path: root/cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_PropertyManager.py

# Copyright 2008 Nanorex, Inc.  See LICENSE file for details.
"""
ProteinDisplayStyle_PropertyManager.py

The ProteinDisplayStyle_PropertyManager class provides a Property Manager 
for the B{Display Style} command on the flyout toolbar in the 
Build > Protein mode. 

@author: Urmi
@version: $Id$ 
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History: Urmi copied this from DnaDisplayStyle_PropertyManager.py and modified
         it to suit the needs of protein display.
         
To do:
- Fix bug: a single rotamer is displayed (i.e. expanded) by default.
- Change "Style" factory setting to "Trace (ball and stick)
- Block widget signals to eliminate unneccessary repaints of the model view.
    (i.e. self.updateProteinDisplayStyleWidgets(blockSignals = True))

"""
import os, time, fnmatch
import foundation.env as env

from utilities.prefs_constants import getDefaultWorkingDirectory
from utilities.prefs_constants import workingDirectory_prefs_key
from utilities.Log import greenmsg
from utilities.constants import yellow, orange, red, magenta 
from utilities.constants import cyan, blue, white, black, gray
from utilities.constants import diPROTEIN

from PyQt4.Qt import SIGNAL
from PyQt4.Qt import Qt
from PyQt4.Qt import QFileDialog, QString, QMessageBox
from PM.PM_GroupBox import PM_GroupBox
from PM.PM_ComboBox import PM_ComboBox
from PM.PM_CheckBox import PM_CheckBox
from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
from PM.PM_ToolButtonRow import PM_ToolButtonRow
from PM.PM_Constants import PM_DONE_BUTTON
from PM.PM_Constants import PM_WHATS_THIS_BUTTON
from PM.PM_ColorComboBox import PM_ColorComboBox
from utilities.prefs_constants import proteinStyle_prefs_key
from utilities.prefs_constants import proteinStyleSmooth_prefs_key
from utilities.prefs_constants import proteinStyleQuality_prefs_key
from utilities.prefs_constants import proteinStyleScaling_prefs_key
from utilities.prefs_constants import proteinStyleScaleFactor_prefs_key
from utilities.prefs_constants import proteinStyleColors_prefs_key
from utilities.prefs_constants import proteinStyleAuxColors_prefs_key
from utilities.prefs_constants import proteinStyleCustomColor_prefs_key 
from utilities.prefs_constants import proteinStyleAuxCustomColor_prefs_key 
from utilities.prefs_constants import proteinStyleColorsDiscrete_prefs_key 
from utilities.prefs_constants import proteinStyleHelixColor_prefs_key 
from utilities.prefs_constants import proteinStyleStrandColor_prefs_key
from utilities.prefs_constants import proteinStyleCoilColor_prefs_key
from utilities.Log import redmsg

from command_support.Command_PropertyManager import Command_PropertyManager

proteinDisplayStylePrefsList = \
                         [proteinStyle_prefs_key,
                          proteinStyleSmooth_prefs_key,
                          proteinStyleQuality_prefs_key, 
                          proteinStyleScaling_prefs_key, 
                          proteinStyleScaleFactor_prefs_key, 
                          proteinStyleColors_prefs_key, 
                          proteinStyleAuxColors_prefs_key, 
                          proteinStyleCustomColor_prefs_key, 
                          proteinStyleAuxCustomColor_prefs_key, 
                          proteinStyleColorsDiscrete_prefs_key, 
                          proteinStyleHelixColor_prefs_key, 
                          proteinStyleStrandColor_prefs_key, 
                          proteinStyleCoilColor_prefs_key ]

# Protein Display Style Favorite File I/O functions. 
def writeProteinDisplayStyleSettingsToFavoritesFile( basename ):
    
    """
    Writes a "favorite file" (with a .txt extension) to store all the
    Protein display style settings (pref keys and their current values).

    @param basename: The filename (without the .fav extension) to write.
    @type  basename: string

    @note: The favorite file is written to the directory
            $HOME/Nanorex/Favorites/ProteinDisplayStyle.
    """
    if not basename:
        return 0, "No name given."

    # Get filename and write the favorite file.
    favfilepath = getFavoritePathFromBasename(basename)
    writeDnaFavoriteFile(favfilepath)
    return 1, basename


def getFavoritePathFromBasename( basename ):
    """
    Returns the full path to the favorite file given a basename.

