    def _resetAminoAcids(self):
        """
        Resets the color and collapse all amino acids of all proteins.
        """

        proteinChunkList = getAllProteinChunksInPart(self.win.assy)

        for proteinChunk in proteinChunkList:
            proteinChunk.protein.collapse_all_rotamers()
            aa_list = proteinChunk.protein.get_amino_acids()
            for aa in aa_list:
                aa.color = None
                aa.collapse()

        self.win.glpane.gl_update()
        return

    def _update_UI_do_updates(self):
        """
        Overrides superclass method.

        @see: Command_PropertyManager._update_UI_do_updates()
        """

        self.proteinChunk1 = None
        self.proteinChunk2 = None
        self.comparePushButton.setEnabled(False)
        self.hidePushButton.setEnabled(False)

        selectedProteinList = self.win.assy.getSelectedProteinChunks()

        if len(selectedProteinList) == 0:
            self.structure1LineEdit.setText("")
            self.structure2LineEdit.setText("")
            msg = (
                "Select two structures of the same length in the graphics area, "
                "then click the <b>Compare</b> button to compare them."
            )

        elif len(selectedProteinList) == 1:
            self.proteinChunk1 = selectedProteinList[0]
            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
            self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)
            self.structure2LineEdit.setText("")
            msg = (
                "Select one more structure in the graphics area that is the same "
                "length as <b>" + self.proteinChunk1.name + "</b>. "
                "Then click the <b>Compare</b> button to compare them."
            )

        elif len(selectedProteinList) == 2:
            self.proteinChunk1 = selectedProteinList[0]
            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
            self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)

            self.proteinChunk2 = selectedProteinList[1]
            aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids()
            self.structure2LineEdit.setText(self.proteinChunk2.name + aa2_count)

            if aa1_count == aa2_count:
                self.comparePushButton.setEnabled(True)
                self.hidePushButton.setEnabled(True)
                msg = "Click the <b>Compare</b> button to compare the two selected structures."
            else:
                msg = "<b>%s</b> and <b>%s</b> are not the same length." % (
                    self.proteinChunk1.name,
                    self.proteinChunk2.name,
                )
                msg = redmsg(msg)

        else:
            self.structure1LineEdit.setText("")
            self.structure2LineEdit.setText("")
            msg = redmsg("Too many proteins selected.")

        self.updateMessage(msg)
        env.history.redmsg(msg)
        return
class InsertNanotube_PropertyManager( DnaOrCnt_PropertyManager):
    """
    The InsertNanotube_PropertyManager class provides a Property Manager
    for the B{Build > Nanotube > CNT} command.

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title         =  "Insert Nanotube"
    pmName        =  title
    iconPath      =  "ui/actions/Tools/Build Structures/InsertNanotube.png"

    def __init__( self, win, editCommand ):
        """
        Constructor for the Nanotube property manager.
        """
        self.endPoint1 = None
        self.endPoint2 = None

        self.nanotube = Nanotube() # A 5x5 CNT.

        _superclass.__init__( self,
                                 win,
                                 editCommand)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect( self.ntTypeComboBox,
                      SIGNAL("currentIndexChanged(const QString&)"),
                      self._ntTypeComboBoxChanged )

        change_connect(self.chiralityNSpinBox,
                       SIGNAL("valueChanged(int)"),
                       self._chiralityFixup)

        change_connect(self.chiralityMSpinBox,
                       SIGNAL("valueChanged(int)"),
                       self._chiralityFixup)

        change_connect(self.endingsComboBox,
                       SIGNAL("currentIndexChanged(const QString&)"),
                       self._endingsComboBoxChanged )

        # This spin box is currently hidden.
        change_connect(self.bondLengthDoubleSpinBox,
                       SIGNAL("valueChanged(double)"),
                       self._bondLengthChanged)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

    def ok_btn_clicked(self):
        """
        Slot for the OK button
        """
        if self.editCommand:
            self.editCommand.preview_or_finalize_structure(previewing = False)
            ##env.history.message(self.editCommand.logMessage)
        self.win.toolsDone()

    def cancel_btn_clicked(self):
        """
        Slot for the Cancel button.
        """
        if self.editCommand:
            self.editCommand.cancelStructure()
        self.win.toolsCancel()


    def _update_widgets_in_PM_before_show(self):
        """
        Update various widgets in this Property manager.
        Overrides MotorPropertyManager._update_widgets_in_PM_before_show.
        The various  widgets , (e.g. spinboxes) will get values from the
        structure for which this propMgr is constructed for
        (self.editcCntroller.struct)

        @see: MotorPropertyManager._update_widgets_in_PM_before_show
        @see: self.show where it is called.
        """
        pass

    def getFlyoutActionList(self):
        """
        Returns custom actionlist that will be used in a specific mode
        or editing a feature etc Example: while in movie mode,
        the _createFlyoutToolBar method calls this.
        """
        #'allActionsList' returns all actions in the flyout toolbar
        #including the subcontrolArea actions
        allActionsList = []

        #Action List for  subcontrol Area buttons.
        #In this mode there is really no subcontrol area.
        #We will treat subcontrol area same as 'command area'
        #(subcontrol area buttons will have an empty list as their command area
        #list). We will set  the Comamnd Area palette background color to the
        #subcontrol area.

        subControlAreaActionList =[]

        self.exitEditCommandAction.setChecked(True)
        subControlAreaActionList.append(self.exitEditCommandAction)

        separator = QAction(self.w)
        separator.setSeparator(True)
        subControlAreaActionList.append(separator)


        allActionsList.extend(subControlAreaActionList)

        #Empty actionlist for the 'Command Area'
        commandActionLists = []

        #Append empty 'lists' in 'commandActionLists equal to the
        #number of actions in subControlArea
        for i in range(len(subControlAreaActionList)):
            lst = []
            commandActionLists.append(lst)

        params = (subControlAreaActionList, commandActionLists, allActionsList)

        return params

    def _addGroupBoxes( self ):
        """
        Add the Insert Nanotube Property Manager group boxes.
        """

        self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" )
        self._loadGroupBox1( self._pmGroupBox1 )
        self._pmGroupBox1.hide()

        self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" )
        self._loadGroupBox2( self._pmGroupBox2 )

        self._displayOptionsGroupBox = PM_GroupBox( self,
                                                    title = "Display Options" )
        self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )

        self._pmGroupBox3 = PM_GroupBox( self, title = "Nanotube Distortion" )
        self._loadGroupBox3( self._pmGroupBox3 )
        self._pmGroupBox3.hide() #@ Temporary.

        self._pmGroupBox4 = PM_GroupBox( self, title = "Multi-Walled CNTs" )
        self._loadGroupBox4( self._pmGroupBox4 )
        self._pmGroupBox4.hide() #@ Temporary.

        self._pmGroupBox5 = PM_GroupBox( self, title = "Advanced Options" )
        self._loadGroupBox5( self._pmGroupBox5 )
        self._pmGroupBox5.hide() #@ Temporary.

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 1.
        """
        #Following toolbutton facilitates entering a temporary NanotubeLineMode
        #to create a CNT using endpoints of the specified line.
        self.specifyCntLineButton = PM_ToolButton(
            pmGroupBox,
            text = "Specify Endpoints",
            iconPath  = "ui/actions/Properties Manager/Pencil.png",
            spanWidth = True
        )
        self.specifyCntLineButton.setCheckable(True)
        self.specifyCntLineButton.setAutoRaise(True)
        self.specifyCntLineButton.setToolButtonStyle(
            Qt.ToolButtonTextBesideIcon)

        #EndPoint1 and endPoint2 coordinates. These widgets are hidden
        # as of 2007- 12 - 05
        self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                label = "End Point 1")
        self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
        self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
        self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox

        self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                label = "End Point 2")
        self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
        self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
        self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox

        self._endPoint1SpinBoxes.hide()
        self._endPoint2SpinBoxes.hide()

    def _loadGroupBox2(self, pmGroupBox):
        """
        Load widgets in group box 2.
        """

        _ntTypeChoices = ['Carbon',
                          'Boron Nitride']
        self.ntTypeComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Type:",
                         choices       =  _ntTypeChoices,
                         setAsDefault  =  True)

        self.ntRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  self.nanotube.getRise(),
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )

        self.ntRiseDoubleSpinBox.hide()

