def __init__ (self):
# parent constructor
wx.Frame.__init__(self, None, -1, "Genome Viewer", size=(self.hsize, self.vsize))
# min size of the frame
self.SetMinSize((self.hsize, self.vsize))
# statusbar
self.statusbar=self.CreateStatusBar()
self.statusbar.SetFieldsCount(3)
self.statusbar.SetStatusWidths([-3, -1, -1])
self.statusbar.SetStatusText("GenomeViewer Version 1.0", 1)
# timer in statusbar
self.timer = wx.PyTimer(self.NotifyTimer)
self.timer.Start(1000)
self.NotifyTimer()
# creates the menubar
self.MakeMenuBar()
self.container = Imports.con
self.genome = Imports.genome
self.genomemodel = GenomeModel()#(self.genome, self.features)
self.genomemodel.setGenome(self.genome)
self.genomemodel.setFeatureListContainer(self.container)
### splitter ###
self.splitLeft = ProportionalSplitter(self, -1, 0.33)
self.splitRight = ProportionalSplitter(self.splitLeft, -1, 0.9)
### treeview ###
self.treeview = TreeView(self.container, self.genomemodel, self.splitLeft)
self.container.addObserver(self.treeview)
### genomeview ###
self.genomeview = GenomeView(self.genomemodel, self.splitRight)
self.genome.addObserver(self.genomeview)
### genomebar ###
self.genomebar = GenomeBar(self.genomemodel, self.splitRight)
self.genomemodel.addObserver(self.genomebar)
self.splitLeft.SplitVertically(self.treeview,self.splitRight)
self.splitRight.SplitHorizontally(self.genomeview, self.genomebar)
self.Centre()
self.Show(True)
class MainFrame(wx.Frame):
"""initialize mainframe"""
hsize = 800
vsize = 600
def __init__ (self):
# parent constructor
wx.Frame.__init__(self, None, -1, "Genome Viewer", size=(self.hsize, self.vsize))
# min size of the frame
self.SetMinSize((self.hsize, self.vsize))
# statusbar
self.statusbar=self.CreateStatusBar()
self.statusbar.SetFieldsCount(3)
self.statusbar.SetStatusWidths([-3, -1, -1])
self.statusbar.SetStatusText("GenomeViewer Version 1.0", 1)
# timer in statusbar
self.timer = wx.PyTimer(self.NotifyTimer)
self.timer.Start(1000)
self.NotifyTimer()
# creates the menubar
self.MakeMenuBar()
self.container = Imports.con
self.genome = Imports.genome
self.genomemodel = GenomeModel()#(self.genome, self.features)
self.genomemodel.setGenome(self.genome)
self.genomemodel.setFeatureListContainer(self.container)
### splitter ###
self.splitLeft = ProportionalSplitter(self, -1, 0.33)
self.splitRight = ProportionalSplitter(self.splitLeft, -1, 0.9)
### treeview ###
self.treeview = TreeView(self.container, self.genomemodel, self.splitLeft)
self.container.addObserver(self.treeview)
### genomeview ###
self.genomeview = GenomeView(self.genomemodel, self.splitRight)
self.genome.addObserver(self.genomeview)
### genomebar ###
self.genomebar = GenomeBar(self.genomemodel, self.splitRight)
self.genomemodel.addObserver(self.genomebar)
self.splitLeft.SplitVertically(self.treeview,self.splitRight)
self.splitRight.SplitHorizontally(self.genomeview, self.genomebar)
self.Centre()
self.Show(True)
def MakeMenuBar(self):
''' creating the menu '''
#menu "File
fileMenu = wx.Menu()
# menu item "Open Genome"
openGenome = fileMenu.Append(-1, "Open genome", "Open new genome-file")
