def loadSequenceTraces(self):
self.numseqs = self.cons.getNumSeqs()
self.seqt1 = self.cons.getSequenceTrace(0)
if self.numseqs == 2:
self.seqt2 = self.cons.getSequenceTrace(1)
else:
self.seqt2 = None
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt1))
if self.numseqs == 2:
viewer = FwdRevSTVDecorator(viewer)
self.viewers = [ viewer ]
if self.seqt2 != None:
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt2))
self.viewers.append(FwdRevSTVDecorator(viewer))
self.consview = ScrolledConsensusSequenceViewer(self.cons)
# add the sequence trace layout to the window
self.stlayout = SequenceTraceLayout(self.consview, self.viewers)
self.vbox.pack_start(self.stlayout, expand=True, fill=True)
# Register callbacks for the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().registerObserver('consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().registerObserver('selection_state', self.selectStateChange)
# register callbacks for the consensus sequence model
self.cons.registerObserver('undo_state_changed', self.undoStateChanged)
self.cons.registerObserver('redo_state_changed', self.redoStateChanged)
title = 'Trace View: ' + self.seqt1.getFileName()
if self.numseqs == 2:
title += ', ' + self.seqt2.getFileName()
self.set_title(title)
def loadSequenceTraces(self):
self.numseqs = self.cons.getNumSeqs()
self.seqt1 = self.cons.getSequenceTrace(0)
if self.numseqs == 2:
self.seqt2 = self.cons.getSequenceTrace(1)
else:
self.seqt2 = None
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt1))
if self.numseqs == 2:
viewer = FwdRevSTVDecorator(viewer)
self.viewers = [viewer]
if self.seqt2 != None:
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt2))
self.viewers.append(FwdRevSTVDecorator(viewer))
self.consview = ScrolledConsensusSequenceViewer(self.cons)
# add the sequence trace layout to the window
self.stlayout = SequenceTraceLayout(self.consview, self.viewers)
self.vbox.pack_start(self.stlayout, expand=True, fill=True)
# Register callbacks for the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().registerObserver(
'consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().registerObserver(
'selection_state', self.selectStateChange)
# register callbacks for the consensus sequence model
self.cons.registerObserver('undo_state_changed', self.undoStateChanged)
self.cons.registerObserver('redo_state_changed', self.redoStateChanged)
title = 'Trace View: ' + self.seqt1.getFileName()
if self.numseqs == 2:
title += ', ' + self.seqt2.getFileName()
self.set_title(title)
class TraceWindow(gtk.Window, CommonDialogs, Observable):
def __init__(self, mod_consseq_builder, is_mainwindow=False, id_num=-1):
gtk.Window.__init__(self, gtk.WINDOW_TOPLEVEL)
self.is_mainwindow = is_mainwindow
self.id_num = id_num
self.cons = mod_consseq_builder
self.infowin = None
# initialize the observable events for this class
self.defineObservableEvents(['consensus_saved'])
# initialize the window GUI elements and event handlers
self.connect('destroy', self.destroyWindow)
self.vbox = gtk.VBox(False, 0)
self.add(self.vbox)
# create the menus and toolbar
menuxml = '''<menubar name="menubar">
<menu action="File">
<menuitem action="Save_Consens" />
<separator />
<menuitem action="Export_Alignment" />
<menuitem action="Export_Consensus" />
<menuitem action="Export_Raw" />
<separator />
<menuitem action="File_Info" />
<separator />
<menuitem action="Close" />
</menu>
<menu action="Edit">
<menuitem action="Undo" />
<menuitem action="Redo" />
<separator />
<menuitem action="Copy" />
<menuitem action="Delete" />
<menuitem action="Modify" />
<separator />
<menuitem action="Recalc_Consens" />
</menu>
<menu action="View">
<menuitem action="Scroll_Lock" />
</menu>
</menubar>
<popup name="editpopup">
<menuitem action="Copy" />
<menuitem action="Delete" />
<menuitem action="Modify" />
<separator />
<menuitem action="Recalc_Consens" />
</popup>
<toolbar name="toolbar">
<toolitem action="File_Info" />
<separator />
<toolitem action="Save_Consens" />
<separator />
<toolitem action="Undo" />
<toolitem action="Redo" />
<separator />
<toolitem action="Copy" />
<toolitem action="Delete" />
<toolitem action="Modify" />
</toolbar>'''
