# -*- coding: utf-8 -*-


import sys

try:
    import wx
    WX_VERSION = int(wx.version()[0])
    hasWx = True

except Exception as e:
    hasWx = False
    WX_VERSION = 0

if hasWx:
    import wx.xrc
    from wx.lib.buttons import GenBitmapTextButton
    from pubsub import pub
    import wx.adv

import os
import time
import datetime
import threading
import numpy
import matplotlib

# Check backends and use the first interactive one
interactive_backends = [i for i in matplotlib.rcsetup.interactive_bk]
goodBackend = False
for backend in interactive_backends:
    if goodBackend: break
    try:
        matplotlib.use(backend,warn=False, force=True)
        from matplotlib import pyplot as plt
        goodBackend = True
    except:
        goodBackend = False


import matplotlib.pyplot as plt
import multiprocessing as mp
import math
import subprocess

from functools import partial

import traceback

import pytransit
import pytransit.analysis
import pytransit.export
import pytransit.trash as trash
import pytransit.transit_tools as transit_tools
import pytransit.tnseq_tools as tnseq_tools
import pytransit.norm_tools as norm_tools
import pytransit.stat_tools as stat_tools
import pytransit.fileDisplay as fileDisplay
import pytransit.qcDisplay as qcDisplay
import pytransit.images as images



method_wrap_width = 250
methods = pytransit.analysis.methods
export_methods = pytransit.export.methods
normmethods = norm_tools.methods


wildcard = "Python source (*.py)|*.py|" \
            "All files (*.*)|*.*"
transit_prefix = "[TRANSIT]"







###########################################################################
## Class MainFrame
###########################################################################

class MainFrame ( wx.Frame ):

    def __init__( self, parent ):
        wx.Frame.__init__ ( self, parent, id = wx.ID_ANY, title = u"TRANSIT", pos = wx.DefaultPosition, size = wx.Size( 1350,975 ), style = wx.DEFAULT_FRAME_STYLE|wx.TAB_TRAVERSAL )


        #Define variables

        #Define Text
        self.instructions_text = """
1. Choose the annotation file ("prot table") that corresponds to the datasets to be analyzed.
2. Add the desired Control and Experimental datasets.
3. (Optional) If you wish to visualize their read counts, select the desired datasets and click on the "View" button.
4. Select the desired analysis method from the dropdown menu on the top-right of the window, and follow its instructions.
"""


        # Define ART
        bmp = wx.ArtProvider.GetBitmap(wx.ART_FILE_OPEN, wx.ART_OTHER, (16, 16))



        #self.SetSizeHintsSz( wx.DefaultSize, wx.DefaultSize )

        bSizer1 = wx.BoxSizer( wx.HORIZONTAL )

        self.mainWindow = wx.ScrolledWindow( self, wx.ID_ANY, wx.DefaultPosition, wx.Size( -1,-1 ), wx.HSCROLL|wx.VSCROLL )
        self.mainWindow.SetScrollRate( 5, 5 )
        self.mainWindow.SetMinSize( wx.Size( 700,-1 ) )

        bSizer4 = wx.BoxSizer( wx.VERTICAL )

        # ANNOTATION
        orgSizer = wx.StaticBoxSizer( wx.StaticBox( self.mainWindow, wx.ID_ANY, u"Organism" ), wx.VERTICAL )

        bSizer10 = wx.BoxSizer( wx.HORIZONTAL )

        self.m_staticText5 = wx.StaticText( self.mainWindow, wx.ID_ANY, u"Annotation File:", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.m_staticText5.Wrap( -1 )
        bSizer10.Add( self.m_staticText5, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )


        self.annotationFilePicker = GenBitmapTextButton(self.mainWindow, 1, bmp, '[Click to add Annotation File (.prot_table or .gff3)]', size= wx.Size(500, -1))

        bSizer10.Add( self.annotationFilePicker, 1, wx.ALIGN_CENTER_VERTICAL, 5 )

        orgSizer.Add( bSizer10, 1, wx.EXPAND, 5 )

        bSizer4.Add( orgSizer, 0, wx.EXPAND, 5 )


