View.py

# -*- coding: utf-8 -*-
'''
Created on 27.05.2009

@author: mirco,phil
'''
import wx
import os
from FeatureListContainer import FeatureListContainer
from Genome import Genome
from GenomeView import GenomeView
from GenomeModel import GenomeModel
from GenomeBar import GenomeBar
from IObserver import IObserver
from TreeView import TreeView
import Imports
from Search import Search
from wx.lib.wordwrap import wordwrap
from ProportionalSplitter import ProportionalSplitter
from sys import platform
from CheckBoxFrame import CheckBoxFrame
import wx.richtext as rt
from TypeColors import TypeColors
import  time
from webbrowser import open

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/')

if __name__ == "__main__":
    app = wx.PySimpleApp()
    frame = MainFrame()
    frame.Show(True)
    app.MainLoop()