# These actions are (usually) always enabled.
self.main_ag = gtk.ActionGroup('main_actions')
self.main_ag.add_actions([
('File', None, '_File'),
('Save_Consens', gtk.STOCK_SAVE, '_Save working sequence to project', None, 'Save the working sequence to the project', self.saveConsensus),
('Export_Consensus', None, 'Export w_orking sequence...', None, 'Export the working sequence to a file', self.exportConsensus),
('Export_Raw', None, 'Export _raw sequence(s)...', None, 'Export the un-edited sequence(s) to a file', self.exportRawSequence),
('File_Info', gtk.STOCK_INFO, '_Information...', None, 'View detailed information about the file(s)', self.fileInfo),
('Close', gtk.STOCK_CLOSE, '_Close', None, 'Close this window', self.closeWindow),
('Edit', None, '_Edit'),
('Recalc_Consens', None, '_Recalculate working seq.', None, 'Recalculate the working sequence', self.recalcConsensus),
('View', None, '_View')])
# These actions are enabled only when there are two sequencing traces in the window.
self.twotrace_ag = gtk.ActionGroup('twotrace_actions')
self.twotrace_ag.add_actions([
('Export_Alignment', None, 'Export _alignment...', None, 'Export the aligned forward and reverse sequences', self.exportAlignment)])
self.twotrace_ag.add_toggle_actions([
('Scroll_Lock', None, '_Synchronize trace scrolling', None, 'Synchronizes the scrolling of the forward and reverse traces', self.lockScrolling, True)])
# these actions are for common edit commands
self.edit_ag = gtk.ActionGroup('edite_actions')
self.edit_ag.add_actions([
('Undo', gtk.STOCK_UNDO, '_Undo', '<ctl>z', 'Undo the last change to the working sequence', self.undoConsChange),
('Redo', gtk.STOCK_REDO, '_Redo', '<ctl>y', 'Redo the last change to the working sequence', self.redoConsChange)])
# these actions are only enabled when there is an active selection
self.sel_edit_ag = gtk.ActionGroup('selected_edit_actions')
self.sel_edit_ag.add_actions([
('Copy', gtk.STOCK_COPY, '_Copy selected base(s) to clipboard', '<ctl>c', 'Copy the selected base(s) to the system clipboard', self.copyConsBases),
('Delete', gtk.STOCK_DELETE, '_Delete selected base(s)', None, 'Delete the selected base(s) from the working sequence', self.deleteConsBases),
('Modify', gtk.STOCK_EDIT, '_Modify selected base(s)...', None, 'Edit the selected base(s)', self.editConsBases)])
self.uim = gtk.UIManager()
self.add_accel_group(self.uim.get_accel_group())
self.uim.insert_action_group(self.main_ag, 0)
self.uim.insert_action_group(self.twotrace_ag, 0)
self.uim.insert_action_group(self.edit_ag, 0)
self.uim.insert_action_group(self.sel_edit_ag, 0)
self.uim.add_ui_from_string(menuxml)
self.vbox.pack_start(self.uim.get_widget('/menubar'), expand=False, fill=False)
toolbar_hbox = gtk.HBox()
self.uim.get_widget('/toolbar').set_show_arrow(False)
self.uim.get_widget('/toolbar').set_icon_size(gtk.ICON_SIZE_LARGE_TOOLBAR)
self.uim.get_widget('/toolbar').set_style(gtk.TOOLBAR_ICONS)
toolbar_hbox.pack_start(self.uim.get_widget('/toolbar'), expand=False, fill=False)
self.vbox.pack_start(toolbar_hbox, expand=False, fill=False)
# disable some menus/toolbar buttons by default
self.edit_ag.get_action('Undo').set_sensitive(False)
self.edit_ag.get_action('Redo').set_sensitive(False)
self.sel_edit_ag.set_sensitive(False)
self.loadSequenceTraces()