        # CONTROL
        ctrlSizer = wx.StaticBoxSizer( wx.StaticBox( self.mainWindow, wx.ID_ANY, u"Control Samples" ), wx.VERTICAL )

        bSizer2 = wx.BoxSizer( wx.HORIZONTAL )

        self.ctrlRemoveButton = wx.Button( self.mainWindow, wx.ID_ANY, u"Remove", wx.DefaultPosition, (96,-1), 0 )
        bSizer2.Add( self.ctrlRemoveButton, 0, wx.ALL, 5 )

        self.ctrlView = wx.Button( self.mainWindow, wx.ID_ANY, u"Track View", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.ctrlView.Hide()

        bSizer2.Add( self.ctrlView, 0, wx.ALL, 5 )

        self.ctrlScatter = wx.Button( self.mainWindow, wx.ID_ANY, u"Scatter", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.ctrlScatter.Hide()

        bSizer2.Add( self.ctrlScatter, 0, wx.ALL, 5 )

        self.ctrlFilePicker = GenBitmapTextButton(self.mainWindow, 1, bmp, '[Click to add Control Dataset(s)]', size= wx.Size(500, -1))
        bSizer2.Add( self.ctrlFilePicker, 1, wx.ALIGN_CENTER_VERTICAL, 5 )

        ctrlSizer.Add( bSizer2, 0, wx.EXPAND, 5 )

        self.list_ctrl = wx.ListCtrl( self.mainWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.LC_REPORT|wx.SUNKEN_BORDER )

        self.list_ctrl.SetMaxSize(wx.Size(-1,200))
        ctrlSizer.Add( self.list_ctrl, 1, wx.ALL|wx.EXPAND, 5 )

        bSizer4.Add( ctrlSizer, 1, wx.EXPAND, 5 )


        # EXPERIMENTAL
        expSizer1 = wx.StaticBoxSizer( wx.StaticBox( self.mainWindow, wx.ID_ANY, u"Experimental Samples" ), wx.VERTICAL )

        bSizer3 = wx.BoxSizer( wx.HORIZONTAL )

        self.expSizer = wx.Button( self.mainWindow, wx.ID_ANY, u"Remove", wx.DefaultPosition, (96,-1), 0 )
        bSizer3.Add( self.expSizer, 0, wx.ALL, 5 )

        self.expView = wx.Button( self.mainWindow, wx.ID_ANY, u"Track View", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.expView.Hide()

        bSizer3.Add( self.expView, 0, wx.ALL, 5 )

        self.expScatter = wx.Button( self.mainWindow, wx.ID_ANY, u"Scatter", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.expScatter.Hide()

        bSizer3.Add( self.expScatter, 0, wx.ALL, 5 )


        self.expFilePicker = GenBitmapTextButton(self.mainWindow, 1, bmp, '[Click to add Experimental Dataset(s)]', size= wx.Size(500, -1))
        bSizer3.Add( self.expFilePicker, 1, wx.ALIGN_CENTER_VERTICAL, 5 )


        expSizer1.Add( bSizer3, 0, wx.EXPAND, 5 )

        self.list_exp = wx.ListCtrl( self.mainWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.LC_REPORT|wx.SUNKEN_BORDER )
        self.list_exp.SetMaxSize(wx.Size(-1, 200))
        expSizer1.Add( self.list_exp, 1, wx.ALL|wx.EXPAND, 5 )


        bSizer4.Add( expSizer1, 1, wx.EXPAND, 5 )



        # RESULTS
        filesSizer = wx.StaticBoxSizer( wx.StaticBox( self.mainWindow, wx.ID_ANY, u"Results Files" ), wx.VERTICAL )

        bSizer141 = wx.BoxSizer( wx.HORIZONTAL )

        self.displayButton = wx.Button( self.mainWindow, wx.ID_ANY, u"Display Table", wx.DefaultPosition, wx.DefaultSize, 0 )
        bSizer141.Add( self.displayButton, 0, wx.ALL, 5 )

        self.fileActionButton = wx.Button( self.mainWindow, wx.ID_ANY, u"Display Graph", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.fileActionButton.Hide()

        bSizer141.Add( self.fileActionButton, 0, wx.ALL, 5 )

        self.addFileButton = GenBitmapTextButton(self.mainWindow, 1 , bmp, 'Add Results File', size= wx.Size(150, 30))


        bSizer141.Add( self.addFileButton, 0, wx.ALL, 5 )