        # Nanotube Length
        self.ntLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Nanotube Length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.ntLengthLineEdit.setDisabled(True)
        self.ntLengthLineEdit.hide()

        # Nanotube diameter
        self.ntDiameterLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Diameter: ",
                         setAsDefault  =  False)

        self.ntDiameterLineEdit.setDisabled(True)
        self.updateNanotubeDiameter()

        self.chiralityNSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (n):",
                        value        = self.nanotube.getChiralityN(),
                        minimum      =  2,
                        maximum      =  100,
                        setAsDefault = True )

        self.chiralityMSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (m):",
                        value        = self.nanotube.getChiralityM(),
                        minimum      =  0,
                        maximum      =  100,
                        setAsDefault = True )

        # How about having user prefs for CNT and BNNT bond lengths?
        # I'm guessing that if the user wants to set these values, they will
        # do it once and would like those bond length values persist forever.
        # Need to discuss with others to determine if this spinbox comes out.
        # --Mark 2008-03-29
        self.bondLengthDoubleSpinBox = \
            PM_DoubleSpinBox( pmGroupBox,
                              label        = "Bond length:",
                              value        = self.nanotube.getBondLength(),
                              setAsDefault = True,
                              minimum      = 1.0,
                              maximum      = 3.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        #self.bondLengthDoubleSpinBox.hide()

        endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"]

        self.endingsComboBox= \
            PM_ComboBox( pmGroupBox,
                         label        = "Endings:",
                         choices      = endingChoices,
                         index        = 0,
                         setAsDefault = True,
                         spanWidth    = False )

    def _loadGroupBox3(self, inPmGroupBox):
        """
        Load widgets in group box 3.
        """

        self.zDistortionDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "Z-distortion:",
                              value        = 0.0,
                              setAsDefault = True,
                              minimum      = 0.0,
                              maximum      = 10.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        self.xyDistortionDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "XY-distortion:",
                              value        = 0.0,
                              setAsDefault = True,
                              minimum      = 0.0,
                              maximum      = 2.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

        self.twistSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Twist:",
                        value        = 0,
                        setAsDefault = True,
                        minimum      = 0,
                        maximum      = 100, # What should maximum be?
                        suffix       = " deg/A" )

        self.bendSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Bend:",
                        value        = 0,
                        setAsDefault = True,
                        minimum      = 0,
                        maximum      = 360,
                        suffix       = " deg" )

    def _loadGroupBox4(self, inPmGroupBox):
        """
        Load widgets in group box 4.
        """

        # "Number of Nanotubes" SpinBox
        self.mwntCountSpinBox = \
            PM_SpinBox( inPmGroupBox,
                        label        = "Number:",
                        value        = 1,
                        setAsDefault = True,
                        minimum      = 1,
                        maximum      = 10,
                        suffix       = " nanotubes" )

        self.mwntCountSpinBox.setSpecialValueText("SWNT")

        # "Spacing" lineedit.
        self.mwntSpacingDoubleSpinBox = \
            PM_DoubleSpinBox( inPmGroupBox,
                              label        = "Spacing:",
                              value        = 2.46,
                              setAsDefault = True,
                              minimum      = 1.0,
                              maximum      = 10.0,
                              singleStep   = 0.1,
                              decimals     = 3,
                              suffix       = " Angstroms" )

    def _loadGroupBox5(self, pmGroupBox):
        """
        Load widgets in group box 5.
        """
        self._rubberbandLineGroupBox = PM_GroupBox(
            pmGroupBox,
            title = 'Rubber band Line:')

        ntLineChoices = ['Ladder']
        self.ntRubberBandLineDisplayComboBox = \
            PM_ComboBox( self._rubberbandLineGroupBox ,
                         label         =  " Display as:",
                         choices       =  ntLineChoices,
                         setAsDefault  =  True)

        self.lineSnapCheckBox = \
            PM_CheckBox(self._rubberbandLineGroupBox ,
                        text         = 'Enable line snap' ,
                        widgetColumn = 1,
                        state        = Qt.Checked
                        )


    def _connect_showCursorTextCheckBox(self):
        """
        Connect the show cursor text checkbox with user prefs_key.
        Overrides
        DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
        """
        connect_checkbox_with_boolean_pref(
            self.showCursorTextCheckBox ,
            insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key )


    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
               [  #Format: (" checkbox text", prefs_key)

                   ("Nanotube length",
                    insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ),

                    ("Angle",
                     insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key )
                 ]

        return params


    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the Insert Nanotube Property Manager.
        """
        pass

    def _setEndPoints(self):
        """
        Set the two endpoints of the nanotube using the values from the
        X, Y, Z coordinate spinboxes in the property manager.

        @note: The group box containing the 2 sets of XYZ spin boxes are
        currently hidden.
        """
        # First endpoint (origin) of nanotube
        x1 = self.x1SpinBox.value()
        y1 = self.y1SpinBox.value()
        z1 = self.z1SpinBox.value()

        # Second endpoint (direction vector/axis) of nanotube.
        x2 = self.x2SpinBox.value()
        y2 = self.y2SpinBox.value()
        z2 = self.z2SpinBox.value()

        if not self.endPoint1:
            self.endPoint1 = V(x1, y1, z1)
        if not self.endPoint2:
            self.endPoint2 = V(x2, y2, z2)

        self.nanotube.setEndPoints(self.endPoint1, self.endPoint2)
            # Need arg "recompute=True", which will recompute the second
            # endpoint (endPoint2) using the nanotube rise.

    def getParameters(self):
        """
        Return the parameters from this property manager to be used to create
        the nanotube.

        @return: A nanotube instance with its attrs set to the current
                 parameters in the property manager.
        @rtype: L{Nanotube}

        @see: L{InsertNanotube_EditCommand._gatherParameters} where this is used
        """
        self._setEndPoints()
        return (self.nanotube)

    def _ntTypeComboBoxChanged( self, type ):
        """
        Slot for the Type combobox. It is called whenever the
        Type choice is changed.

        @param inIndex: The new index.
        @type  inIndex: int
        """
        self.nanotube.setType(str(type))
        print "Bond Length =", self.nanotube.getBondLength()
        self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength())
        #self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex])

    def _bondLengthChanged(self, bondLength):
        """
        Slot for the B{Bond Length} spinbox.
        """
        self.nanotube.setBondLength(bondLength)
        self.updateNanotubeDiameter()
        return

    def _chiralityFixup(self, spinBoxValueJunk = None):
        """
        Slot for several validators for different parameters.
        This gets called whenever the user changes the n, m chirality values.

        @param spinBoxValueJunk: This is the Spinbox value from the valueChanged
                                 signal. It is not used. We just want to know
                                 that the spinbox value has changed.
        @type  spinBoxValueJunk: double or None
        """
        _n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(),
                                            self.chiralityMSpinBox.value())

        #self.n, self.m = self.nanotube.getChirality()

        self.connect_or_disconnect_signals(isConnect = False)
        self.chiralityNSpinBox.setValue(_n)
        self.chiralityMSpinBox.setValue(_m)
        self.connect_or_disconnect_signals(isConnect = True)

        self.updateNanotubeDiameter()

    def updateNanotubeDiameter(self):
        """
        Update the nanotube Diameter lineEdit widget.
        """
        diameterText = "%-7.4f Angstroms" %  (self.nanotube.getDiameter())
        self.ntDiameterLineEdit.setText(diameterText)

        # ntRiseDoubleSpinBox is currently hidden.
        self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise())

    def _endingsComboBoxChanged(self, endings):
        """
        Slot for the B{Ending} combobox.