# If there is only one trace file, disable the actions that require two traces.
if self.numseqs < 2:
self.twotrace_ag.set_sensitive(False)
# get the trace file(s) toolbar
trace_tb = self.stlayout.getTraceToolBar()
for cnt in range(0, 2):
blank = gtk.SeparatorToolItem()
blank.set_draw(False)
#self.uim.get_widget('/toolbar').insert(blank, 0)
trace_tb.insert(blank, 0)
toolbar_hbox.pack_start(trace_tb, True, True)
# add a consensus sequence status bar at the bottom of the window
sbar = ConsensSeqStatusBar(self.cons)
self.vbox.pack_start(sbar, False)
self.vbox.show_all()
self.vbox.show()
# by default, do not show the "Save_Consens" action UI elements
self.main_ag.get_action('Save_Consens').set_visible(False)
self.setDefaultGeometry()
self.show()
self.set_focus(None)
def setDefaultGeometry(self):
#print self.get_size()
width, height = self.get_size()
screen = self.get_screen()
# calculate the default width based on the screen size
new_width = (screen.get_width() * 5) / 6
# calculate the default height based on the preferred size of the sequence trace viewers
v_height = self.viewers[0].getDefaultHeight()
v_pref_height = self.viewers[0].getPreferredHeight()
diff = v_pref_height - v_height
new_height = height + self.numseqs * diff
#print new_width, new_height
self.set_default_size(new_width, new_height)
self.set_position(gtk.WIN_POS_CENTER)
def setSaveEnabled(self, state):
self.main_ag.get_action('Save_Consens').set_sensitive(state)
def registerObserver(self, event_name, handler):
"""
Extends the registerObserver() method in Observable to allow GUI elements to respond
to observer registration.
"""
Observable.registerObserver(self, event_name, handler)
if event_name == 'consensus_saved':
# Show the "Save_Consens" action UI elements since someone's actually listening for this signal.
self.main_ag.get_action('Save_Consens').set_visible(True)
def saveConsensus(self, widget):
self.notifyObservers('consensus_saved',
(self, self.cons.getCompactConsensus(), self.cons.getConsensus()))
def getIdNum(self):
return self.id_num
def loadSequenceTraces(self):
self.numseqs = self.cons.getNumSeqs()
self.seqt1 = self.cons.getSequenceTrace(0)
if self.numseqs == 2:
self.seqt2 = self.cons.getSequenceTrace(1)
else:
self.seqt2 = None
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt1))
if self.numseqs == 2:
viewer = FwdRevSTVDecorator(viewer)
self.viewers = [ viewer ]
if self.seqt2 != None:
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt2))
self.viewers.append(FwdRevSTVDecorator(viewer))
self.consview = ScrolledConsensusSequenceViewer(self.cons)
# add the sequence trace layout to the window
self.stlayout = SequenceTraceLayout(self.consview, self.viewers)
self.vbox.pack_start(self.stlayout, expand=True, fill=True)
# Register callbacks for the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().registerObserver('consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().registerObserver('selection_state', self.selectStateChange)
# register callbacks for the consensus sequence model
self.cons.registerObserver('undo_state_changed', self.undoStateChanged)
self.cons.registerObserver('redo_state_changed', self.redoStateChanged)
title = 'Trace View: ' + self.seqt1.getFileName()
if self.numseqs == 2:
title += ', ' + self.seqt2.getFileName()
self.set_title(title)
def lockScrolling(self, widget):
"""
Responds to clicks on the synchronize scrolling checkbox menu item.