        fileActionChoiceChoices = [ u"[Choose Action]"]
        self.fileActionChoice = wx.Choice( self.mainWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, fileActionChoiceChoices, 0 )
        self.fileActionChoice.SetSelection( 0 )
        bSizer141.Add( self.fileActionChoice, 0, wx.ALL, 5 )


        filesSizer.Add( bSizer141, 0, 0, 5 )

        self.list_files = wx.ListCtrl( self.mainWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.LC_REPORT|wx.SUNKEN_BORDER )
        self.list_files.SetMaxSize(wx.Size(-1,200))
        filesSizer.Add( self.list_files, 1, wx.ALL|wx.EXPAND, 5 )


        bSizer4.Add( filesSizer, 1, wx.EXPAND, 5 )


        self.mainWindow.SetSizer( bSizer4 )
        self.mainWindow.Layout()
        bSizer4.Fit( self.mainWindow )
        bSizer1.Add( self.mainWindow, 1, wx.ALL|wx.EXPAND, 5 )

        self.m_panel5 = wx.Panel( self, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.DOUBLE_BORDER|wx.TAB_TRAVERSAL )
        self.m_panel5.SetMaxSize( wx.Size( 2,-1 ) )

        bSizer1.Add( self.m_panel5, 0, wx.ALL|wx.EXPAND, 5 )

        self.optionsWindow = wx.ScrolledWindow( self, wx.ID_ANY, wx.DefaultPosition, wx.Size( -1,-1 ), wx.HSCROLL|wx.VSCROLL |wx.EXPAND)
        self.optionsWindow.SetScrollRate( 5, 5 )
        self.optionsWindow.SetMinSize( wx.Size( 310,1000 ) )


        self.optionsSizer = wx.BoxSizer( wx.VERTICAL )

        # Logo Section
        self.logoImg = wx.StaticBitmap( self.optionsWindow, wx.ID_ANY, wx.NullBitmap, wx.DefaultPosition, wx.DefaultSize, 0 )
        self.optionsSizer.Add( self.logoImg, 0, wx.ALL|wx.ALIGN_CENTER, 5 )

        self.versionLabel = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"", wx.DefaultPosition, wx.DefaultSize, wx.ALIGN_CENTRE )
        self.versionLabel.Wrap( -1 )
        self.versionLabel.SetFont( wx.Font( 10, 74, 90, 92, False, "Sans" ) )

        self.optionsSizer.Add( self.versionLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )


        # Method Information
        self.methodInfoText = wx.StaticBox( self.optionsWindow, wx.ID_ANY, u"Instructions" )
        self.methodInfoText.SetFont(wx.Font(10, wx.DEFAULT, wx.NORMAL, wx.BOLD))
        self.methodInfoSizer = wx.StaticBoxSizer( self.methodInfoText, wx.VERTICAL )

        self.methodShortText = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.methodShortText.Wrap(250)
        self.methodShortText.Hide()
        self.methodInfoSizer.Add( self.methodShortText, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
        self.methodLongText = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.methodLongText.Wrap(250)
        self.methodLongText.Hide()
        self.methodInfoSizer.Add( self.methodLongText, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )

        self.methodDescText = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.methodDescText.Wrap(250)
        self.methodDescText.Hide()
        self.methodInfoSizer.Add( self.methodDescText, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )

        self.methodTnText = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.methodTnText.Wrap(250)

        font = wx.Font(8, wx.DEFAULT, wx.NORMAL, wx.BOLD)
        self.methodTnText.SetFont(font)
        self.methodTnText.Hide()

        self.methodInfoSizer.Add( self.methodTnText, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )


        self.methodInstructions = wx.StaticText( self.optionsWindow, wx.ID_ANY, self.instructions_text, wx.DefaultPosition, wx.DefaultSize, 0 )
        self.methodInstructions.Wrap( 250 )
        self.methodInfoSizer.Add( self.methodInstructions, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
        self.optionsSizer.Add( self.methodInfoSizer, 0, wx.ALL|wx.EXPAND, 5 )