self.Bind(wx.EVT_MENU, self.OnOpenGenomeFile, openGenome)
# menu item "Open PTT annotation"
openPttAnnotation = fileMenu.Append(-1, "Open PTT annotation", "Open new ptt annotation-file")
self.Bind(wx.EVT_MENU, self.OnOpenPttAnnotation, openPttAnnotation)
# menu item "Open GFF annotation"
openGffAnnotation = fileMenu.Append(-1, "Open GFF annotation", "Open new gff annotation-file")
self.Bind(wx.EVT_MENU, self.OnOpenGffAnnotation, openGffAnnotation)
fileMenu.AppendSeparator()
saveTxt = fileMenu.Append(-1, "Save Text", "Saves Sequence As Shown In The Text Field")
self.Bind(wx.EVT_MENU, self.OnSaveTxt, saveTxt)
saveTxtAs = fileMenu.Append(-1, "Save Text As...", "Saves Sequence As Shown In The Text Field")
self.Bind(wx.EVT_MENU, self.OnSaveTxtAs, saveTxtAs)
fileMenu.AppendSeparator()
# menu item "Exit"
exit = fileMenu.Append(-1, "Exit", "Exit Program")
self.Bind(wx.EVT_MENU, self.OnExit, exit)
#menu "Edit
editMenu = wx.Menu()
edit = editMenu.Append(-1, "Feature Selection", "Edit Feature Selection")
self.Bind(wx.EVT_MENU, self.OnOpenCheckFrame, edit)
changeTypeCol = editMenu.Append(-1, "Change Feature Colors", "Change Colors of Features")
self.Bind(wx.EVT_MENU, self.OnOpenTypeColors, changeTypeCol)
#menu SearchMenu
searchMenu = wx.Menu()
# menu item
openRegExSearch = searchMenu.Append(-1, "Regular Expression", "Search with regular expressions")
self.Bind(wx.EVT_MENU, self.OnOpenRegExSearch, openRegExSearch)
# menu item
openGeneSearch = searchMenu.Append(-1, "Gene Finding", "Search with sequence string")
self.Bind(wx.EVT_MENU, self.OnOpenGeneSearch, openGeneSearch)
#self.Bind(wx.EVT_MENU, self.onOpenFeatureSelection, openFeatureSelection)
#menu Format
formatMenu = wx.Menu()
reset= formatMenu.Append(-1, "Reset", "Reset Format")
self.Bind(wx.EVT_MENU, self.OnReset, reset)
formatMenu.AppendSeparator()
upperCase = formatMenu.AppendCheckItem(-1, "Capitals", "Upper Case")
self.Bind(wx.EVT_MENU, self.OnUpperCase, upperCase)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateUpperCase, upperCase)
bold = formatMenu.AppendCheckItem(-1, "Bold", "Bold")
self.Bind(wx.EVT_MENU, self.OnBold, bold)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateBold, bold)
italic = formatMenu.AppendCheckItem(-1, "Italic", "Italic")
self.Bind(wx.EVT_MENU, self.OnItalic, italic)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateItalic, italic)
formatMenu.AppendSeparator()
increaseSize = formatMenu.Append(-1, "Increase Size", "Increases Font Size")
self.Bind(wx.EVT_MENU, self.OnIncreaseSize, increaseSize)
decreaseSize = formatMenu.Append(-1, "Decrease Size", "Decreases Font Size")
self.Bind(wx.EVT_MENU, self.OnDecreaseSize, decreaseSize)
formatMenu.AppendSeparator()
increaseLineSp = formatMenu.Append(-1, "Increase Line Spacing", "Increases Line Spacing")
self.Bind(wx.EVT_MENU, self.OnIncreaseLineSp, increaseLineSp)
decreaseLineSp = formatMenu.Append(-1, "Decrease Line Spacing", "Decreases Line Spacing")
self.Bind(wx.EVT_MENU, self.OnDecreaseLineSp, decreaseLineSp)
formatMenu.AppendSeparator()
indentMore = formatMenu.Append(-1, "Indent More", "Indents More")
self.Bind(wx.EVT_MENU, self.OnIndentMore, indentMore)