"""
if widget.get_active():
self.stlayout.lockScrolling()
else:
self.stlayout.unlockScrolling()
def consensusSeqClicked(self, select_start, select_end, event):
if event.button == 3:
self.uim.get_widget('/editpopup').popup(None, None, None, event.button, event.time)
def selectStateChange(self, selection_exists):
if selection_exists:
self.sel_edit_ag.set_sensitive(True)
else:
self.sel_edit_ag.set_sensitive(False)
def undoStateChanged(self, has_undo):
if has_undo:
self.edit_ag.get_action('Undo').set_sensitive(True)
else:
self.edit_ag.get_action('Undo').set_sensitive(False)
def redoStateChanged(self, has_redo):
if has_redo:
self.edit_ag.get_action('Redo').set_sensitive(True)
else:
self.edit_ag.get_action('Redo').set_sensitive(False)
def undoConsChange(self, widget):
self.cons.undo()
self.setSaveEnabled(True)
def redoConsChange(self, widget):
self.cons.redo()
self.setSaveEnabled(True)
def copyConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
seq = self.cons.getConsensus(sel[0], sel[1])
pyperclip.copy(seq)
def deleteConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
self.cons.deleteBases(sel[0], sel[1])
self.setSaveEnabled(True)
def editConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
seq = self.cons.getConsensus(sel[0], sel[1])
# Create a text-entry dialog to allow the user to modify the selected base(s).
diag = EntryDialog(self, 'Edit Sequence',
'You may make changes to the selected base(s) below.\n\nOriginal sequence: {0} ({1} bases)\n'.format(seq, len(seq)),
seq, 50)
# Build a regular expression object for checking if the characters in the new
# string are all valid bases.
reo = re.compile('[' + ''.join(ConsensSeqBuilder.allbases) + ' ]*')
# Display the dialog until the user presses cancel, closes the dialog, or submits
# an acceptable string.
stringok = False
while not(stringok):
response = diag.run()
if (response == gtk.RESPONSE_CANCEL) or (response == gtk.RESPONSE_DELETE_EVENT):
break
newseq = diag.get_text().upper()
match = reo.match(newseq)
# Verify that newseq is of the correct length and only contains valid bases.
if len(newseq) != len(seq):
self.showMessage('The number of bases in the edited sequence must match the the selection.')
elif match.end() - match.start() != len(newseq):
self.showMessage('The edited sequence contains invalid characters. You may only use IUPAC nucleotide codes or spaces.')
else:
stringok = True
diag.destroy()
if response == gtk.RESPONSE_OK:
self.cons.modifyBases(sel[0], sel[1], newseq)
self.setSaveEnabled(True)
def recalcConsensus(self, widget):
response = self.showYesNoDialog('Are you sure you want to recalculate the working sequence? This will overwrite any edits you have made.')
if response != gtk.RESPONSE_YES:
return
self.cons.recalcConsensusSequence()
self.setSaveEnabled(True)
def fileInfo(self, widget):
seqtraces = list()
self.numseqs = self.cons.getNumSeqs()
seqtraces.append(self.cons.getSequenceTrace(0))
if self.numseqs == 2:
seqtraces.append(self.cons.getSequenceTrace(1))
if self.infowin != None:
self.infowin.present()
else:
self.infowin = TraceFileInfoWin(seqtraces)
self.infowin.connect('destroy', self.fileInfoDestroyed)
def fileInfoDestroyed(self, win):
self.infowin = None
def exportConsensus(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Consensus Sequence')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequence
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage('The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.')
return
desc = 'consensus'
seqfname = self.cons.getSequenceTrace(0).getFileName()
if self.numseqs == 2:
seqfname += ', ' + self.cons.getSequenceTrace(1).getFileName()
sw.addUnalignedSequence(self.cons.getCompactConsensus(), seqfname, desc)
sw.write()
def exportRawSequence(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Raw Sequence(s)')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequence
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage('The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.')
return
for cnt in range(0, self.numseqs):
seqfname = self.cons.getSequenceTrace(cnt).getFileName()
desc = 'raw sequence'
if self.cons.getSequenceTrace(cnt).isReverseComplemented():
desc += ' (reverse complemented)'
sw.addUnalignedSequence(self.cons.getSequenceTrace(cnt).getBaseCalls(), seqfname, desc)
sw.write()
def exportAlignment(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Alignment')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequences
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage('The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.')