    @param basename: The favorite filename (without the .txt extension).
    @type  basename: string

    @note: The (default) directory for all favorite files is
           $HOME/Nanorex/Favorites/ProteinDisplayStyle.
    """
    _ext = "txt"

    # Make favorite filename (i.e. ~/Nanorex/Favorites/ProteinDisplayStyleFavorites/basename.txt)
    from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
    _dir = find_or_make_Nanorex_subdir('Favorites/ProteinDisplayStyle')
    return os.path.join(_dir, "%s.%s" % (basename, _ext))

def writeDnaFavoriteFile( filename ):
    """
    Writes a favorite file to I{filename}.
    """
    f = open(filename, 'w')

    # Write header
    f.write ('!\n! Protein display style favorite file')
    f.write ('\n!Created by NanoEngineer-1 on ')
    timestr = "%s\n!\n" % time.strftime("%Y-%m-%d at %H:%M:%S")
    f.write(timestr)

    #write preference list in file without the NE version
    for pref_key in proteinDisplayStylePrefsList:
        val = env.prefs[pref_key]

        pref_keyArray = pref_key.split("/")
        pref_key = pref_keyArray[1]

        if isinstance(val, int):
            f.write("%s = %d\n" % (pref_key, val))
        elif isinstance(val, float):
            f.write("%s = %-6.2f\n" % (pref_key, val))
        elif isinstance(val, bool):
            f.write("%s = %d\n" % (pref_key, val))
        else:
            print "Not sure what pref_key '%s' is." % pref_key

    f.close()


def loadFavoriteFile( filename ):
    """
    Loads a favorite file from anywhere in the disk.

    @param filename: The full path for the favorite file.
    @type  filename: string
    """
    if os.path.exists(filename):
        favoriteFile = open(filename, 'r')
    else:
        env.history.message("Favorite file to be loaded does not exist.")
        return 0

    # do syntax checking on the file to figure out whether this is a valid
    # favorite file
    line = favoriteFile.readline()
    line = favoriteFile.readline()

    if line != "! DNA display style favorite file\n":
        env.history.message(" Not a proper favorite file")
        favoriteFile.close()
        return 0

    while 1:
        line = favoriteFile.readline()
        # marks the end of file
        if line == "":
            break

        # process each line to obtain pref_keys and their corresponding values
        if line[0] != '!':

            keyValuePair = line.split('=')
            pref_keyString = keyValuePair[0].strip()
            pref_value=keyValuePair[1].strip()

            # check if pref_value is an integer or float. Booleans currently
            # stored as integer as well.
            try:
                int(pref_value)
                pref_valueToStore = int(pref_value)
            except ValueError:
                pref_valueToStore = float(pref_value)

            # match pref_keyString with its corresponding variable name in the
            # preference key list
            pref_key = findPrefKey( pref_keyString )
            #add preference key and its corresponding value to the dictionary
            if pref_key:
                env.prefs[pref_key] = pref_valueToStore
    favoriteFile.close()

    #check if a copy of this file exists in the favorites directory. If not make
    # a copy of it in there
    favName = os.path.basename(str(filename))
    name = favName[0:len(favName)-4]
    favfilepath = getFavoritePathFromBasename(name)

    if not os.path.exists(favfilepath):
        saveFavoriteFile(favfilepath, filename)
    return 1


def findPrefKey( pref_keyString ):
    """
    Matches prefence key in the proteinDisplayStylePrefsList with pref_keyString
    from the favorte file that we intend to load.

    @param pref_keyString: preference from the favorite file to be loaded.
    @type  pref_keyString: string

    @note: very inefficient since worst case time taken is proportional to the
    size of the list. If original preference strings are in a dictionary, access
    can be done in constant time

    """

    for keys in proteinDisplayStylePrefsList:
        #split keys in dnaDisplayStylePrefList into version number and pref_key
        pref_array= keys.split("/")
        if pref_array[1] == pref_keyString:
            return keys
    return None

def saveFavoriteFile( savePath, fromPath ):
    """
    Save favorite file to anywhere in the disk

    @param savePath: full path for the location where the favorite file is to be saved.
    @type  savePath: string

    @param savePath: ~/Nanorex/Favorites/DnaDisplayStyle/$FAV_NAME.txt
    @type  fromPath: string
    """
    if savePath:
        saveFile = open(savePath, 'w')
    if fromPath:
        fromFile = open(fromPath, 'r')

    lines=fromFile.readlines()
    saveFile.writelines(lines)

    saveFile.close()
    fromFile.close()

    return

# =
_superclass = Command_PropertyManager
class ProteinDisplayStyle_PropertyManager(Command_PropertyManager):
    """
    The ProteinDisplayStyle_PropertyManager class provides a Property Manager 
    for the B{Display Style} command on the flyout toolbar in the 
    Build > Protein 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         =  "Edit Protein Display Style"
    pmName        =  title
    iconPath      =  "ui/actions/Edit/EditProteinDisplayStyle.png"
    
    def __init__( self, command ):
        """
        Constructor for the property manager.
        """