indentLess = formatMenu.Append(-1, "Indent Less", "Indents Less")
self.Bind(wx.EVT_MENU, self.OnIndentLess, indentLess)
formatMenu.AppendSeparator()
seqColor= formatMenu.Append(-1, "Sequence Color", "Change Color Of Sequence")
self.Bind(wx.EVT_MENU, self.OnSeqColor, seqColor)
numColor= formatMenu.Append(-1, "Numeration Color", "Change Color Of Numeration")
self.Bind(wx.EVT_MENU, self.OnNumColor, numColor)
formatMenu.AppendSeparator()
charsPerLine = formatMenu.Append(-1, "Chars Per Line", "Set Number Of Characters Per Line")
self.Bind(wx.EVT_MENU, self.OnCharsPerLine, charsPerLine)
#menu Help
helpMenu = wx.Menu()
about = helpMenu.Append(-1, "About", "About GenomeViewer")
self.Bind(wx.EVT_MENU, self.OnAbout, about)
#NCBI
stuff = helpMenu.Append(-1, "download files from NCBI", "download files")
self.Bind(wx.EVT_MENU, self.OnStuff, stuff)
#uni-tue
uni = helpMenu.Append(-1, "Uni Tuebingen", "official website")
self.Bind(wx.EVT_MENU, self.OnUni, uni)
#append items to menu bar
menuBar = wx.MenuBar()
menuBar.Append(fileMenu, "File")
menuBar.Append(editMenu, "Edit")
menuBar.Append(searchMenu, "Search")
#menuBar.Append(featureselectMenu, "Feature Selection")
menuBar.Append(formatMenu, "Format")
menuBar.Append(helpMenu, "Help")
self.SetMenuBar(menuBar)
def OnUni(self, evt):
open('www.uni-tuebingen.de')
def NotifyTimer(self):
t = time.localtime(time.time())
st = time.strftime("%d-%b-%Y %I:%M:%S", t)
self.statusbar.SetStatusText(st, 2)
def OnCharsPerLine(self, evt):
cpl=self.genomemodel.getCharsPerLine()
#self.genomemodel.getCharsPerLine()
dlg = wx.NumberEntryDialog(self, "", "Enter Characters Per Line:",
"CharsPerLine", cpl, 20, 150)
if dlg.ShowModal() == wx.ID_OK:
self.genomemodel.setCharsPerLine(dlg.GetValue())
dlg.Destroy()
def OnSaveTxt(self, evt):
if not self.genomeview.getRtc().GetFilename():
self.OnSaveTxtAs(evt)
return
self.genomeview.getRtc().SaveFile()
def OnSaveTxtAs(self, evt):
wildcard, types = rt.RichTextBuffer.GetExtWildcard(save=True)
dlg = wx.FileDialog(self, "Choose a filename",
wildcard=wildcard,
style=wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
if path:
fileType = types[dlg.GetFilterIndex()]
ext = rt.RichTextBuffer.FindHandlerByType(fileType).GetExtension()
if not path.endswith(ext):
path += '.' + ext
self.genomeview.getRtc().SaveFile(path, fileType)
dlg.Destroy()
def OnUpperCase(self, evt):
self.genomemodel.changeUpperCase()
def OnUpdateUpperCase(self, evt):
evt.Check(self.genomemodel.isUpperCase())
def OnReset(self, evt):
self.genomemodel.resetLayout()
def OnSeqColor(self, evt):
colourData = wx.ColourData()
colourData.SetColour(self.genomemodel.getSeqColor())
dlg = wx.ColourDialog(self, colourData)
if dlg.ShowModal() == wx.ID_OK:
colourData = dlg.GetColourData()
colour = colourData.GetColour()
self.genomemodel.setSeqColor(colour)
dlg.Destroy()
def OnNumColor(self, evt):
colourData = wx.ColourData()
colourData.SetColour(self.genomemodel.getNumColor())
dlg = wx.ColourDialog(self, colourData)
if dlg.ShowModal() == wx.ID_OK:
colourData = dlg.GetColourData()
colour = colourData.GetColour()
self.genomemodel.setNumColor(colour)