return
for cnt in range(0, self.numseqs):
seqfname = self.cons.getSequenceTrace(cnt).getFileName()
desc = 'sequence ' + str(cnt)
if self.cons.getSequenceTrace(cnt).isReverseComplemented():
desc += ' (reverse complemented)'
sw.addAlignedSequence(self.cons.getAlignedSequence(cnt), seqfname, desc)
sw.write()
def closeWindow(self, widget):
self.destroy()
def destroyWindow(self, widget, data=None):
# close the file information window, if it exists
if self.infowin != None:
self.infowin.destroy()
# Unregister this window as an observer of the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().unregisterObserver('consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().unregisterObserver('selection_state', self.selectStateChange)
# Unregister this window as an observer of the consensus sequence.
self.cons.unregisterObserver('undo_state_changed', self.undoStateChanged)
self.cons.unregisterObserver('redo_state_changed', self.redoStateChanged)
if self.is_mainwindow:
gtk.main_quit()
class TraceWindow(gtk.Window, CommonDialogs, Observable):
def __init__(self, mod_consseq_builder, is_mainwindow=False, id_num=-1):
gtk.Window.__init__(self, gtk.WINDOW_TOPLEVEL)
self.is_mainwindow = is_mainwindow
self.id_num = id_num
self.cons = mod_consseq_builder
self.infowin = None
# initialize the observable events for this class
self.defineObservableEvents(['consensus_saved'])
# initialize the window GUI elements and event handlers
self.connect('destroy', self.destroyWindow)
self.vbox = gtk.VBox(False, 0)
self.add(self.vbox)
# create the menus and toolbar
menuxml = '''<menubar name="menubar">
<menu action="File">
<menuitem action="Save_Consens" />
<separator />
<menuitem action="Export_Alignment" />
<menuitem action="Export_Consensus" />
<menuitem action="Export_Raw" />
<separator />
<menuitem action="File_Info" />
<separator />
<menuitem action="Close" />
</menu>
<menu action="Edit">
<menuitem action="Undo" />
<menuitem action="Redo" />
<separator />
<menuitem action="Copy" />
<menuitem action="Delete" />
<menuitem action="Modify" />
<separator />
<menuitem action="Recalc_Consens" />
</menu>
<menu action="View">
<menuitem action="Scroll_Lock" />
</menu>
</menubar>
<popup name="editpopup">
<menuitem action="Copy" />
<menuitem action="Delete" />
<menuitem action="Modify" />
<separator />
<menuitem action="Recalc_Consens" />
</popup>
<toolbar name="toolbar">
<toolitem action="File_Info" />
<separator />
<toolitem action="Save_Consens" />
<separator />
<toolitem action="Undo" />
<toolitem action="Redo" />
<separator />
<toolitem action="Copy" />
<toolitem action="Delete" />
<toolitem action="Modify" />
</toolbar>'''
# These actions are (usually) always enabled.
self.main_ag = gtk.ActionGroup('main_actions')
self.main_ag.add_actions([
('File', None, '_File'),
('Save_Consens', gtk.STOCK_SAVE,
'_Save working sequence to project', None,
'Save the working sequence to the project', self.saveConsensus),
('Export_Consensus', None, 'Export w_orking sequence...', None,
'Export the working sequence to a file', self.exportConsensus),
('Export_Raw', None, 'Export _raw sequence(s)...', None,
'Export the un-edited sequence(s) to a file',
self.exportRawSequence),
('File_Info', gtk.STOCK_INFO, '_Information...', None,
'View detailed information about the file(s)', self.fileInfo),
('Close', gtk.STOCK_CLOSE, '_Close', None, 'Close this window',
self.closeWindow), ('Edit', None, '_Edit'),
('Recalc_Consens', None, '_Recalculate working seq.', None,
'Recalculate the working sequence', self.recalcConsensus),
('View', None, '_View')
])