                     
        self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
        
        _superclass.__init__(self, command)        
        

        self.showTopRowButtons( PM_DONE_BUTTON | \
                                PM_WHATS_THIS_BUTTON)
        
     
        msg = "Modify the protein display settings below."
        self.updateMessage(msg)

    def connect_or_disconnect_signals(self, isConnect = True):
        """
        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 
        
        # Favorite buttons signal-slot connections.
        change_connect( self.applyFavoriteButton,
                        SIGNAL("clicked()"), 
                       self.applyFavorite)
        

        change_connect( self.addFavoriteButton,
                        SIGNAL("clicked()"), 
                       self.addFavorite)
        
        change_connect( self.deleteFavoriteButton,
                        SIGNAL("clicked()"), 
                       self.deleteFavorite)
        
        change_connect( self.saveFavoriteButton,
                        SIGNAL("clicked()"), 
                       self.saveFavorite)
        
        change_connect( self.loadFavoriteButton,
                        SIGNAL("clicked()"), 
                       self.loadFavorite)
        
        #Display group box signal slot connections
        change_connect(self.proteinStyleComboBox,
                       SIGNAL("currentIndexChanged(int)"),
                       self.changeProteinDisplayStyle)
        
        change_connect(self.smoothingCheckBox,
                       SIGNAL("stateChanged(int)"),
                       self.smoothProteinDisplay)
        change_connect(self.scaleComboBox,
                       SIGNAL("currentIndexChanged(int)"),
                       self.changeProteinDisplayScale)
        change_connect(self.splineDoubleSpinBox,
                       SIGNAL("valueChanged(double)"),
                       self.changeProteinSplineValue)
        change_connect(self.scaleFactorDoubleSpinBox,
                       SIGNAL("valueChanged(double)"),
                       self.changeProteinScaleFactor)
        
        #color groupbox
        change_connect(self.proteinComponentComboBox,
                       SIGNAL("currentIndexChanged(int)"),
                       self.chooseProteinComponent)
        
        change_connect(self.proteinAuxComponentComboBox,
                       SIGNAL("currentIndexChanged(int)"),
                       self.chooseAuxilliaryProteinComponent)        
        
        change_connect(self.customColorComboBox,
                       SIGNAL("editingFinished()"),
                       self.chooseCustomColor)
        
        change_connect(self.auxColorComboBox,
                       SIGNAL("editingFinished()"),
                       self.chooseAuxilliaryColor)
        
        #change_connect(self.discColorCheckBox,
        #               SIGNAL("stateChanged(int)"),
        #               self.setDiscreteColors)
        
        change_connect(self.helixColorComboBox,
                       SIGNAL("editingFinished()"),
                       self.chooseHelixColor)
        
        change_connect(self.strandColorComboBox,
                       SIGNAL("editingFinished()"),
                       self.chooseStrandColor)
        
        change_connect(self.coilColorComboBox,
                       SIGNAL("editingFinished()"),
                       self.chooseCoilColor)

    #Protein Display methods         
        
    def  changeProteinDisplayStyle(self, idx):
        """
        Change protein display style
        
        @param idx: index of the protein display style combo box
        @type idx: int
        """
        env.prefs[proteinStyle_prefs_key] = idx
        return
    
    def  changeProteinDisplayQuality(self, idx):
        
        env.prefs[proteinStyleQuality_prefs_key] = idx
        return
    
    def  smoothProteinDisplay(self, state):
        """
        Smoooth protein display.
        
