# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details. """ DnaGeneratorPropertyManager.py WARNING: this file has been mostly superseded by DnaDuplexPropertyManager.py. @author: Will Ware @version: $Id$ @copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details. History: Ninad (Nov2006 and later): Ported it to Property manager with further enhancements Mark 2007-05-14: Organized code, added docstrings and renamed variables to make code more readable and understandable. Jeff 2007-06-13: - Major code cleanup (removed most abbreviations, standardized method names); - Added helper function getDuplexRise. - Added Duplex Length spinbox and handler methods (duplexLengthChange, update duplex length) - Revamped approach to sequence checking and editing. Jeff 2007-06-19: - Renamed class DnaPropMgr to DnaPropertyManager Mark 2007-08-07: - Now uses new PM module. Also renamed DnaPropertyManager to DnaGeneratorPropertyManager. Mark 2007-10-18: - Major rewrite of this module, superseding it -- DnaDuplexPropertyManager.py. """ # To do: # 1) Cursor/insertion point visibility: # - changes to the interior (not end) of the sequence/strand length must # be changed manually via direct selection and editing. # - try using a blinking vertical bar via HTML to represent the cursor # 2) Actions (reverse, complement, etc in _getSequence() should not purge # unrecognized characters. import foundation.env as env from dna.model.Dna_Constants import basesDict, dnaDict from dna.model.Dna_Constants import getComplementSequence from dna.model.Dna_Constants import getReverseSequence from dna.model.Dna_Constants import replaceUnrecognized from utilities.Log import redmsg, greenmsg, orangemsg from PyQt4.Qt import SIGNAL from PyQt4.Qt import QRegExp from PyQt4.Qt import QString from PyQt4.Qt import QTextCursor from PyQt4.Qt import QTextOption from PM.PM_ComboBox import PM_ComboBox from PM.PM_DoubleSpinBox import PM_DoubleSpinBox from PM.PM_GroupBox import PM_GroupBox from PM.PM_SpinBox import PM_SpinBox from PM.PM_TextEdit import PM_TextEdit from PM.PM_Dialog import PM_Dialog from widgets.DebugMenuMixin import DebugMenuMixin # DNA model type variables # (indices for model... and conformation... comboboxes). #@REDUCED_MODEL = 0 #@ATOMISTIC_MODEL = 1 BDNA = 0 ZDNA = 1 # Do not commit with DEBUG set to True. Mark 2007-08-07 DEBUG = False class DnaGeneratorPropertyManager( PM_Dialog, DebugMenuMixin ): """ The DnaGeneratorPropertyManager class provides a Property Manager for the "Build > Atoms" command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str @ivar validSymbols: Miscellaneous symbols that may appear in the sequence (but are ignored). The hyphen '-' is a special case that must be dealt with individually; it is not included because it can confuse regular expressions. @type validSymbols: QString """ title = "DNA" pmName = title iconPath = "ui/actions/Tools/Build Structures/DNA.png" validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?') # The following class variables guarantee the UI's menu items # are synchronized with their action code. The arrays should # not be changed, unless an item is removed or inserted. # Changes should be made via only the _action... variables. # e.g., Change _action_Complement from "Complement" # to "Complement Sequences". The menu item will # change and its related code will need no update. _action_Complement = "Complement" _action_Reverse = "Reverse" _action_RemoveUnrecognized = 'Remove unrecognized letters' _action_ConvertUnrecognized = 'Convert unrecognized letters to "N"' _actionChoices = [ "Action", "---", _action_Complement, _action_Reverse, _action_RemoveUnrecognized, _action_ConvertUnrecognized ] _modeltype_PAM3 = "PAM3" _modeltype_PAM5 = "PAM5" _modeltype_Atomistic = "Atomistic" # deprecated _modelChoices = [ _modeltype_PAM3, _modeltype_PAM5 ] def __init__( self ): """ Constructor for the DNA Generator property manager. """ PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title ) DebugMenuMixin._init1( self ) msg = "Edit the DNA parameters and select Preview to \ preview the structure. Click Done to insert it into \ the model." # This causes the "Message" box to be displayed as well. # setAsDefault=True causes this message to be reset whenever # this PM is (re)displayed via show(). Mark 2007-06-01. self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = True ) def _addGroupBoxes( self ): """ Add the DNA Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Strand Sequence" ) self._loadGroupBox1( self._pmGroupBox1 ) self._pmGroupBox2 = PM_GroupBox( self, title = "DNA Parameters" ) self._loadGroupBox2( self._pmGroupBox2 ) self._pmGroupBox3 = PM_GroupBox( self, title = "Endpoints" ) self._loadGroupBox3( self._pmGroupBox3 ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 1. """ # Duplex Length self.duplexLengthSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Duplex Length: ", value = 0, setAsDefault = False, minimum = 0, maximum = 34000, singleStep = self.getDuplexRise("B-DNA"), decimals = 3, suffix = ' Angstroms') self.connect( self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"), self.duplexLengthChanged ) # Strand Length self.strandLengthSpinBox = \ PM_SpinBox( pmGroupBox, label = "Strand Length :", value = 0, setAsDefault = False, minimum = 0, maximum = 10000, suffix = ' bases' ) self.connect( self.strandLengthSpinBox, SIGNAL("valueChanged(int)"), self.strandLengthChanged ) # New Base choices newBaseChoices = [] for theBase in basesDict.keys(): newBaseChoices = newBaseChoices \ + [ theBase + ' (' \ + basesDict[theBase]['Name'] + ')' ] try: defaultBaseChoice = basesDict.keys().index('N') except: defaultBaseChoice = 0 # Strand Sequence self.sequenceTextEdit = \ PM_TextEdit( pmGroupBox, label = "", spanWidth = True ) self.sequenceTextEdit.setCursorWidth(2) self.sequenceTextEdit.setWordWrapMode( QTextOption.WrapAnywhere ) self.connect( self.sequenceTextEdit, SIGNAL("textChanged()"), self.sequenceChanged ) self.connect( self.sequenceTextEdit, SIGNAL("cursorPositionChanged()"), self.cursorPosChanged ) # Actions self.actionsComboBox = \ PM_ComboBox( pmGroupBox, label = '', choices = self._actionChoices, index = 0, setAsDefault = True, spanWidth = True ) # If SIGNAL("activate(const QString&)") is used, we get a TypeError. # This is a bug that needs Bruce. Using currentIndexChanged(int) as # a workaround, but there is still a bug when the "Reverse" action # is selected. Mark 2007-08-15 self.connect( self.actionsComboBox, SIGNAL("currentIndexChanged(int)"), self.actionsComboBoxChanged ) def _loadGroupBox2( self, pmGroupBox ): """ Load widgets in group box 2. """ self.modelComboBox = \ PM_ComboBox( pmGroupBox, label = "Model :", choices = self._modelChoices, setAsDefault = True) self.conformationComboBox = \ PM_ComboBox( pmGroupBox, label = "Conformation :", choices = ["B-DNA"], setAsDefault = True) self.connect( self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged ) self.basesPerTurnComboBox= \ PM_ComboBox( pmGroupBox, label = "Bases Per Turn :", choices = ["10.0", "10.5", "10.67"], setAsDefault = True) # I may decide to reintroduce "base-pair chunks" at a later time. # Please talk to me if you have a strong feeling about including # this. Mark 2007-08-19. createChoices = ["Strand chunks", \ "Single chunk" ] #@ "Base-pair chunks"] self.createComboBox = \ PM_ComboBox( pmGroupBox, label = "Create :", choices = createChoices, index = 0, setAsDefault = True, spanWidth = False ) def _loadGroupBox3(self, pmGroupBox): """ Load widgets in group box 3. """ self._endPoint1GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint1" ) self._endPoint2GroupBox = PM_GroupBox( pmGroupBox, title = "Endpoint2" ) # Point 1 self.x1SpinBox = \ PM_DoubleSpinBox( self._endPoint1GroupBox, label = \ "ui/actions/Properties Manager/X_Coordinate.png", value = 0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') self.y1SpinBox = \ PM_DoubleSpinBox( self._endPoint1GroupBox, label = \ "ui/actions/Properties Manager/Y_Coordinate.png", value = 0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') self.z1SpinBox = \ PM_DoubleSpinBox( self._endPoint1GroupBox, label = \ "ui/actions/Properties Manager/Z_Coordinate.png", value = 0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') # Point 2 self.x2SpinBox = \ PM_DoubleSpinBox( self._endPoint2GroupBox, label = \ "ui/actions/Properties Manager/X_Coordinate.png", value = 10.0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') self.y2SpinBox = \ PM_DoubleSpinBox( self._endPoint2GroupBox, label = \ "ui/actions/Properties Manager/Y_Coordinate.png", value = 0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') self.z2SpinBox = \ PM_DoubleSpinBox( self._endPoint2GroupBox, label = \ "ui/actions/Properties Manager/Z_Coordinate.png", value = 0, setAsDefault = True, minimum = -100.0, maximum = 100.0, decimals = 3, suffix = ' Angstroms') def _addWhatsThisText( self ): """ What's This text for some of the widgets in the DNA Property Manager. @note: Many PM widgets are still missing their "What's This" text. """ self.conformationComboBox.setWhatsThis("""Conformation