# These actions are enabled only when there are two sequencing traces in the window.
self.twotrace_ag = gtk.ActionGroup('twotrace_actions')
self.twotrace_ag.add_actions([
('Export_Alignment', None, 'Export _alignment...', None,
'Export the aligned forward and reverse sequences',
self.exportAlignment)
])
self.twotrace_ag.add_toggle_actions([
('Scroll_Lock', None, '_Synchronize trace scrolling', None,
'Synchronizes the scrolling of the forward and reverse traces',
self.lockScrolling, True)
])
# these actions are for common edit commands
self.edit_ag = gtk.ActionGroup('edite_actions')
self.edit_ag.add_actions([
('Undo', gtk.STOCK_UNDO, '_Undo', '<ctl>z',
'Undo the last change to the working sequence',
self.undoConsChange),
('Redo', gtk.STOCK_REDO, '_Redo', '<ctl>y',
'Redo the last change to the working sequence',
self.redoConsChange)
])
# these actions are only enabled when there is an active selection
self.sel_edit_ag = gtk.ActionGroup('selected_edit_actions')
self.sel_edit_ag.add_actions([
('Copy', gtk.STOCK_COPY, '_Copy selected base(s) to clipboard',
'<ctl>c', 'Copy the selected base(s) to the system clipboard',
self.copyConsBases),
('Delete', gtk.STOCK_DELETE, '_Delete selected base(s)', None,
'Delete the selected base(s) from the working sequence',
self.deleteConsBases),
('Modify', gtk.STOCK_EDIT, '_Modify selected base(s)...', None,
'Edit the selected base(s)', self.editConsBases)
])
self.uim = gtk.UIManager()
self.add_accel_group(self.uim.get_accel_group())
self.uim.insert_action_group(self.main_ag, 0)
self.uim.insert_action_group(self.twotrace_ag, 0)
self.uim.insert_action_group(self.edit_ag, 0)
self.uim.insert_action_group(self.sel_edit_ag, 0)
self.uim.add_ui_from_string(menuxml)
self.vbox.pack_start(self.uim.get_widget('/menubar'),
expand=False,
fill=False)
toolbar_hbox = gtk.HBox()
self.uim.get_widget('/toolbar').set_show_arrow(False)
self.uim.get_widget('/toolbar').set_icon_size(
gtk.ICON_SIZE_LARGE_TOOLBAR)
self.uim.get_widget('/toolbar').set_style(gtk.TOOLBAR_ICONS)
toolbar_hbox.pack_start(self.uim.get_widget('/toolbar'),
expand=False,
fill=False)
self.vbox.pack_start(toolbar_hbox, expand=False, fill=False)
# disable some menus/toolbar buttons by default
self.edit_ag.get_action('Undo').set_sensitive(False)
self.edit_ag.get_action('Redo').set_sensitive(False)
self.sel_edit_ag.set_sensitive(False)
self.loadSequenceTraces()
# If there is only one trace file, disable the actions that require two traces.
if self.numseqs < 2:
self.twotrace_ag.set_sensitive(False)
# get the trace file(s) toolbar
trace_tb = self.stlayout.getTraceToolBar()
for cnt in range(0, 2):
blank = gtk.SeparatorToolItem()
blank.set_draw(False)
#self.uim.get_widget('/toolbar').insert(blank, 0)
trace_tb.insert(blank, 0)
toolbar_hbox.pack_start(trace_tb, True, True)
# add a consensus sequence status bar at the bottom of the window
sbar = ConsensSeqStatusBar(self.cons)
self.vbox.pack_start(sbar, False)
self.vbox.show_all()
self.vbox.show()
# by default, do not show the "Save_Consens" action UI elements
self.main_ag.get_action('Save_Consens').set_visible(False)
self.setDefaultGeometry()
self.show()
self.set_focus(None)
def setDefaultGeometry(self):
#print self.get_size()
width, height = self.get_size()
screen = self.get_screen()
# calculate the default width based on the screen size
new_width = (screen.get_width() * 5) / 6
# calculate the default height based on the preferred size of the sequence trace viewers
v_height = self.viewers[0].getDefaultHeight()
v_pref_height = self.viewers[0].getPreferredHeight()
diff = v_pref_height - v_height
new_height = height + self.numseqs * diff
#print new_width, new_height
self.set_default_size(new_width, new_height)
self.set_position(gtk.WIN_POS_CENTER)
def setSaveEnabled(self, state):
self.main_ag.get_action('Save_Consens').set_sensitive(state)
def registerObserver(self, event_name, handler):
"""
Extends the registerObserver() method in Observable to allow GUI elements to respond
to observer registration.