        @param state: state of the smooth protein display check box.
        @type state: int
        """
        if state == Qt.Checked:
            env.prefs[proteinStyleSmooth_prefs_key] = True
        else:
            env.prefs[proteinStyleSmooth_prefs_key] = False
        return
    
    def  changeProteinDisplayScale(self, idx):
        """
        Change protein display scale
        
        @param idx: index of the protein display scaling choices combo box
        @type idx: int
        """
        env.prefs[proteinStyleScaling_prefs_key] = idx
        return
    
    def changeProteinSplineValue(self, val):
        """
        Change protein display resolution
        @param val: value in the protein display resolution double spinbox
        @type val: double
        """
        env.prefs[proteinStyleQuality_prefs_key] = val
        return
    
    def changeProteinScaleFactor(self, val):
        """
        Change protein display scale factor
        
        @param val: value in the protein display scale factor double spinbox
        @type val: double
        """
        env.prefs[proteinStyleScaleFactor_prefs_key] = val
        return
    
    def chooseProteinComponent(self, idx):
        """
        Choose protein component to set the color of 
        
        @param idx: index of the protein component choices combo box
        @type idx: int
        """
        env.prefs[proteinStyleColors_prefs_key] = idx
        return
    
    def chooseAuxilliaryProteinComponent(self, idx):
        """
        Choose auxilliary protein component to set the color of 
        
        @param idx: index of the auxilliary protein component choices combo box
        @type idx: int
        """
        env.prefs[proteinStyleAuxColors_prefs_key] = idx - 1
        return
    
    def chooseCustomColor(self):
        """
        Choose custom color of the chosen protein component
        """
        color = self.customColorComboBox.getColor()
        env.prefs[proteinStyleCustomColor_prefs_key] = color
        return
    
    def chooseAuxilliaryColor(self):
        """
        Choose custom color of the chosen auxilliary protein component
        """
        color = self.auxColorComboBox.getColor()
        env.prefs[proteinStyleAuxCustomColor_prefs_key] = color
        return  
    
        
    def chooseHelixColor(self):
        """
        Choose helix color
        """
        color = self.helixColorComboBox.getColor()
        env.prefs[proteinStyleHelixColor_prefs_key] = color
        return
    
    def chooseStrandColor(self):
        """
        Choose strand color
        """
        color = self.strandColorComboBox.getColor()
        env.prefs[proteinStyleStrandColor_prefs_key] = color
        return     
    
    def chooseCoilColor(self):
        """
        Choose coil color
        """
        color = self.coilColorComboBox.getColor()
        env.prefs[proteinStyleCoilColor_prefs_key] = color
        return     
    
    def setDiscreteColors(self, state):
        """
        Set discrete colors.
        
        @param state: state of the set discrete colors check box.
        @type state: int
        """
        if state == Qt.Checked:
            env.prefs[proteinStyleColorsDiscrete_prefs_key] = True
        else:
            env.prefs[proteinStyleColorsDiscrete_prefs_key] = False
        return
    
    
    def show_OLD(self):
        """
        Shows the Property Manager.Extends superclass method. 
        """
        #@REVIEW: See comment in CompareProteins_PropertyManager
        self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
        self.sequenceEditor.hide()        
        
        self.updateProteinDisplayStyleWidgets()
        
        _superclass.show(self)
        
    def show(self):
        """
        Shows the Property Manager. Extends superclass method
        """
        _superclass.show(self)
        
        #@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
        #-- Ninad 2008-10-02

        # Force the Global Display Style to "DNA Cylinder" so the user
        # can see the display style setting effects on any DNA in the current
        # model. The current global display style will be restored when leaving
        # this command (via self.close()).
        self.originalDisplayStyle = self.o.displayMode
            # TODO: rename that public attr of GLPane (widely used)
            # from displayMode to displayStyle. [bruce 080910 comment]
        self.o.setGlobalDisplayStyle(diPROTEIN)

        # Update all PM widgets, .
        # note: It is important to update the widgets by blocking the 
        # 'signals'. If done in the reverse order, it will generate signals 
        #when updating the PM widgets (via updateDnaDisplayStyleWidgets()), 
        #causing unneccessary repaints of the model view.
        self.updateProteinDisplayStyleWidgets()#@@@ blockSignals = True)
        return
    
    def close(self):
        """
        Closes the Property Manager. Extends superclass method.
        """
        _superclass.close(self)

        # Restore the original global display style.
        self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
        return
    
    def _addGroupBoxes( self ):
        """
        Add the Property Manager group boxes.
        """
        self._pmGroupBox1 = PM_GroupBox( self,
                                         title = "Favorites")
        self._loadGroupBox1( self._pmGroupBox1 )

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

        self._pmGroupBox3 = PM_GroupBox( self,
                                         title = "Color")
        self._loadGroupBox3( self._pmGroupBox3 )

    def _loadGroupBox1(self, pmGroupBox):
        """
        Load widgets in group box.
        @param pmGroupBox: group box that contains various favorite buttons
        @see: L{PM_GroupBox}  
        """
        # Other info
        # Not only loads the factory default settings but also all the favorite
        # files stored in the ~/Nanorex/Favorites/ProteinDisplayStyle directory
        favoriteChoices = ['Factory default settings']