        @param endings: The option's text.
        @type  endings: string
        """
        self.nanotube.setEndings(str(endings))
        return

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_InsertNanotube_PropertyManager(self)
        return
Exemplo n.º 10
0
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager):
    """
    The DnaStrand_PropertyManager class provides a Property Manager
    for the DnaStrand_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 = "DnaStrand Properties"
    iconPath = "ui/actions/Properties Manager/Strand.png"

    def __init__(self, command):
        """
        Constructor for the Build DNA property manager.
        """

        self.sequenceEditor = None

        self._numberOfBases = 0
        self._conformation = 'B-DNA'
        self.dnaModel = 'PAM3'

        _superclass.__init__(self, command)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        return

    def _addGroupBoxes(self):
        """
        Add group boxes to this PM.
        """

        self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
        self._loadGroupBox1(self._pmGroupBox1)
        self._displayOptionsGroupBox = PM_GroupBox(self,
                                                   title="Display Options")
        self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)

        #Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here
        #so that the sequence editor gets connected! Perhaps
        #superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03
        self._loadSequenceEditor()
        return

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 1.
        """

        self.nameLineEdit = PM_LineEdit(pmGroupBox,
                                        label="Name:",
                                        text="",
                                        setAsDefault=False)

        self.numberOfBasesSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label         =  "Number of bases:",
                        value         =  self._numberOfBases,
                        setAsDefault  =  False,
                        minimum       =  2,
                        maximum       =  10000 )

        self.disableStructHighlightingCheckbox = \
            PM_CheckBox( pmGroupBox,
                         text         = "Don't highlight while editing DNA",
                         widgetColumn  = 0,
                         state        = Qt.Unchecked,
                         setAsDefault = True,
                         spanWidth = True
                         )

        #As of 2008-03-31, the properties such as number of bases will be
        #editable only by using the resize handles.
        self.numberOfBasesSpinBox.setEnabled(False)
        return

    def _loadSequenceEditor(self):
        """
        Temporary code  that shows the Sequence editor ..a doc widget docked
        at the bottom of the mainwindow. The implementation is going to change
        before 'rattleSnake' product release.
        As of 2007-11-20: This feature (sequence editor) is waiting
        for the ongoing dna model work to complete.
        """
        self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
        self.sequenceEditor.hide()
        return

    def _loadDisplayOptionsGroupBox(self, pmGroupBox):
        """
        Overrides superclass method.
        Also loads the color chooser widget.
        """
        self._loadColorChooser(pmGroupBox)
        _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
        return

    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,
            dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
        return

    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 bases",
                   dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),

                  ("Number of bases to be changed",
                   dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
                 ]

        return params

    def getParameters(self):
        name = self.nameLineEdit.text()
        numberOfBases = self.numberOfBasesSpinBox.value()
        dnaForm = self._conformation
        dnaModel = self.dnaModel
        color = self._colorChooser.getColor()

        return (numberOfBases, dnaForm, dnaModel, color, name)

    def setParameters(self, params):
        """
        This is usually called when you are editing an existing structure.
        It also gets called when selecting a new strand (within this command).
        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?
        """
        numberOfBases, \
            dnaForm, \
            dnaModel, \
            color, \
            name = params

        if numberOfBases is not None:
            self.numberOfBasesSpinBox.setValue(numberOfBases)
        if dnaForm is not None:
            self._conformation = dnaForm
        if dnaModel is not None:
            self.dnaModel = dnaModel

        if color is not None:
            self._colorChooser.setColor(color)

        if name:  # Minimal test. Should add a validator. --Mark 2008-12-16
            self.nameLineEdit.setText(name)

        # This gets called when we enter the command *and* when selecting a new
        # strand. In either case, we must update the sequence in the sequenece
        # editor. Fixes bug 2951. --Mark 2008-12-16
        if self.command and self.command.hasValidStructure():
            #print "setParameters(): loading sequence in sequence editor for ", name
            self.updateSequence(strand=self.command.struct)
        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 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

        if self.sequenceEditor:
            self.sequenceEditor.connect_or_disconnect_signals(isConnect)

        _superclass.connect_or_disconnect_signals(self, isConnect)

        change_connect(self.disableStructHighlightingCheckbox,
                       SIGNAL('stateChanged(int)'),
                       self.change_struct_highlightPolicy)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

        change_connect(self.nameLineEdit, SIGNAL("editingFinished()"),
                       self._nameChanged)
        return

    def _update_UI_do_updates(self):
        """
        @see: Command_PropertyManager. _update_UI_do_updates()
        @see: DnaStrand_EditCommand.command_update_UI()
        @see: DnaStrand_EditCommand.hasResizableStructure()
        """
        if not self.command.hasValidStructure():
            print "DnaStrand not a valid structure."
            self._pmGroupBox1.setEnabled(False)
            self._displayOptionsGroupBox.setEnabled(False)
            self.sequenceEditor.updateSequence(strand=" ")
            self.sequenceEditor.setEnabled(False)
            self.nameLineEdit.setText("")
            self.numberOfBasesSpinBox.setValue(0)
            return
        else:
            self._pmGroupBox1.setEnabled(True)
            self._displayOptionsGroupBox.setEnabled(True)
            self.sequenceEditor.setEnabled(True)

        isStructResizable, why_not = self.command.hasResizableStructure()
        if not isStructResizable:
            #disable all widgets
            if self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(False)
                msg1 = ("Attention: ") % (self.command.struct.name)
                msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \
                              (self.command.struct.name, why_not))
                self.updateMessage(msg1 + msg2)
        else:
            if not self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(True)
            msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name)
            msg2 = "Use resize handles to resize the strand. "\
                 "Use the <i>Sequence Editor</i> to edit the sequence."
            self.updateMessage(msg1 + msg2)
        return

    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)

        if self.sequenceEditor:
            self.sequenceEditor.close()

        _superclass.close(self)
        return

    def updateSequence(self, strand=None):
        """
        Public method provided for convenience. If any callers outside of this
        command need to update the sequence in the sequence editor, they can simply
        do DnaStrand_ProprtyManager.updateSequence() rather than
        DnaStrand_ProprtyManager.sequenceEditor.updateSequence()
        @see: Ui_DnaSequenceEditor.updateSequence()
        """
        if self.sequenceEditor:
            self.sequenceEditor.updateSequence(strand=strand)
        return

    def change_struct_highlightPolicy(self, checkedState=False):
        """
        Change the 'highlight policy' of the structure being edited
        (i.e. self.command.struct) .
        @param checkedState: The checked state of the checkbox that says
                             'Don't highlight while editing DNA'. So, it
                             its True, the structure being edited won't get
                             highlighted.
        @see: DnaStrand.setHighlightPolicy for more comments
        """
        if self.command and self.command.hasValidStructure():
            highlight = not checkedState
            self.command.struct.setHighlightPolicy(highlight=highlight)
        return

    def _addWhatsThisText(self):
        """
        Add what's this text.
        Abstract method.
        """
        pass

    def _nameChanged(self):  # Added by Mark. 2008-12-16
        """
        Slot for "Name" field. Changes the name of the strand if the user types
        in a new name.

        @warning: this lacks a validator. User can type in a name with invalid
                  characters.
        """
        if not self.command.hasValidStructure():
            return

        name = str(self.nameLineEdit.text())

        if not name:  # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16
            if self.command.hasValidStructure():
                self.nameLineEdit.setText(self.command.getStructureName())

            return

        self.command.setStructureName(name)

        self._update_UI_do_updates()  # Updates the message box.

        return
Exemplo n.º 11
0
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager):
    """
    The DnaStrand_PropertyManager class provides a Property Manager 
    for the DnaStrand_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 = "DnaStrand Properties"
    pmName = title
    iconPath = "ui/actions/Properties Manager/Strand.png"

    def __init__(self, win, editCommand):
        """
        Constructor for the Build DNA property manager.
        """

        #For model changed signal
        self.previousSelectionParams = None

        #see self.connect_or_disconnect_signals for comment about this flag
        self.isAlreadyConnected = False
        self.isAlreadyDisconnected = False

        self.sequenceEditor = None

        self._numberOfBases = 0
        self._conformation = 'B-DNA'
        self.duplexRise = 3.18
        self.basesPerTurn = 10
        self.dnaModel = 'PAM3'

        _superclass.__init__(self, win, editCommand)



        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

        self._loadSequenceEditor()

        msg = "Use resize handles to resize the strand. Use sequence editor"\
                   "to assign a new sequence or the current one to a file."
        self.updateMessage(msg)

    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="Strand name:",
                                        text="",
                                        setAsDefault=False)

        self.numberOfBasesSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label         =  "Number of bases:",
                        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.duplexRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  self.duplexRise,
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )

        self.disableStructHighlightingCheckbox = \
            PM_CheckBox( pmGroupBox,
                         text         = "Don't highlight while editing DNA",
                         widgetColumn  = 0,
                         state        = Qt.Unchecked,
                         setAsDefault = True,
                         spanWidth = True
                         )