"""
Observable.registerObserver(self, event_name, handler)
if event_name == 'consensus_saved':
# Show the "Save_Consens" action UI elements since someone's actually listening for this signal.
self.main_ag.get_action('Save_Consens').set_visible(True)
def saveConsensus(self, widget):
self.notifyObservers(
'consensus_saved',
(self, self.cons.getCompactConsensus(), self.cons.getConsensus()))
def getIdNum(self):
return self.id_num
def loadSequenceTraces(self):
self.numseqs = self.cons.getNumSeqs()
self.seqt1 = self.cons.getSequenceTrace(0)
if self.numseqs == 2:
self.seqt2 = self.cons.getSequenceTrace(1)
else:
self.seqt2 = None
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt1))
if self.numseqs == 2:
viewer = FwdRevSTVDecorator(viewer)
self.viewers = [viewer]
if self.seqt2 != None:
viewer = ScrollAndZoomSTVDecorator(SequenceTraceViewer(self.seqt2))
self.viewers.append(FwdRevSTVDecorator(viewer))
self.consview = ScrolledConsensusSequenceViewer(self.cons)
# add the sequence trace layout to the window
self.stlayout = SequenceTraceLayout(self.consview, self.viewers)
self.vbox.pack_start(self.stlayout, expand=True, fill=True)
# Register callbacks for the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().registerObserver(
'consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().registerObserver(
'selection_state', self.selectStateChange)
# register callbacks for the consensus sequence model
self.cons.registerObserver('undo_state_changed', self.undoStateChanged)
self.cons.registerObserver('redo_state_changed', self.redoStateChanged)
title = 'Trace View: ' + self.seqt1.getFileName()
if self.numseqs == 2:
title += ', ' + self.seqt2.getFileName()
self.set_title(title)
def lockScrolling(self, widget):
"""
Responds to clicks on the synchronize scrolling checkbox menu item.
"""
if widget.get_active():
self.stlayout.lockScrolling()
else:
self.stlayout.unlockScrolling()
def consensusSeqClicked(self, select_start, select_end, event):
if event.button == 3:
self.uim.get_widget('/editpopup').popup(None, None, None,
event.button, event.time)
def selectStateChange(self, selection_exists):
if selection_exists:
self.sel_edit_ag.set_sensitive(True)
else:
self.sel_edit_ag.set_sensitive(False)
def undoStateChanged(self, has_undo):
if has_undo:
self.edit_ag.get_action('Undo').set_sensitive(True)
else:
self.edit_ag.get_action('Undo').set_sensitive(False)
def redoStateChanged(self, has_redo):
if has_redo:
self.edit_ag.get_action('Redo').set_sensitive(True)
else:
self.edit_ag.get_action('Redo').set_sensitive(False)
def undoConsChange(self, widget):
self.cons.undo()
self.setSaveEnabled(True)
def redoConsChange(self, widget):
self.cons.redo()
self.setSaveEnabled(True)
def copyConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
seq = self.cons.getConsensus(sel[0], sel[1])
pyperclip.copy(seq)
def deleteConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
self.cons.deleteBases(sel[0], sel[1])
self.setSaveEnabled(True)
def editConsBases(self, widget):
csv = self.consview.getConsensusSequenceViewer()
sel = csv.getSelection()
seq = self.cons.getConsensus(sel[0], sel[1])