        #look for all the favorite files in the favorite folder and add them to
        # the list
        from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
        _dir = find_or_make_Nanorex_subdir('Favorites/ProteinDisplayStyle')

        for file in os.listdir(_dir):
            fullname = os.path.join( _dir, file)
            if os.path.isfile(fullname):
                if fnmatch.fnmatch( file, "*.txt"):
                    # leave the extension out
                    favoriteChoices.append(file[0:len(file)-4])
        self.favoritesComboBox  = \
            PM_ComboBox( pmGroupBox,
                         choices       =  favoriteChoices,
                         spanWidth  =  True)
        self.favoritesComboBox.setWhatsThis(
            """<b> List of Favorites </b>
            <p>
            Creates a list of favorite Protein display styles. Once favorite
            styles have been added to the list using the Add Favorite button,
            the list will display the chosen favorites.
            To change the current favorite, select a current favorite from
            the list, and push the Apply Favorite button.""")

        # PM_ToolButtonRow ===============

        # Button list to create a toolbutton row.
        # Format:
        # - QToolButton, buttonId, buttonText,
        # - iconPath,
        # - tooltip, shortcut, column

        BUTTON_LIST = [
            ( "QToolButton", 1,  "APPLY_FAVORITE","ui/actions/Properties Manager/ApplyPeptideDisplayStyleFavorite.png",
              "Apply Favorite", "", 0),   
            ( "QToolButton", 2,  "ADD_FAVORITE",
              "ui/actions/Properties Manager/AddFavorite.png","Add Favorite", "", 1),
            ( "QToolButton", 3,  "DELETE_FAVORITE", "ui/actions/Properties Manager/DeleteFavorite.png",
              "Delete Favorite", "", 2),
            ( "QToolButton", 4,  "SAVE_FAVORITE",
              "ui/actions/Properties Manager/SaveFavorite.png",
              "Save Favorite", "", 3),
            ( "QToolButton", 5,  "LOAD_FAVORITE",
              "ui/actions/Properties Manager/LoadFavorite.png",
              "Load Favorite", \
              "", 4)
            ]

        self.favsButtonGroup = \
            PM_ToolButtonRow( pmGroupBox,
                              title        = "",
                              buttonList   = BUTTON_LIST,
                              spanWidth    = True,
                              isAutoRaise  = False,
                              isCheckable  = False,
                              setAsDefault = True,
                              )

        self.favsButtonGroup.buttonGroup.setExclusive(False)
        self.applyFavoriteButton  = self.favsButtonGroup.getButtonById(1)
        self.addFavoriteButton    = self.favsButtonGroup.getButtonById(2)
        self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
        self.saveFavoriteButton   = self.favsButtonGroup.getButtonById(4)
        self.loadFavoriteButton   = self.favsButtonGroup.getButtonById(5)

    def _loadGroupBox2(self, pmGroupBox):
        """
        Load widgets in group box.
        
        @param pmGroupBox: group box that contains protein display choices
        @see: L{PM_GroupBox}  
        
        """
        proteinStyleChoices = ['CA trace (wire)', 
                               'CA trace (cylinders)', 
                               'CA trace (ball and stick)',
                               'Tube',
                               'Ladder',
                               'Zigzag',
                               'Flat ribbon',
                               'Solid ribbon',
                               'Cartoons',
                               'Fancy cartoons',
                               'Peptide tiles'
                               ]

        self.proteinStyleComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Style:",
                         choices       =  proteinStyleChoices,
                         setAsDefault  =  True)
            
        scaleChoices = ['Constant', 'Secondary structure', 'B-factor']

        self.scaleComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Scaling:",
                         choices       =  scaleChoices,
                         setAsDefault  =  True)
        self.scaleFactorDoubleSpinBox = \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Scaling factor:",
                              value         =  1.00,
                              setAsDefault  =  True,
                              minimum       =  0.1,
                              maximum       =  3.0,
                              decimals      =  1,
                              singleStep    =  0.1 )
   
        self.splineDoubleSpinBox = \
            PM_DoubleSpinBox( pmGroupBox,
                              label         =  "Resolution:",
                              value         =  3,
                              setAsDefault  =  True,
                              minimum       =  2,
                              maximum       =  8,
                              decimals      =  0,
                              singleStep    =  1 )
        