        #As of 2008-03-31, the properties such as number of bases will be
        #editable only by using the resize handles. post FNANO we will support
        #the
        self.numberOfBasesSpinBox.setEnabled(False)
        self.basesPerTurnDoubleSpinBox.setEnabled(False)
        self.duplexRiseDoubleSpinBox.setEnabled(False)

    def _loadSequenceEditor(self):
        """
        Temporary code  that shows the Sequence editor ..a doc widget docked
        at the bottom of the mainwindow. The implementation is going to change
        before 'rattleSnake' product release.
        As of 2007-11-20: This feature (sequence editor) is waiting 
        for the ongoing dna model work to complete.
        """
        self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
        self.sequenceEditor.hide()

    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,
            dnaStrandEditCommand_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 bases",
                   dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),

                  ("Number of bases to be changed",
                   dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
                 ]

        return params

    def getParameters(self):
        numberOfBases = self.numberOfBasesSpinBox.value()
        dnaForm = self._conformation
        dnaModel = self.dnaModel
        basesPerTurn = self.basesPerTurn
        duplexRise = self.duplexRise
        color = self._colorChooser.getColor()

        return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise,
                color)

    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?  
        """
        #Set the duplex rise and bases per turn spinbox values.

        numberOfBases, \
                     dnaForm, \
                     dnaModel, \
                     basesPerTurn, \
                     duplexRise, \
                     color  = params

        if numberOfBases is not None:
            self.numberOfBasesSpinBox.setValue(numberOfBases)
        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 color is not None:
            self._colorChooser.setColor(color)

    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

        if self.sequenceEditor:
            self.sequenceEditor.connect_or_disconnect_signals(isConnect)

        _superclass.connect_or_disconnect_signals(self, isConnect)

        change_connect(self.disableStructHighlightingCheckbox,
                       SIGNAL('stateChanged(int)'),
                       self.change_struct_highlightPolicy)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

    def model_changed(self):
        """
        @see: DnaStrand_EditCommand.model_changed()
        @see: DnaStrand_EditCommand.hasResizableStructure()
        """
        isStructResizable, why_not = self.editCommand.hasResizableStructure()
        if not isStructResizable:
            #disable all widgets
            if self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(False)
                msg1 = ("Viewing properties of %s <br>") % (
                    self.editCommand.struct.name)
                msg2 = redmsg("DnaStrand is not resizable. Reason: %s" %
                              (why_not))
                self.updateMessage(msg1 + msg2)
        else:
            if not self._pmGroupBox1.isEnabled():
                self._pmGroupBox1.setEnabled(True)
                msg1 = ("Viewing properties of %s <br>") % (
                    self.editCommand.struct.name)
                msg2 = "Use resize handles to resize the strand. Use sequence editor"\
                    "to assign a new sequence or the current one to a file."
                self.updateMessage(msg1 + msg2)

    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
        This method also retrives the name information from the 
        editCommand's structure for its name line edit field. 
        @see: DnaStrand_EditCommand.getStructureName()
        @see: self.close()
        """
        _superclass.show(self)
        self._showSequenceEditor()

        if self.editCommand is not None:
            name = self.editCommand.getStructureName()
            if name is not None:
                self.nameLineEdit.setText(name)

    def close(self):
        """
        Close this property manager. 
        Also sets the name of the self.editCommand's structure to the one 
        displayed in the line edit field.
        @see self.show()
        @see: DnaSegment_EditCommand.setStructureName
        """
        if self.editCommand is not None:
            name = str(self.nameLineEdit.text())
            self.editCommand.setStructureName(name)

        if self.sequenceEditor:
            self.sequenceEditor.close()

        _superclass.close(self)

    def _showSequenceEditor(self):
        if self.sequenceEditor:
            if not self.sequenceEditor.isVisible():
                #Show the sequence editor
                #ATTENTION: the sequence editor also closes (temporarily) the
                #reports dockwidget (if visible) Its state is later restored when
                #the sequuence Editor is closed.
                self.sequenceEditor.show()

            self.updateSequence()

    def updateSequence(self):
        """
        Update the sequence string in the sequence editor
        @see: DnaSequenceEditor.setSequence()
        @see DnaSequenceEditor._determine_complementSequence()
        @see: DnaSequenceEditor.setComplementSequence()
        @see: DnaStrand.getStrandSequenceAndItsComplement()
        """
        #Read in the strand sequence of the selected strand and
        #show it in the text edit in the sequence editor.
        ##strand = self.strandListWidget.getPickedItem()

        if not self.editCommand.hasValidStructure():
            return

        strand = self.editCommand.struct

        titleString = 'Sequence Editor for ' + strand.name

        self.sequenceEditor.setWindowTitle(titleString)
        sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement(
        )
        if sequenceString:
            sequenceString = QString(sequenceString)
            sequenceString = sequenceString.toUpper()
            #Set the initial sequence (read in from the file)
            self.sequenceEditor.setSequence(sequenceString)

            #Set the initial complement sequence for DnaSequence editor.
            #do this independently because 'complementSequenceString' may have
            #some characters (such as * ) that denote a missing base on the
            #complementary strand. this information is used by the sequence
            #editor. See DnaSequenceEditor._determine_complementSequence()
            #for more details. See also bug 2787
            self.sequenceEditor.setComplementSequence(complementSequenceString)

    def change_struct_highlightPolicy(self, checkedState=False):
        """
        Change the 'highlight policy' of the structure being edited 
        (i.e. self.editCommand.struct) . 
        @param checkedState: The checked state of the checkbox that says 
                             'Don't highlight while editing DNA'. So, it 
                             its True, the structure being edited won't get
                             highlighted. 
        @see: DnaStrand.setHighlightPolicy for more comments        
        """
        if self.editCommand and self.editCommand.hasValidStructure():
            highlight = not checkedState
            self.editCommand.struct.setHighlightPolicy(highlight=highlight)

    def _addWhatsThisText(self):
        """
        Add what's this text. 
        Abstract method.
        """
        pass
class CompareProteins_PropertyManager(Command_PropertyManager):
    """
    The CompareProteins_PropertyManager class provides a Property Manager 
    for the B{Compare Proteins} command on the Build Protein flyout toolbar. 

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    
    @ivar proteinChunk1: The first currently selected protein to be compared.
    @type proteinChunk1: protein chunk
    
    @ivar proteinChunk2: The second currently selected protein to be compared.
    @type proteinChunk2: protein chunk
    """

    title = "Compare Proteins"
    pmName = title
    iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png"
    proteinChunk1 = None
    proteinChunk2 = None

    def __init__(self, command):
        """
        Constructor for the property manager.
        """
        self.threshold = 10.0

        _superclass.__init__(self, command)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        return

    def connect_or_disconnect_signals(self, isConnect=True):

        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.comparePushButton, SIGNAL("clicked()"),
                       self._compareProteins)

        change_connect(self.thresholdDoubleSpinBox,
                       SIGNAL("valueChanged(double)"), self._thresholdChanged)

        change_connect(self.hidePushButton, SIGNAL("clicked()"),
                       self._hideDifferences)
        return

    def close(self):
        """
        Closes the Property Manager. Overrides EditCommand_PM.close()
        """

        env.history.statusbar_msg("")
        self._resetAminoAcids()
        _superclass.close(self)

        # Restore the original global display style.
        self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
        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.
        """
        _superclass.show(self)
        env.history.statusbar_msg("")

        # Force the Global Display Style to "Protein" since this is the only way
        # to see comparisons. The global display style will be restored when leaving
        # this command (via self.close()).
        self.originalDisplayStyle = self.o.displayMode
        self.o.setGlobalDisplayStyle(diPROTEIN)
        return

    def _addGroupBoxes(self):
        """
        Add the Property Manager group boxes.
        """
        self._pmGroupBox1 = PM_GroupBox(self, title="Compare")
        self._loadGroupBox1(self._pmGroupBox1)
        return

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.  
        """
        pass

    def _addToolTipText(self):
        """
        Tool Tip text for widgets in this Property Manager.  
        """
        pass

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        """

        self.structure1LineEdit = \
            PM_LineEdit( pmGroupBox,
                         label         =  "First structure:",
                         setAsDefault  =  False)
        self.structure1LineEdit.setEnabled(False)

        self.structure2LineEdit = \
            PM_LineEdit( pmGroupBox,
                         label         =  "Second structure:",
                         setAsDefault  =  False)
        self.structure2LineEdit.setEnabled(False)

        self.thresholdDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Threshold:",
                              value         =  self.threshold,
                              setAsDefault  =  True,
                              minimum       =  0.0,
                              maximum       =  360.0,
                              decimals      =  1,
                              singleStep    =  30.0,
                              suffix        = " deg",
                              spanWidth = False)

        self.comparePushButton  = \
            PM_PushButton( pmGroupBox,
                         text         =  "Compare",
                         setAsDefault  =  True)

        self.hidePushButton  = \
            PM_PushButton( pmGroupBox,
                         text         =  "Hide differences",
                         setAsDefault  =  True)
        return

    def _compareProteins(self):
        """
        Slot for Compare button.
        