# Create a text-entry dialog to allow the user to modify the selected base(s).
diag = EntryDialog(
self, 'Edit Sequence',
'You may make changes to the selected base(s) below.\n\nOriginal sequence: {0} ({1} bases)\n'
.format(seq, len(seq)), seq, 50)
# Build a regular expression object for checking if the characters in the new
# string are all valid bases.
reo = re.compile('[' + ''.join(ConsensSeqBuilder.allbases) + ' ]*')
# Display the dialog until the user presses cancel, closes the dialog, or submits
# an acceptable string.
stringok = False
while not (stringok):
response = diag.run()
if (response
== gtk.RESPONSE_CANCEL) or (response
== gtk.RESPONSE_DELETE_EVENT):
break
newseq = diag.get_text().upper()
match = reo.match(newseq)
# Verify that newseq is of the correct length and only contains valid bases.
if len(newseq) != len(seq):
self.showMessage(
'The number of bases in the edited sequence must match the the selection.'
)
elif match.end() - match.start() != len(newseq):
self.showMessage(
'The edited sequence contains invalid characters. You may only use IUPAC nucleotide codes or spaces.'
)
else:
stringok = True
diag.destroy()
if response == gtk.RESPONSE_OK:
self.cons.modifyBases(sel[0], sel[1], newseq)
self.setSaveEnabled(True)
def recalcConsensus(self, widget):
response = self.showYesNoDialog(
'Are you sure you want to recalculate the working sequence? This will overwrite any edits you have made.'
)
if response != gtk.RESPONSE_YES:
return
self.cons.recalcConsensusSequence()
self.setSaveEnabled(True)
def fileInfo(self, widget):
seqtraces = list()
self.numseqs = self.cons.getNumSeqs()
seqtraces.append(self.cons.getSequenceTrace(0))
if self.numseqs == 2:
seqtraces.append(self.cons.getSequenceTrace(1))
if self.infowin != None:
self.infowin.present()
else:
self.infowin = TraceFileInfoWin(seqtraces)
self.infowin.connect('destroy', self.fileInfoDestroyed)
def fileInfoDestroyed(self, win):
self.infowin = None
def exportConsensus(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Consensus Sequence')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequence
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
desc = 'consensus'
seqfname = self.cons.getSequenceTrace(0).getFileName()
if self.numseqs == 2:
seqfname += ', ' + self.cons.getSequenceTrace(1).getFileName()
sw.addUnalignedSequence(self.cons.getCompactConsensus(), seqfname,
desc)
sw.write()
def exportRawSequence(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Raw Sequence(s)')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequence
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
for cnt in range(0, self.numseqs):
seqfname = self.cons.getSequenceTrace(cnt).getFileName()
desc = 'raw sequence'
if self.cons.getSequenceTrace(cnt).isReverseComplemented():
desc += ' (reverse complemented)'
sw.addUnalignedSequence(
self.cons.getSequenceTrace(cnt).getBaseCalls(), seqfname, desc)
sw.write()
def exportAlignment(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Alignment')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != gtk.RESPONSE_OK:
return
# write out the sequences
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
for cnt in range(0, self.numseqs):
seqfname = self.cons.getSequenceTrace(cnt).getFileName()
desc = 'sequence ' + str(cnt)
if self.cons.getSequenceTrace(cnt).isReverseComplemented():
desc += ' (reverse complemented)'
sw.addAlignedSequence(self.cons.getAlignedSequence(cnt), seqfname,
desc)
sw.write()
def closeWindow(self, widget):
self.destroy()
def destroyWindow(self, widget, data=None):
# close the file information window, if it exists
if self.infowin != None:
self.infowin.destroy()
# Unregister this window as an observer of the consensus sequence viewer.
self.consview.getConsensusSequenceViewer().unregisterObserver(
'consensus_clicked', self.consensusSeqClicked)
self.consview.getConsensusSequenceViewer().unregisterObserver(
'selection_state', self.selectStateChange)
# Unregister this window as an observer of the consensus sequence.
self.cons.unregisterObserver('undo_state_changed',
self.undoStateChanged)
self.cons.unregisterObserver('redo_state_changed',
self.redoStateChanged)
if self.is_mainwindow:
gtk.main_quit()