        self.smoothingCheckBox = \
            PM_CheckBox( pmGroupBox,
                         text         = "Smoothing",
                         setAsDefault = True)
        
    def _loadGroupBox3(self, pmGroupBox):
        """
        Load widgets in group box.
        @param pmGroupBox: group box that contains various color choices
        @see: L{PM_GroupBox} 
        """
        colorChoices = ['Chunk', 'Chain', 'Order', 'Hydropathy', 'Polarity',
                        'Acidity', 'Size', 'Character', 'Number of contacts',
                        'Secondary structure type', 'Secondary structure order',
                        'B-factor', 'Occupancy', 'Custom']

        self.proteinComponentComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Color by:",
                         choices       =  colorChoices,
                         setAsDefault  =  True)

        colorList = [orange, yellow, red, magenta, 
                       cyan, blue, white, black, gray]
        
        colorNames = ["Orange(default)", "Yellow", "Red", "Magenta", 
                        "Cyan", "Blue", "White", "Black", "Other color..."]
        
        self.customColorComboBox = \
            PM_ColorComboBox(pmGroupBox,
                            colorList = colorList,
                            colorNames = colorNames,
                            label      = "Custom:",
                            color      = orange,
                            setAsDefault  =  True)
                            
        colorChoices1 = [ 'Same as main color', 'Lighter', 'Darker', 
                          'Gray', 'Custom']
        
        self.proteinAuxComponentComboBox  = \
            PM_ComboBox( pmGroupBox,
                         label         =  "Aux:",
                         choices       =  colorChoices1,
                         setAsDefault  =  True)
        
        colorListAux = [orange, yellow, red, magenta,cyan, blue, white, black, gray]
        
        colorNamesAux = ["Orange(default)", "Yellow", "Red", "Magenta", "Cyan", 
                         "Blue", "White", "Black", "Other color..."]
        
        self.auxColorComboBox = \
            PM_ColorComboBox(pmGroupBox,
                             colorList = colorListAux,
                             colorNames = colorNamesAux, 
                             label = "Custom aux:",
                             color = gray,
                             setAsDefault  =  True)

        #self.discColorCheckBox = \
        #    PM_CheckBox( pmGroupBox,
        #                 text = "Discretize colors",
        #                 setAsDefault = True
        #                 )
        # 
        colorListHelix = [red, yellow, gray, magenta, 
                          cyan, blue, white, black, orange]
        
        colorNamesHelix = ["Red(default)", "Yellow", "Gray", "Magenta", 
                           "Cyan", "Blue", "White", "Black", "Other color..."]
        
        self.helixColorComboBox = \
            PM_ColorComboBox(pmGroupBox,
                            colorList = colorListHelix,
                            colorNames = colorNamesHelix,  
                            label      = "Helix:",
                            color      = red,
                            setAsDefault  =  True)
        
        colorListStrand = [cyan, yellow, gray, magenta, 
                           red, blue, white, black, orange]
        
        colorNamesStrand = ["Cyan(default)", "Yellow", "Gray", "Magenta", 
                            "Red", "Blue", "White", "Black", "Other color..."]
        
        self.strandColorComboBox = \
            PM_ColorComboBox(pmGroupBox,
                            colorList = colorListStrand,
                            colorNames = colorNamesStrand, 
                            label      = "Strand:",
                            color      = cyan,
                            setAsDefault  =  True)

        self.coilColorComboBox = \
            PM_ColorComboBox(pmGroupBox,
                            colorList = colorListAux,
                            colorNames = colorNamesAux,
                            label      = "Coil:",
                            color      = orange,
                            setAsDefault  =  True)