There are three DNA geometries, A-DNA, B-DNA, and Z-DNA. Only B-DNA and Z-DNA are currently supported.

""") self.sequenceTextEdit.setWhatsThis("""Strand Sequence

Type in the strand sequence you want to generate here (5' => 3')

Recognized base letters:

A = Adenosine
C = Cytosine
G = Guanosine
T = Thymidine
N = aNy base
X = Unassigned

Other base letters currently recognized:

B = C,G, or T
D = A,G, or T
H = A,C, or T
V = A,C, or G
R = A or G (puRine)
Y = C or T (pYrimidine)
K = G or T (Keto)
M = A or C (aMino)
S = G or C (Strong -3H bonds)
W = A or T (Weak - 2H bonds)

""") self.actionsComboBox.setWhatsThis("""Action

Select an action to perform on the sequence.

""") def conformationComboBoxChanged( self, inIndex ): """ Slot for the Conformation combobox. It is called whenever the Conformation choice is changed. @param inIndex: The new index. @type inIndex: int """ self.basesPerTurnComboBox.clear() conformation = self.conformationComboBox.currentText() if conformation == "B-DNA": self.basesPerTurnComboBox.insertItem(0, "10.0") self.basesPerTurnComboBox.insertItem(1, "10.5") self.basesPerTurnComboBox.insertItem(2, "10.67") #10.5 is the default value for Bases per turn. #So set the current index to 1 self.basesPerTurnComboBox.setCurrentIndex(1) elif conformation == "Z-DNA": self.basesPerTurnComboBox.insertItem(0, "12.0") elif inIndex == -1: # Caused by clear(). This is tolerable for now. Mark 2007-05-24. conformation = "B-DNA" # Workaround for "Restore Defaults". pass else: msg = redmsg("conformationComboBoxChanged(): \ Error - unknown DNA conformation. Index = "+ inIndex) env.history.message(msg) self.duplexLengthSpinBox.setSingleStep( self.getDuplexRise(conformation) ) def modelComboBoxChanged( self, inIndex ): """ Slot for the Model combobox. It is called whenever the Model choice is changed. @param inIndex: The new index. @type inIndex: int """ conformation = self._modelChoices[ inIndex ] self.disconnect( self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged ) self.conformationComboBox.clear() # Generates signal! if conformation == self._modeltype_PAM3: self.conformationComboBox.addItem("B-DNA") elif conformation == self._modeltype_PAM5: self.conformationComboBox.addItem("B-DNA") elif conformation == self._modeltype_Atomistic: self.conformationComboBox.addItem("B-DNA") self.conformationComboBox.addItem("Z-DNA") elif inIndex == -1: # Caused by clear(). This is tolerable for now. Mark 2007-05-24. pass else: msg = "Error - unknown model representation. Index = " + inIndex env.history.message(redmsg(msg)) self.connect( self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged) # GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox. def getDuplexRise( self, inConformation ): """ Return the 'rise' between base pairs of the specified DNA type (conformation). @param inConformation: The current conformation. @type inConformation: int """ return dnaDict[str(inConformation)]['DuplexRise'] def synchronizeLengths( self ): """ Guarantees the values of the duplex length and strand length spinboxes agree with the strand sequence (textedit). """ self.updateStrandLength() self.updateDuplexLength() return # Added :jbirac 20070613: def duplexLengthChanged( self, inDuplexLength ): """ Slot for the duplex length spinbox, called whenever the value of the Duplex Length spinbox changes. @param inDuplexLength: The duplex length. @type inDuplexLength: float """ conformation = self.conformationComboBox.currentText() duplexRise = self.getDuplexRise( conformation ) newStrandLength = inDuplexLength / duplexRise + 0.5 newStrandLength = int( newStrandLength ) self.strandLengthChanged( newStrandLength ) def updateDuplexLength( self ): # Added :jbirac 20070615: """ Update the Duplex Length spinbox; always the length of the strand sequence multiplied by the 'rise' of the duplex. This method is called by slots of other controls (i.e., this itself is not a slot.) """ conformation = self.conformationComboBox.currentText() newDuplexLength = self.getDuplexRise( conformation ) \ * self.getSequenceLength() self.disconnect( self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"), self.duplexLengthChanged) self.duplexLengthSpinBox.setValue( newDuplexLength ) self.connect( self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"), self.duplexLengthChanged) # Renamed from length_changed :jbirac 20070613: def