dlg.Destroy()
def OnIncreaseLineSp(self, evt):
self.genomemodel.increaseLineSp(10)
def OnDecreaseLineSp(self, evt):
self.genomemodel.decreaseLineSp(10)
def OnIndentMore(self, evt):
self.genomemodel.indentMore(20)
def OnIndentLess(self, evt):
self.genomemodel.indentLess(20)
def OnUpdateBold(self, evt):
evt.Check(self.genomemodel.isBold())
def OnUpdateItalic(self, evt):
evt.Check(self.genomemodel.isItalic())
def OnBold(self, evt):
self.genomemodel.changeSeqWeight()
def OnItalic(self, evt):
self.genomemodel.changeSeqStyle()
def OnIncreaseSize(self, evt):
self.genomemodel.incSeqSize(2)
self.genomemodel.incNumSize(2)
def OnDecreaseSize(self, evt):
self.genomemodel.decSeqSize(2)
self.genomemodel.decNumSize(2)
def OnOpenCheckFrame(self, evt):
check = CheckBoxFrame()
def OnOpenTypeColors(self, evt):
TypeColors(self, self.genomemodel.getTypeDict())
def OnAbout(self, event):
info = wx.AboutDialogInfo()
info.Name = "GenomeViewer"
info.Version = "1.0"
info.Copyright = "(C) 2009"
info.Description = wordwrap(
"A \"GenomeViewer\" is a software program that views genome sequences ",
350, wx.ClientDC(self))
info.WebSite = ("http://www.uni-tuebingen.de", "Our home page")
info.Developers = [ "Mirco",
"Phil",
"Julian",
"Matze" ]
licenseText = "Everybody is free, so everything is free...."
info.Licence = wordwrap(licenseText, 500, wx.ClientDC(self))
wx.AboutBox(info)
def OnExit(self, event):
children=self.Children
for child in children:
child.Close(True)
self.Close(True)
def OnOpenGenomeFile(self, event):
if platform == "win32":
wildcard = ""
else:
wildcard="*"
dialog = wx.FileDialog(None, "Choose a genome-file", os.getcwd(),
"", wildcard, wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
fasta = Imports.Fasta()
fasta.importfasta(dialog.GetPath())
dialog.Destroy()
def OnOpenGffAnnotation(self, event):
if platform == "win32":
wildcard = ""
else:
wildcard="*"
dialog = wx.FileDialog(None, "Choose an GFF-annotation-file", os.getcwd(),
"", wildcard, wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
gff = Imports.Gff()
gff.importgff(dialog.GetPath())
dialog.Destroy()
def OnOpenPttAnnotation(self, event):
if platform == "win32":
wildcard = ""
else:
wildcard="*"
dialog = wx.FileDialog(None, "Choose an PTT-annotation-file", os.getcwd(),
"", wildcard, wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
ptt = Imports.Ptt()
ptt.importptt(dialog.GetPath())
dialog.Destroy()
def OnOpenRegExSearch(self,event):
dialog = wx.TextEntryDialog(None, "Please enter regular expression here:",
"Regular Expression Search","",
style=wx.OK|wx.CANCEL)
if dialog.ShowModal() == wx.ID_OK:
print "You have entered: %s" % dialog.GetValue()
search=Search(self.genomemodel, self.treeview)
search.regexsearch(dialog.GetValue())
def OnOpenGeneSearch(self,event):
dialog = wx.TextEntryDialog(None, "Please enter sequence string here:",
"Gene finding","",
style=wx.OK|wx.CANCEL)
if dialog.ShowModal() == wx.ID_OK:
print "You have entered: %s" % dialog.GetValue()
search=Search(self.genomemodel, self.treeview)
search.genesearch(dialog.GetValue())
def OnStuff(self,event):
open('http://www.ncbi.nlm.nih.gov/Ftp/')