    def updateProteinDisplayStyleWidgets( self ):
        """
        Updates all the Protein Display style widgets based on the current pref keys
        values
        """
        self.proteinStyleComboBox.setCurrentIndex(env.prefs[proteinStyle_prefs_key]) 
        self.splineDoubleSpinBox.setValue(env.prefs[proteinStyleQuality_prefs_key])  
        if env.prefs[proteinStyleSmooth_prefs_key] == True:        
            self.smoothingCheckBox.setCheckState(Qt.Checked)
        else:
            self.smoothingCheckBox.setCheckState(Qt.Unchecked)
        self.scaleComboBox.setCurrentIndex(env.prefs[proteinStyleScaling_prefs_key])
        self.scaleFactorDoubleSpinBox.setValue(env.prefs[proteinStyleScaleFactor_prefs_key])         
        self.proteinComponentComboBox.setCurrentIndex(env.prefs[proteinStyleColors_prefs_key])         
        self.customColorComboBox.setColor(env.prefs[proteinStyleCustomColor_prefs_key])
        self.proteinAuxComponentComboBox.setCurrentIndex(env.prefs[proteinStyleAuxColors_prefs_key])        
        self.auxColorComboBox.setColor(env.prefs[proteinStyleAuxCustomColor_prefs_key])
        #if env.prefs[proteinStyleColorsDiscrete_prefs_key] == True:        
        #    self.discColorCheckBox.setCheckState(Qt.Checked)  
        #else:
        #    self.discColorCheckBox.setCheckState(Qt.Unchecked)   
        self.helixColorComboBox.setColor(env.prefs[proteinStyleHelixColor_prefs_key])
        self.strandColorComboBox.setColor(env.prefs[proteinStyleStrandColor_prefs_key])
        self.coilColorComboBox.setColor(env.prefs[proteinStyleCoilColor_prefs_key])      
        return

    def applyFavorite(self):
        """
        Apply a favorite to the current display chosen in the favorites combo box
        """
        current_favorite = self.favoritesComboBox.currentText()
        if current_favorite == 'Factory default settings':
            env.prefs.restore_defaults(proteinDisplayStylePrefsList)
        else:
            favfilepath = getFavoritePathFromBasename(current_favorite)
            loadFavoriteFile(favfilepath)

        self.updateProteinDisplayStyleWidgets()
        return

    def addFavorite(self):
        """
        create and add favorite to favorites directory and favorites combo box
        in PM
        @note: Rules and other info:
         - The new favorite is defined by the current Protein display style 
           settings.
         - The user is prompted to type in a name for the new
           favorite.
         - The Protein display style settings are written to a file in a special
           directory on the disk
          (i.e. $HOME/Nanorex/Favorites/ProteinDisplayStyle/$FAV_NAME.txt).
         - The name of the new favorite is added to the list of favorites in
           the combobox, which becomes the current option.
           Existence of a favorite with the same name is checked in the above
           mentioned location and if a duplicate exists, then the user can either
           overwrite and provide a new name.
        """


        # Prompt user for a favorite name to add.
        from widgets.simple_dialogs import grab_text_line_using_dialog

        ok1, name = \
          grab_text_line_using_dialog(
              title = "Add new favorite",
              label = "favorite name:",
              iconPath = "ui/actions/Properties Manager/AddFavorite.png",
              default = "" )
        if ok1:
            # check for duplicate files in the
            # $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory

            fname = getFavoritePathFromBasename( name )
            if os.path.exists(fname):

                #favorite file already exists!

                _ext= ".txt"
                ret = QMessageBox.warning( self, "Warning!",
                "The favorite file \"" + name + _ext + "\"already exists.\n"
                "Do you want to overwrite the existing file?",
                "&Overwrite", "&Cancel", "",
                0,    # Enter == button 0
                1)   # Escape == button 1

                if ret == 0:
                    #overwrite favorite file
                    ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
                    indexOfDuplicateItem = self.favoritesComboBox.findText(name)
                    self.favoritesComboBox.removeItem(indexOfDuplicateItem)
                    print "Add Favorite: removed duplicate favorite item."
                else:
                    env.history.message("Add Favorite: cancelled overwriting favorite item.")
                    return

            else:
                ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
        else:
            # User cancelled.
            return
        if ok2:

            self.favoritesComboBox.addItem(name)
            _lastItem = self.favoritesComboBox.count()
            self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
            msg = "New favorite [%s] added." % (text)
        else:
            msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not

        env.history.message(msg)

        return

    def deleteFavorite(self):
        """
        Delete favorite file from the favorites directory
        """
        currentIndex = self.favoritesComboBox.currentIndex()
        currentText = self.favoritesComboBox.currentText()
        if currentIndex == 0:
            msg = "Cannot delete '%s'." % currentText
        else:
            self.favoritesComboBox.removeItem(currentIndex)
            # delete file from the disk
            deleteFile= getFavoritePathFromBasename( currentText )
            os.remove(deleteFile)
            msg = "Deleted favorite named [%s].\n" \
                "and the favorite file [%s.txt]." \
                % (currentText, currentText)
        env.history.message(msg)
        return