        Compares two selected proteins of the same length.
        Amino acids that differ greater than the "threshold" 
        value are displayed in two colors (red for the first protein 
        and yellow for the second protein) and are only visible when
        the two proteins are displayed in the
        reduced display style.
        """
        from utilities.constants import red, orange, green, cyan

        if not self.proteinChunk1 or \
           not self.proteinChunk2:
            return

        protein_1 = self.proteinChunk1.protein
        protein_2 = self.proteinChunk2.protein

        if protein_1 and \
           protein_2:
            aa_list_1 = protein_1.get_amino_acids()
            aa_list_2 = protein_2.get_amino_acids()
            protein_1.collapse_all_rotamers()
            protein_2.collapse_all_rotamers()
            if len(aa_list_1) == len(aa_list_2):
                for aa1, aa2 in zip(aa_list_1, aa_list_2):
                    aa1.color = None
                    aa2.color = None
                    #aa1.collapse()
                    #aa2.collapse()
                    if aa1.get_one_letter_code() != aa2.get_one_letter_code():
                        aa1.set_color(red)
                        aa1.expand()
                        aa2.set_color(yellow)
                        aa2.expand()
                    else:
                        max = 0.0
                        for chi in range(0, 3):
                            angle1 = aa1.get_chi_angle(chi)
                            angle2 = aa2.get_chi_angle(chi)
                            if angle1 and \
                               angle2:
                                if angle1 < 0.0:
                                    angle1 += 360.0
                                if angle2 < 0.0:
                                    angle2 += 360.0
                                diff = abs(angle1 - angle2)
                                if diff > max:
                                    max = diff
                        if max >= self.threshold:
                            # This be a parameter.
                            aa1.set_color(green)
                            aa1.expand()
                            aa2.set_color(cyan)
                            aa2.expand()

                self.win.glpane.gl_update()
            else:
                msg = "The lengths of compared proteins are not equal."
                self.updateMessage(msg)
                env.history.redmsg(msg)
        return

    def _hideDifferences(self):
        """
        Slot for the "Hide differences" button.
        
        Hides amino acids that differ greater than the "threshold" value. 
        
        @warning: Untested. Code looks suspicious.
        """
        if not self.proteinChunk1 or \
           not self.proteinChunk2:
            return

        protein_1 = self.proteinChunk1.protein
        protein_2 = self.proteinChunk2.protein

        if protein_1 and \
           protein_2:
            aa_list_1 = protein_1.get_amino_acids()
            aa_list_2 = protein_2.get_amino_acids()
            if len(aa_list_1) == len(aa_list_2):
                protein_1.collapse_all_rotamers()  #@@@
                protein_2.collapse_all_rotamers()  #@@@
                for aa1, aa2 in zip(aa_list_1, aa_list_2):
                    aa1.color = None
                    aa2.color = None
                    aa1.collapse()
                    aa2.collapse()
            self.win.glpane.gl_update()
        return

    def _thresholdChanged(self, value):
        """
        Slot for Threshold spinbox.
        """
        self.threshold = value
        self._compareProteins()
        return

    def _resetAminoAcids(self):
        """
        Resets the color and collapse all amino acids of all proteins.
        """

        proteinChunkList = getAllProteinChunksInPart(self.win.assy)

        for proteinChunk in proteinChunkList:
            proteinChunk.protein.collapse_all_rotamers()
            aa_list = proteinChunk.protein.get_amino_acids()
            for aa in aa_list:
                aa.color = None
                aa.collapse()

        self.win.glpane.gl_update()
        return

    def _update_UI_do_updates(self):
        """
        Overrides superclass method. 
        
        @see: Command_PropertyManager._update_UI_do_updates()
        """

        self.proteinChunk1 = None
        self.proteinChunk2 = None
        self.comparePushButton.setEnabled(False)
        self.hidePushButton.setEnabled(False)

        selectedProteinList = self.win.assy.getSelectedProteinChunks()

        if len(selectedProteinList) == 0:
            self.structure1LineEdit.setText("")
            self.structure2LineEdit.setText("")
            msg = "Select two structures of the same length in the graphics area, "\
                "then click the <b>Compare</b> button to compare them."

        elif len(selectedProteinList) == 1:
            self.proteinChunk1 = selectedProteinList[0]
            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids(
            )
            self.structure1LineEdit.setText(self.proteinChunk1.name +
                                            aa1_count)
            self.structure2LineEdit.setText("")
            msg = "Select one more structure in the graphics area that is the same "\
                "length as <b>" + self.proteinChunk1.name + "</b>. "\
                "Then click the <b>Compare</b> button to compare them."

        elif len(selectedProteinList) == 2:
            self.proteinChunk1 = selectedProteinList[0]
            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids(
            )
            self.structure1LineEdit.setText(self.proteinChunk1.name +
                                            aa1_count)

            self.proteinChunk2 = selectedProteinList[1]
            aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids(
            )
            self.structure2LineEdit.setText(self.proteinChunk2.name +
                                            aa2_count)

            if aa1_count == aa2_count:
                self.comparePushButton.setEnabled(True)
                self.hidePushButton.setEnabled(True)
                msg = "Click the <b>Compare</b> button to compare the two selected structures."
            else:
                msg = "<b>%s</b> and <b>%s</b> are not the same length." % \
                    (self.proteinChunk1.name, self.proteinChunk2.name)
                msg = redmsg(msg)

        else:
            self.structure1LineEdit.setText("")
            self.structure2LineEdit.setText("")
            msg = redmsg("Too many proteins selected.")

        self.updateMessage(msg)
        env.history.redmsg(msg)
        return
Exemplo n.º 13
0
class EditNanotube_PropertyManager(DnaOrCnt_PropertyManager):
    """
    The NanotubeSegmenta_PropertyManager class provides a Property Manager
    for the EditNanotube_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 = "Nanotube Properties"
    pmName = title
    iconPath = "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png"

    def __init__(self, command):
        """
        Constructor for the Cnt Segment Properties property manager.
        """

        #For model changed signal
        self.previousSelectionParams = None

        #see self.connect_or_disconnect_signals for comment about this flag
        self.isAlreadyConnected = False
        self.isAlreadyDisconnected = False

        # Initialized here. Their values will be set in
        # _update_widgets_in_PM_before_show()
        self.endPoint1 = V(0, 0, 0)
        self.endPoint2 = V(0, 0, 0)

        _superclass.__init__(self, command)


        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect

        change_connect(self.nameLineEdit, SIGNAL("editingFinished()"),
                       self._nameChanged)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)
        return

    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: EditNanotube_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: EditNanotube_EditCommand.setStructureName
        """
        if self.command is not None:
            name = str(self.nameLineEdit.text())
            self.command.setStructureName(name)
        _superclass.close(self)

    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,
            editNanotubeEditCommand_showCursorTextCheckBox_prefs_key)

    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
               [  #Format: (" checkbox text", prefs_key)

                  ("Nanotube length",
                   editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key)
                 ]

        return params

    def setParameters(self, params):
        """
        This is called when entering "Nanotube Segment Properties
        (i.e. "Edit properties...") to retrieve and set parameters of the
        nanotube segment that might be modified during this command and
        are needed to regenerate the nanotube segment.

        @param params: The parameters of the nanotube segment.
                       These parameters are retreived via
                       L{NanotubeSegment.getProps()}, called from
                       L{EditNanotube_EditCommand.editStructure()}.

                       Parameters:
                       - n, m (chirality)
                       - type (i.e. carbon or boron nitride)
                       - endings (none, hydrogen, nitrogen)
                       - endpoints (endPoint1, endPoint2)
        @type params: list (n, m), type, endings, (endPoint1, endPoint2)

        @note: Any widgets in the property manager that display these
        parameters should be updated here.