strandLengthChanged( self, inStrandLength ): """ Slot for the Strand Length spin box, called whenever the value of the Strand Length spin box changes. @param inStrandLength: The number of bases in the strand sequence. @type inStrandLength: int """ theSequence = self.getPlainSequence() sequenceLen = len( theSequence ) lengthChange = inStrandLength - self.getSequenceLength() # Preserve the cursor's position/selection cursor = self.sequenceTextEdit.textCursor() #cursorPosition = cursor.position() selectionStart = cursor.selectionStart() selectionEnd = cursor.selectionEnd() if inStrandLength < 0: return # Should never happen. if lengthChange < 0: # If length is less than the previous length, # simply truncate the current sequence. theSequence.chop( -lengthChange ) elif lengthChange > 0: # If length has increased, add the correct number of base # letters to the current strand sequence. numNewBases = lengthChange # Get current base selected in combobox. chosenBase = 'X' # Unassigned. basesToAdd = chosenBase * numNewBases theSequence.append( basesToAdd ) else: env.history.message( orangemsg( "strandLengthChanged(): Length has not changed." )) self.setSequence( theSequence ) return # Renamed from updateLength :jbirac 20070613: def updateStrandLength( self ): """ Update the Strand Length spinbox; always the length of the strand sequence. """ self.disconnect( self.strandLengthSpinBox, SIGNAL("valueChanged(int)"), self.strandLengthChanged ) self.strandLengthSpinBox.setValue( self.getSequenceLength() ) self.connect( self.strandLengthSpinBox, SIGNAL("valueChanged(int)"), self.strandLengthChanged ) return def sequenceChanged( self ): """ Slot for the Strand Sequence textedit widget. Assumes the sequence changed directly by user's keystroke in the textedit. Other methods... """ cursorPosition = self.getCursorPosition() theSequence = self.getPlainSequence() # Disconnect while we edit the sequence. self.disconnect( self.sequenceTextEdit, SIGNAL("textChanged()"), self.sequenceChanged ) # How has the text changed? if theSequence.length() == 0: # There is no sequence. self.updateStrandLength() self.updateDuplexLength() else: # Insert the sequence; it will be "stylized" by setSequence(). self.setSequence( theSequence ) # Reconnect to respond when the sequence is changed. self.connect( self.sequenceTextEdit, SIGNAL("textChanged()"), self.sequenceChanged ) self.synchronizeLengths() return def getPlainSequence( self, inOmitSymbols = False ): """ Returns a plain text QString (without HTML stylization) of the current sequence. All characters are preserved (unless specified explicitly), including valid base letters, punctuation symbols, whitespace and invalid letters. @param inOmitSymbols: Omits characters listed in self.validSymbols. @type inOmitSymbols: bool @return: The current DNA sequence in the PM. @rtype: QString """ outSequence = self.sequenceTextEdit.toPlainText() if inOmitSymbols: # This may look like a sloppy piece of code, but Qt's QRegExp # class makes it pretty tricky to remove all punctuation. theString = '[<>' \ + str( QRegExp.escape(self.validSymbols) ) \ + ']|-' outSequence.remove(QRegExp( theString )) return outSequence def stylizeSequence( self, inSequence ): """ Converts a plain text string of a sequence (including optional symbols) to an HTML rich text string. @param inSequence: A DNA sequence. @type inSequence: QString @return: The sequence. @rtype: QString """ outSequence = str(inSequence) # Verify that all characters (bases) in the sequence are "valid". invalidSequence = False basePosition = 0 sequencePosition = 0 invalidStartTag = "" invalidEndTag = "" previousChar = chr(1) # Null character; may be revised. # Some characters must be substituted to preserve # whitespace and tags in HTML code. substituteDict = { ' ':' ', '<':'<', '>':'>' } while basePosition < len(outSequence): theSeqChar = outSequence[basePosition] if ( theSeqChar in basesDict or theSeqChar in self.validSymbols ): # Close any preceding invalid sequence segment. if invalidSequence == True: outSequence = outSequence[:basePosition] \ + invalidEndTag \ + outSequence[basePosition:] basePosition += len(invalidEndTag) invalidSequence = False # Color the valid characters. if theSeqChar != previousChar: # We only need to insert 'color' tags in places where # the adjacent characters are different. if theSeqChar in basesDict: theTag = '' elif not previousChar in