    def saveFavorite(self):
        """
        Save favorite file in a user chosen location
        """
        cmd = greenmsg("Save Favorite File: ")
        env.history.message(greenmsg("Save Favorite File:"))
        current_favorite = self.favoritesComboBox.currentText()
        favfilepath = getFavoritePathFromBasename(current_favorite)
        formats = \
                "Favorite (*.txt);;"\
                "All Files (*.*)"
        directory = self.currentWorkingDirectory
        saveLocation = directory + "/" + current_favorite + ".txt"
        fn = QFileDialog.getSaveFileName(
            self,
            "Save Favorite As", # caption
            favfilepath, #where to save
            formats, # file format options
            QString("Favorite (*.txt)") # selectedFilter
            )
        if not fn:
            env.history.message(cmd + "Cancelled")
        else:
            dir, fil = os.path.split(str(fn))
            self.setCurrentWorkingDirectory(dir)
            saveFavoriteFile(str(fn), favfilepath)
        return

    def setCurrentWorkingDirectory(self, dir = None):
        """
        Set dir as current working diretcory
        
        @param dir: dirname
        @type dir: str
        """
        if os.path.isdir(dir):
            self.currentWorkingDirectory = dir
            self._setWorkingDirectoryInPrefsDB(dir)
        else:
            self.currentWorkingDirectory =  getDefaultWorkingDirectory()
        return    
    
    def _setWorkingDirectoryInPrefsDB(self, workdir = None):
        """
        Set workdir as current working diretcory in prefDB
        
        @param workdir: dirname
        @type workdir: str
        """
        if not workdir:
            return    
        workdir = str(workdir)
        if os.path.isdir(workdir):
            workdir = os.path.normpath(workdir)
            env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.            
        else:
            msg = "[" + workdir + "] is not a directory. Working directory was not changed."
            env.history.message( redmsg(msg))
        return
    
    def loadFavorite(self):
        """
        Load a favorite file
        """ 
        # If the file already exists in the favorites folder then the user is
        # given the option of overwriting it or renaming it

        env.history.message(greenmsg("Load Favorite File:"))
        formats = \
                    "Favorite (*.txt);;"\
                    "All Files (*.*)"

        directory = self.currentWorkingDirectory
        if directory == '':
            directory= getDefaultWorkingDirectory()
        fname = QFileDialog.getOpenFileName(self,
                                         "Choose a file to load",
                                         directory,
                                         formats)
        if not fname:
            env.history.message("User cancelled loading file.")
            return
        else:
            dir, fil = os.path.split(str(fname))
            self.setCurrentWorkingDirectory(dir)
            canLoadFile=loadFavoriteFile(fname)
            if canLoadFile == 1:
                #get just the name of the file for loading into the combobox
                favName = os.path.basename(str(fname))
                name = favName[0:len(favName)-4]
                indexOfDuplicateItem = self.favoritesComboBox.findText(name)
                #duplicate exists in combobox
                if indexOfDuplicateItem != -1:
                    ret = QMessageBox.warning( self, "Warning!",
                                               "The favorite file \"" + name +
                                               "\"already exists.\n"
                                               "Do you want to overwrite the existing file?",
                                               "&Overwrite", "&Rename", "&Cancel",
                                               0,    # Enter == button 0
                                               1   # button 1
                                               )
                    if ret == 0:
                        self.favoritesComboBox.removeItem(indexOfDuplicateItem)
                        self.favoritesComboBox.addItem(name)
                        _lastItem = self.favoritesComboBox.count()
                        self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
                        ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
                        msg = "Overwrote favorite [%s]." % (text)
                        env.history.message(msg)
                    elif ret == 1:
                        # add new item to favorites folder as well as combobox
                        self.addFavorite()
                    else:
                        #reset the display setting values to factory default
                        factoryIndex = self.favoritesComboBox.findText(
                                             'Factory default settings')
                        self.favoritesComboBox.setCurrentIndex(factoryIndex)
                        env.prefs.restore_defaults(proteinDisplayStylePrefsList)

                        env.history.message("Cancelled overwriting favorite file.")
                        return
                else:
                    self.favoritesComboBox.addItem(name)
                    _lastItem = self.favoritesComboBox.count()
                    self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
                    msg = "Loaded favorite [%s]." % (name)
                    env.history.message(msg) 
                self.updateProteinDisplayStyleWidgets()  
        return

    def _addWhatsThisText( self ):
        """
        Add what's this text for this PM
        """
        from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
        WhatsThis_EditDnaDisplayStyle_PropertyManager(self)

    def _addToolTipText(self):
        """
        Add tool tip text to all widgets.
        """
        from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager 
        ToolTip_EditProteinDisplayStyle_PropertyManager(self)