        @see: L{NanotubeSegment.getProps()}

        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?
        """
        (self.n, self.m), self.type, self.endings,\
            (self.endPoint1, self.endPoint2) = params

        # This is needed to update the endpoints since the Nanotube segment
        # may have been moved (i.e. translated or rotated). In that case,
        # the endpoints are not updated, so we recompute them here.
        nanotubeChunk = self.command.struct.members[0]
        self.endPoint1, self.endPoint2, radius = \
            self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk)

        if 0:
            print "\n--------------"
            print "setParameters():"
            print "Struct=", self.command.struct
            print "N, M:", self.n, self.m
            print "type:", self.type
            print "endings:", self.endings
            print "pt1, pt2:", self.endPoint1, self.endPoint2

    def getParameters(self):
        """
        Get the parameters that the edit command will use to determine if
        any have changed. If any have, then the nanotube will be modified.
        """
        if 0:
            print "\n--------------"
            print "getParameters():"
            print "Struct=", self.command.struct
            print "N, M:", self.n, self.m
            print "type:", self.type
            print "endings:", self.endings
            print "pt1, pt2:", self.endPoint1, self.endPoint2

        return (self.n, self.m, self.type, self.endings, self.endPoint1,
                self.endPoint2)

    def _update_widgets_in_PM_before_show(self):
        """
        This is called only when user is editing an existing structure.
        Its different than self.update_widgets_in_pm_before_show. (that method
        is called just before showing the property manager)
        @see: EditNanotube_EditCommand.editStructure()

        """
        if self.command and self.command.hasValidStructure():

            self.nanotube = self.command.struct.nanotube

            self.n, self.m = self.nanotube.getChirality()
            self.type = self.nanotube.getType()
            self.endings = self.nanotube.getEndings()
            self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints()
            pass

        # Note that _update_widgets_in_PM_before_show() is called in
        # self.show, before you connect the signals. So, for the
        # 'first show' we will need to manually set the value of any
        # widgets that need updated. But later, when a different
        # NanotubeSegment is clicked, (while still in
        # EditNanotube_EditCommand, the propMgr will already be connected
        # so any calls in that case is redundant.
        self.updateNameField()
        self.updateLength()
        self.updateNanotubeDiameter()
        self.updateChirality()

        return

    def _update_UI_do_updates(self):
        """
        Overrides superclass method.

        @see: Command_PropertyManager._update_UI_do_updates()
        """
        self._update_widgets_in_PM_before_show()

        if self.command.struct:
            msg = "Editing structure <b>%s</b>." % \
                self.command.getStructureName()
        else:
            msg = "Select a nanotube to edit."
        self.updateMessage(msg)
        return

    def _addGroupBoxes(self):
        """
        Add the 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="Name:",
                                        text="",
                                        setAsDefault=False)

        # Nanotube Length
        self.ntLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.ntLengthLineEdit.setDisabled(True)

        # Nanotube Radius
        self.ntDiameterLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Nanotube Diameter: ",
                         setAsDefault  =  False)

        self.ntDiameterLineEdit.setDisabled(True)

        # Nanotube chirality. These are disabled (read-only) for now. --Mark
        self.chiralityNSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (n) :",
                        minimum      =  2,
                        maximum      =  100,
                        setAsDefault = True )
        self.chiralityNSpinBox.setDisabled(True)

        self.chiralityMSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label        = "Chirality (m) :",
                        minimum      =  0,
                        maximum      =  100,
                        setAsDefault = True )
        self.chiralityMSpinBox.setDisabled(True)

    def _addWhatsThisText(self):
        """
        Add what's this text.
        """
        pass

    def _addToolTipText(self):
        """
        Add Tooltip text
        """
        pass

    def _nameChanged(self):
        """
        Slot for "Name" field.

        @TODO: Include a validator for the name field.
        """

        _name = str(self.nameLineEdit.text())

        if not _name:  # Minimal test. Need to implement a validator.
            self.updateNameField()
            return

        self.command.setStructureName(_name)
        msg = "Editing structure <b>%s</b>." % _name
        self.updateMessage(msg)

        return

    def updateNameField(self):
        """
        Update the name field showing the name of the currently selected protein.
        clear the combobox list.
        """

        if self.command.hasValidStructure():
            self.nameLineEdit.setEnabled(True)
            self.nameLineEdit.setText(self.command.getStructureName())
        else:
            self.nameLineEdit.setDisabled(True)
            self.nameLineEdit.setText("")
        return

    def updateLength(self):
        """
        Update the nanotube Length lineEdit widget.
        """
        if self.command.hasValidStructure():
            _nanotubeLength = vlen(self.endPoint1 - self.endPoint2)
            _lengthText = "%-7.4f Angstroms" % (_nanotubeLength)
        else:
            _lengthText = ""
        self.ntLengthLineEdit.setText(_lengthText)
        return

    def updateNanotubeDiameter(self):
        """
        Update the nanotube Diameter lineEdit widget.
        """
        if self.command.hasValidStructure():
            _diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
        else:
            _diameterText = ""
        self.ntDiameterLineEdit.setText(_diameterText)
        return

    def updateChirality(self):
        """
        Update the nanotube chirality spinboxes (read-only).
        """
        if self.command.hasValidStructure():
            n, m = self.nanotube.getChirality()
        else:
            n = 0
            m = 0
        self.chiralityNSpinBox.setValue(n)
        self.chiralityMSpinBox.setValue(m)
        return

    pass  # End of EditNanotube_PropertyManager class
class DnaDuplexPropertyManager( DnaOrCnt_PropertyManager ):
    """
    The DnaDuplexPropertyManager class provides a Property Manager
    for the B{Build > DNA > Duplex} command.

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title         =  "Insert DNA"
    pmName        =  title
    iconPath      =  "ui/actions/Tools/Build Structures/InsertDsDna.png"

    def __init__( self, win, editCommand ):
        """
        Constructor for the DNA Duplex property manager.
        """
        self.endPoint1 = None
        self.endPoint2 = None

        self._conformation  = "B-DNA"
        self._numberOfBases = 0
        self._basesPerTurn  = getDuplexBasesPerTurn(self._conformation)
        self._duplexRise    = getDuplexRise(self._conformation)
        self._duplexLength  = getDuplexLength(self._conformation,
                                              self._numberOfBases)


        _superclass.__init__( self,
                              win,
                              editCommand)

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_CANCEL_BUTTON | \
                                PM_WHATS_THIS_BUTTON)


    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect


        change_connect(self._placementOptions.buttonGroup,
                       SIGNAL("buttonClicked(int)"),
                       self.activateSpecifyReferencePlaneTool)

        change_connect( self.conformationComboBox,
                        SIGNAL("currentIndexChanged(int)"),
                        self.conformationComboBoxChanged )

        change_connect( self.numberOfBasePairsSpinBox,
                        SIGNAL("valueChanged(int)"),
                        self.numberOfBasesChanged )

        change_connect( self.basesPerTurnDoubleSpinBox,
                        SIGNAL("valueChanged(double)"),
                        self.basesPerTurnChanged )

        change_connect( self.duplexRiseDoubleSpinBox,
                        SIGNAL("valueChanged(double)"),
                        self.duplexRiseChanged )

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)
        
        self.duplexRiseDoubleSpinBox.connectWithState(
            Preferences_StateRef_double( bdnaRise_prefs_key, 
                                         env.prefs[bdnaRise_prefs_key] )
            )
        
        self.basesPerTurnDoubleSpinBox.connectWithState(
            Preferences_StateRef_double( bdnaBasesPerTurn_prefs_key, 
                                         env.prefs[bdnaBasesPerTurn_prefs_key] )
            )

        
                
 
    def ok_btn_clicked(self):
        """
        Slot for the OK button
        """
        if self.editCommand:
            self.editCommand.preview_or_finalize_structure(previewing = False)
            ##env.history.message(self.editCommand.logMessage)
        self.win.toolsDone()

    def cancel_btn_clicked(self):
        """
        Slot for the Cancel button.
        """
        if self.editCommand:
            self.editCommand.cancelStructure()
        self.win.toolsCancel()


    def _update_widgets_in_PM_before_show(self):
        """
        Update various widgets  in this Property manager.
        Overrides superclass method

        @see: MotorPropertyManager._update_widgets_in_PM_before_show
        @see: self.show where it is called.
        """
        pass

    def getFlyoutActionList(self):
        """ returns custom actionlist that will be used in a specific mode
        or editing a feature etc Example: while in movie mode,
        the _createFlyoutToolBar method calls
        this """