self.validSymbols: # The character is a 'valid' symbol to be greyed # out. Only one 'color' tag is needed for a # group of adjacent symbols. theTag = '' else: theTag = '' outSequence = outSequence[:basePosition] \ + theTag + outSequence[basePosition:] basePosition += len(theTag) # Any character must be substituted with an # ASCII code tag because the HTML engine will collapse # whitespace to a single character; whitespace # is truncated from the end of HTML by default. # Also, many symbol characters must be substituted # because they confuse the HTML syntax. #if str( outSequence[basePosition] ) in substituteDict: if outSequence[basePosition] in substituteDict: #theTag = substituteDict[theSeqChar] theTag = substituteDict[ outSequence[basePosition] ] outSequence = outSequence[:basePosition] \ + theTag \ + outSequence[basePosition + 1:] basePosition += len(theTag) - 1 else: # The sequence character is invalid (but permissible). # Tags (e.g., and ) must be inserted at both the # beginning and end of a segment of invalid characters. if invalidSequence == False: outSequence = outSequence[:basePosition] \ + invalidStartTag \ + outSequence[basePosition:] basePosition += len(invalidStartTag) invalidSequence = True basePosition += 1 previousChar = theSeqChar #basePosition += 1 # Specify that theSequence is definitely HTML format, because # Qt can get confused between HTML and Plain Text. outSequence = "" + outSequence outSequence += "" return outSequence def setSequence( self, inSequence, inStylize = True, inRestoreCursor = True ): """ Replace the current strand sequence with the new sequence text. @param inSequence: The new sequence. @type inSequence: QString @param inStylize: If True, inSequence will be converted from a plain text string (including optional symbols) to an HTML rich text string. @type inStylize: bool @param inRestoreCursor: Not implemented yet. @type inRestoreCursor: bool @attention: Signals/slots must be managed before calling this method. The textChanged() signal will be sent to any connected widgets. """ cursor = self.sequenceTextEdit.textCursor() selectionStart = cursor.selectionStart() selectionEnd = cursor.selectionEnd() if inStylize: inSequence = self.stylizeSequence( inSequence ) self.sequenceTextEdit.insertHtml( inSequence ) if inRestoreCursor: cursor.setPosition( min(selectionStart, self.getSequenceLength()), QTextCursor.MoveAnchor ) cursor.setPosition( min(selectionEnd, self.getSequenceLength()), QTextCursor.KeepAnchor ) self.sequenceTextEdit.setTextCursor( cursor ) return def getSequenceLength( self ): """ Returns the number of characters in the strand sequence textedit widget. """ theSequence = self.getPlainSequence( inOmitSymbols = True ) outLength = theSequence.length() return outLength def getCursorPosition( self ): """ Returns the cursor position in the strand sequence textedit widget. """ cursor = self.sequenceTextEdit.textCursor() return cursor.position() def cursorPosChanged( self ): """ Slot called when the cursor position changes. """ cursor = self.sequenceTextEdit.textCursor() if 0: env.history.message( greenmsg( "cursorPosChanged: Selection (" + str(cursor.selectionStart()) + " thru " + str(cursor.selectionEnd())+')' ) ) return def actionsComboBoxChanged( self, inIndex ): """ Slot for the Actions combobox. It is called whenever the Action choice is changed. @param inIndex: The index of the selected action choice. @type inIndex: int """ if inIndex == 0: # Very important. return actionName = str(self.actionsComboBox.currentText()) self.actionsComboBox.setCurrentIndex( 0 ) # Generates signal! self.invokeAction( actionName ) return def invokeAction( self, inActionName ): """ Applies an action on the current sequence displayed in the PM. @param inActionName: The action name. @type inActionName: str @return: The sequence after the action has been applied. @rtype: str """ sequence, allKnown = self._getSequence() outResult = "" if inActionName == self._action_Complement: outResult = getComplementSequence(sequence) elif inActionName == self._action_Reverse: outResult = getReverseSequence(sequence) elif inActionName == self._action_ConvertUnrecognized: outResult = replaceUnrecognized(sequence, replaceBase = 'N') self.setSequence( outResult ) elif inActionName == self._action_RemoveUnrecognized: outResult = replaceUnrecognized(sequence, replaceBase = '') self.setSequence( outResult ) return