        #'allActionsList' returns all actions in the flyout toolbar
        #including the subcontrolArea actions
        allActionsList = []

        #Action List for  subcontrol Area buttons.
        #In this mode there is really no subcontrol area.
        #We will treat subcontrol area same as 'command area'
        #(subcontrol area buttons will have an empty list as their command area
        #list). We will set  the Comamnd Area palette background color to the
        #subcontrol area.

        subControlAreaActionList =[]

        self.exitEditCommandAction.setChecked(True)
        subControlAreaActionList.append(self.exitEditCommandAction)

        separator = QAction(self.w)
        separator.setSeparator(True)
        subControlAreaActionList.append(separator)


        allActionsList.extend(subControlAreaActionList)

        #Empty actionlist for the 'Command Area'
        commandActionLists = []

        #Append empty 'lists' in 'commandActionLists equal to the
        #number of actions in subControlArea
        for i in range(len(subControlAreaActionList)):
            lst = []
            commandActionLists.append(lst)

        params = (subControlAreaActionList, commandActionLists, allActionsList)

        return params

    def _addGroupBoxes( self ):
        """
        Add the DNA Property Manager group boxes.
        """
        self._pmReferencePlaneGroupBox = PM_GroupBox( self,
                                                      title = "Placement Options" )
        self._loadReferencePlaneGroupBox( self._pmReferencePlaneGroupBox )

        self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" )
        self._loadGroupBox1( self._pmGroupBox1 )

        self._pmGroupBox1.hide()

        self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" )
        self._loadGroupBox2( self._pmGroupBox2 )

        self._displayOptionsGroupBox = PM_GroupBox( self,
                                                    title = "Display Options" )
        self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )


    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box 3.
        """
        #Folllowing toolbutton facilitates entering a temporary DnaLineMode
        #to create a DNA using endpoints of the specified line.
        self.specifyDnaLineButton = PM_ToolButton(
            pmGroupBox,
            text = "Specify Endpoints",
            iconPath  = "ui/actions/Properties Manager/Pencil.png",
            spanWidth = True
        )
        self.specifyDnaLineButton.setCheckable(True)
        self.specifyDnaLineButton.setAutoRaise(True)
        self.specifyDnaLineButton.setToolButtonStyle(
            Qt.ToolButtonTextBesideIcon)

        #EndPoint1 and endPoint2 coordinates. These widgets are hidden
        # as of 2007- 12 - 05
        self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label = "End Point 1")
        self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
        self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
        self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox

        self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
                                                          label = "End Point 2")
        self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
        self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
        self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox

        self._endPoint1SpinBoxes.hide()
        self._endPoint2SpinBoxes.hide()

    def _loadGroupBox2(self, pmGroupBox):
        """
        Load widgets in group box 4.
        """

        self.conformationComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Conformation:",
                         choices       =  ["B-DNA"],
                         setAsDefault  =  True)

        dnaModelChoices = ['PAM3', 'PAM5']
        self.dnaModelComboBox = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Model:",
                         choices       =  dnaModelChoices,
                         setAsDefault  =  True)


        self.basesPerTurnDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Bases per turn:",
                              value         =  env.prefs[bdnaBasesPerTurn_prefs_key],
                              setAsDefault  =  True,
                              minimum       =  8.0,
                              maximum       =  20.0,
                              decimals      =  2,
                              singleStep    =  0.1 )
        
        
        self.duplexRiseDoubleSpinBox  =  \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Rise:",
                              value         =  env.prefs[bdnaRise_prefs_key],
                              setAsDefault  =  True,
                              minimum       =  2.0,
                              maximum       =  4.0,
                              decimals      =  3,
                              singleStep    =  0.01 )
        
        
        

        # Strand Length (i.e. the number of bases)
        self.numberOfBasePairsSpinBox = \
            PM_SpinBox( pmGroupBox,
                        label         =  "Base pairs:",
                        value         =  self._numberOfBases,
                        setAsDefault  =  False,
                        minimum       =  0,
                        maximum       =  10000 )

        self.numberOfBasePairsSpinBox.setDisabled(True)

        # Duplex Length
        self.duplexLengthLineEdit  =  \
            PM_LineEdit( pmGroupBox,
                         label         =  "Duplex length: ",
                         text          =  "0.0 Angstroms",
                         setAsDefault  =  False)

        self.duplexLengthLineEdit.setDisabled(True)


    def _loadDisplayOptionsGroupBox(self, pmGroupBox):
        """
        Load widgets in the Display Options GroupBox
        @see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
        """
        #Call the superclass method that loads the cursor text checkboxes.
        #Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
        #only loads the cursor text groupboxes. Subclasses like this can
        #call custom methods like self._loadCursorTextCheckBoxes etc if they
        #don't need all groupboxes that the superclass loads.
        _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)

        self._rubberbandLineGroupBox = PM_GroupBox(
            pmGroupBox,
            title = 'Rubber band line:')

        dnaLineChoices = ['Ribbons', 'Ladder']
        self.dnaRubberBandLineDisplayComboBox = \
            PM_ComboBox( self._rubberbandLineGroupBox ,
                         label         =  " Display as:",
                         choices       =  dnaLineChoices,
                         setAsDefault  =  True)

        self.lineSnapCheckBox = \
            PM_CheckBox(self._rubberbandLineGroupBox ,
                        text         = 'Enable line snap' ,
                        widgetColumn = 1,
                        state        = Qt.Checked
                    )

    def _connect_showCursorTextCheckBox(self):
        """
        Connect the show cursor text checkbox with user prefs_key.
        Overrides
        DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
        """
        connect_checkbox_with_boolean_pref(
            self.showCursorTextCheckBox ,
            dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)


    def _params_for_creating_cursorTextCheckBoxes(self):
        """
        Returns params needed to create various cursor text checkboxes connected
        to prefs_keys  that allow custom cursor texts.
        @return: A list containing tuples in the following format:
                ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
                uses this data to create checkboxes with the the given names and
                connects them to the provided preference keys. (Note that
                PM_PrefsCheckBoxes puts thes within a GroupBox)
        @rtype: list
        @see: PM_PrefsCheckBoxes
        @see: self._loadDisplayOptionsGroupBox where this list is used.
        @see: Superclass method which is overridden here --
        DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
        """
        params = \
        [  #Format: (" checkbox text", prefs_key)
            ("Number of base pairs",
             dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),

            ("Number of turns",
             dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),

            ("Duplex length",
             dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),

            ("Angle",
             dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]

        return params


    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the DNA Property Manager.
        """
        pass


    def conformationComboBoxChanged( self, inIndex ):
        """
        Slot for the Conformation combobox. It is called whenever the
        Conformation choice is changed.

        @param inIndex: The new index.
        @type  inIndex: int
        """
        conformation  =  self.conformationComboBox.currentText()

        if conformation == "B-DNA":
            self.basesPerTurnDoubleSpinBox.setValue("10.0")

        elif conformation == "Z-DNA":
            self.basesPerTurnDoubleSpinBox.setValue("12.0")

        else:
            msg = redmsg("conformationComboBoxChanged(): \
                         Error - unknown DNA conformation. Index = "+ inIndex)
            env.history.message(msg)

        self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))

    def numberOfBasesChanged( self, numberOfBases ):
        """
        Slot for the B{Number of Bases} spinbox.
        """
        # Update the Duplex Length lineEdit widget.
        text = str(getDuplexLength(self._conformation,
                                   numberOfBases,
                                   self._duplexRise)) \
             + " Angstroms"
        self.duplexLengthLineEdit.setText(text)
        return

    def basesPerTurnChanged( self, basesPerTurn ):
        """
        Slot for the B{Bases per turn} spinbox.
        """
        self.editCommand.basesPerTurn = basesPerTurn
        self._basesPerTurn = basesPerTurn
        return

    def duplexRiseChanged( self, rise ):
        """
        Slot for the B{Rise} spinbox.
        """
        self.editCommand.duplexRise = rise
        self._duplexRise = rise
        return

    def getParameters(self):
        """
        Return the parameters from this property manager
        to be used to create the DNA duplex.
        @return: A tuple containing the parameters
        @rtype: tuple
        @see: L{DnaDuplex_EditCommand._gatherParameters} where this is used
        """
        numberOfBases = self.numberOfBasePairsSpinBox.value()
        dnaForm  = str(self.conformationComboBox.currentText())
        basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
        duplexRise = self.duplexRiseDoubleSpinBox.value()

        dnaModel = str(self.dnaModelComboBox.currentText())

        # First endpoint (origin) of DNA duplex
        x1 = self.x1SpinBox.value()
        y1 = self.y1SpinBox.value()
        z1 = self.z1SpinBox.value()

        # Second endpoint (direction vector/axis) of DNA duplex.
        x2 = self.x2SpinBox.value()
        y2 = self.y2SpinBox.value()
        z2 = self.z2SpinBox.value()

        if not self.endPoint1:
            self.endPoint1 = V(x1, y1, z1)
        if not self.endPoint2:
            self.endPoint2 = V(x2, y2, z2)

        return (numberOfBases,
                dnaForm,
                dnaModel,
                basesPerTurn,
                duplexRise,
                self.endPoint1,
                self.endPoint2)

    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_DnaDuplexPropertyManager(self)
Exemplo n.º 15
0
class OrderDna_PropertyManager(Command_PropertyManager):
    """
    The OrderDna_PropertyManager class provides a Property Manager 
    for the B{Order Dna} command on the flyout toolbar in the 
    Build > Dna mode. 

    @ivar title: The title that appears in the property manager header.
    @type title: str

    @ivar pmName: The name of this property manager. This is used to set
                  the name of the PM_Dialog object via setObjectName().
    @type name: str

    @ivar iconPath: The relative path to the PNG file that contains a
                    22 x 22 icon image that appears in the PM header.
    @type iconPath: str
    """

    title         =  "Order DNA"
    pmName        =  title
    iconPath      =  "ui/actions/Command Toolbar/BuildDna/OrderDna.png"
    
    def __init__( self, command ):
        """
        Constructor for the property manager.
        """
        
        _superclass.__init__(self, command)
        
        self.assy = self.win.assy

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        
        self.update_includeStrands() # Updates the message box.
        return
        
        
    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot 
                          method. 
        @type  isConnect: boolean
        """
        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect 
        
        change_connect( self.viewDnaOrderFileButton,
                        SIGNAL("clicked()"), 
                        self.viewDnaOrderFile)
        
        change_connect( self.includeStrandsComboBox,
                      SIGNAL("activated(int)"),
                      self.update_includeStrands )
        return
       
    def _addGroupBoxes( self ):
        """
        Add the Property Manager group boxes.
        """        
        self._pmGroupBox1 = PM_GroupBox( self, title = "Options" )
        self._loadGroupBox1( self._pmGroupBox1 )
    
    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        """
        
        includeStrandsChoices = ["All strands in model",
                                 "Selected strands only"]
        
        self.includeStrandsComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Include strands:", 
                         choices       =  includeStrandsChoices,
                         setAsDefault  =  True)
        
        self.numberOfBasesLineEdit  = \
            PM_LineEdit( pmGroupBox,
                         label  =  "Total nucleotides:",
                         text   = str(self.getNumberOfBases()))
        self.numberOfBasesLineEdit.setEnabled(False)
        
        self.numberOfXBasesLineEdit  = \
            PM_LineEdit( pmGroupBox,
                         label  =  "Unassigned:",
                         text   = str(self.getNumberOfBases(unassignedOnly = True)))
        self.numberOfXBasesLineEdit.setEnabled(False)
        
        self.viewDnaOrderFileButton = \
            PM_PushButton( pmGroupBox,
                           label     = "",
                           text      = "View DNA Order File...",
                           spanWidth = True)
        return
    
    def _addWhatsThisText(self):
        """
        What's This text for widgets in this Property Manager.
        """
        whatsThis_OrderDna_PropertyManager(self)
        return
    
    def _addToolTipText(self):
        """
        Tool Tip text for widgets in the DNA Property Manager.  
        """
        pass
    
    # Ask Bruce where this should live (i.e. class Part?) --Mark
    def getAllDnaStrands(self, selectedOnly = False):
        """
        Returns a list of all the DNA strands in the current part, or only
        the selected strands if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the selected DNA strands.
        @type  selectedOnly: bool
        """
        
        dnaStrandList = []
         
        def func(node):
            if isinstance(node, DnaStrand):
                if selectedOnly:
                    if node.picked:
                        dnaStrandList.append(node)
                else:
                    dnaStrandList.append(node)
                    
        self.win.assy.part.topnode.apply2all(func)
        
        return dnaStrandList
    
    def getNumberOfBases(self, selectedOnly = False, unassignedOnly = False):
        """
        Returns the number of bases count for all the DNA strands in the 
        current part, or only the selected strand if I{selectedOnly} is True.
        
        @param selectedOnly: If True, return only the number of bases in the
                             selected DNA strands.
        @type  selectedOnly: bool
        
        @param unassignedOnly: If True, return only the number of unassigned
                               bases (i.e. base letters = X).
        @type  unassignedOnly: bool
        """
        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)
        
        for strand in strandList:
            strandSequenceString = str(strand.getStrandSequence())
            dnaSequenceString += strandSequenceString
        
        if unassignedOnly:
            return dnaSequenceString.count("X")
        
        return len(dnaSequenceString)
    
    def _update_UI_do_updates(self):
        """
        Overrides superclass method.
        """
        self.update_includeStrands()
        return
        
    def getDnaSequence(self, format = 'CSV'):
        """
        Return the complete Dna sequence information string (i.e. all strand 
        sequences) in the specified format. 
        
        @return: The Dna sequence string
        @rtype: string
        
        """
        if format == 'CSV': #comma separated values.
            separator = ','
            
        dnaSequenceString = ''
        selectedOnly = self.includeStrandsComboBox.currentIndex()
        strandList = self.getAllDnaStrands(selectedOnly)
        
        for strand in strandList:
            dnaSequenceString = dnaSequenceString + strand.name + separator
            strandSequenceString = str(strand.getStrandSequence())
            if strandSequenceString: 
                strandSequenceString = strandSequenceString.upper()
                strandLength = str(len(strandSequenceString)) + separator
                dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString
                
            dnaSequenceString = dnaSequenceString + "\n"
            
        return dnaSequenceString
        
    def viewDnaOrderFile(self, openFileInEditor = True):
        """
        Writes a DNA Order file in comma-separated values (CSV) format 
        and opens it in a text editor.

        The user must save the file to a permanent location using the 
        text editor.

        @see: Ui_DnaFlyout.orderDnaCommand
        @see: writeDnaOrderFile()
        @TODO: assy.getAllDnaObjects(). 
        """
        dnaSequence = self.getDnaSequence(format = 'CSV')

        if dnaSequence: 
            tmpdir = find_or_make_Nanorex_subdir('temp')
            fileBaseName = 'DnaOrder'
            temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)            
            writeDnaOrderFile(temporaryFile, 
                              self.assy,
                              self.getNumberOfBases(),
                              self.getNumberOfBases(unassignedOnly = True),
                              dnaSequence)      

            if openFileInEditor:
                open_file_in_editor(temporaryFile)
                
        return

    def update_includeStrands(self, ignoreVal = 0):
        """
        Slot method for "Include (strands)" combobox.
        """
        
        idx = self.includeStrandsComboBox.currentIndex()
        
        includeType = ["model", "selection"]
        
        _numberOfBases = self.getNumberOfBases()
        self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases")
        
        _numberOfXBases = self.getNumberOfBases(unassignedOnly = True)
        self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases")
        
        # Make the background color red if there are any unassigned bases.
        if _numberOfXBases:
            self.numberOfXBasesLineEdit.setStyleSheet(\
                "QLineEdit {"\
                "background-color: rgb(255, 0, 0)"\
                "}")
        else:
            self.numberOfXBasesLineEdit.setStyleSheet(\
                "QLineEdit {"\
                "background-color: rgb(255, 255, 255)"\
                "}")
        
        if _numberOfBases > 0:
            self.viewDnaOrderFileButton.setEnabled(True)
            msg = "Click on <b>View DNA Order File...</b> to preview a " \
                "DNA order for all DNA strands in the current %s." \
                % includeType[idx]
        else:
            self.viewDnaOrderFileButton.setEnabled(False)
            msg = "<font color=red>" \
                "There are no DNA strands in the current %s." \
                % includeType[idx]
                
        self.updateMessage(msg)
        return