        # Method Options
        self.methodSizerText = wx.StaticBox( self.optionsWindow, wx.ID_ANY, u"Method Options" )
        self.methodSizerText.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
        self.methodSizer = wx.StaticBoxSizer( self.methodSizerText, wx.VERTICAL )


        self.m_panel1 = wx.Panel( self.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
        self.m_panel1.SetMinSize( wx.Size( 50,1 ) )

        self.methodSizer.Add( self.m_panel1, 0, wx.ALL, 5 )

        self.globalLabel = wx.StaticText( self.optionsWindow, wx.ID_ANY, u"Global Options", wx.DefaultPosition, (130,20), 0 )
        self.globalLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
        self.methodSizer.Add( self.globalLabel, 0, wx.ALIGN_CENTER_HORIZONTAL, 5 )

        self.globalPanel = wx.Panel( self.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
        self.globalPanel.SetMinSize( wx.Size( 280,150 ) )
        self.globalPanel.SetMaxSize( wx.Size(-1,-1) )


        globalSizerVT = wx.BoxSizer( wx.VERTICAL )
        nTermSizer = wx.BoxSizer( wx.HORIZONTAL )
        cTermSizer = wx.BoxSizer( wx.HORIZONTAL )


        # N TERMINUS - GLOBAL
        self.globalNTerminusLabel = wx.StaticText( self.globalPanel, wx.ID_ANY, u"Ignore N-Terminus %:", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.globalNTerminusLabel.Wrap( -1 )

        self.globalNTerminusText = wx.TextCtrl( self.globalPanel, wx.ID_ANY, u"0", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.globalNTerminusIcon = pytransit.analysis.base.InfoIcon(self.globalPanel, wx.ID_ANY, tooltip="Ignores a fraction of the ORF, beginning at the N-terminal end. Useful for ignoring read-counts that may occur at the terminal ends, even though they do not truly disrupt a genes function.")
        nTermSizer.Add( self.globalNTerminusLabel, 1, wx.ALIGN_CENTER, 5 )
        nTermSizer.Add( self.globalNTerminusText, 1, wx.ALIGN_CENTER, 5 )
        nTermSizer.Add( self.globalNTerminusIcon, 1, wx.ALIGN_CENTER, 5 )


        # C TERMINUS - GLOBAL
        self.globalCTerminusLabel = wx.StaticText( self.globalPanel, wx.ID_ANY, u"Ignore C-Terminus %:", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.globalCTerminusLabel.Wrap( -1 )
        self.globalCTerminusText = wx.TextCtrl( self.globalPanel, wx.ID_ANY, u"0", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.globalCTerminusIcon = pytransit.analysis.base.InfoIcon(self.globalPanel, wx.ID_ANY, tooltip="Ignores a fraction of the ORF, beginning at the C-terminal end. Useful for ignoring read-counts that may occur at the terminal ends, even though they do not truly disrupt a genes function.")

        cTermSizer.Add( self.globalCTerminusLabel, 1, wx.ALIGN_CENTER_VERTICAL, 5 )
        cTermSizer.Add( self.globalCTerminusText, 1, wx.ALIGN_CENTER_VERTICAL, 5 )
        cTermSizer.Add( self.globalCTerminusIcon, 1, wx.ALIGN_CENTER, 5 )

        # Control Libraries text - GLOBAL
        ctrlLibSizer = wx.BoxSizer( wx.HORIZONTAL )
        self.ctrlLibLabel = wx.StaticText(self.globalPanel, wx.ID_ANY, u"Control Libraries:",
            wx.DefaultPosition, (170,-1), 0)
        self.ctrlLibLabel.Wrap( -1 )
        self.ctrlLibText = wx.TextCtrl( self.globalPanel, wx.ID_ANY, "",
            wx.DefaultPosition, (-1,-1), 0 )
        self.ctrlLibTip = pytransit.analysis.base.InfoIcon(self.globalPanel, wx.ID_ANY,
            tooltip="String of letters representing an \
            identifier for the libraries the datasets belong to. For example, if adding three \
            datasets of different libraries, change the string to 'ABC'. Set of letters used  \
            must match those in Experimental datasets. Keep empty or with all letters equal, e.g. \
            'AAA', to do regular resampling.")

        self.ctrlLibText.Disable()
        ctrlLibSizer.Add(self.ctrlLibLabel, 0, wx.ALIGN_CENTER_VERTICAL, 5 )
        ctrlLibSizer.Add(self.ctrlLibText, 0, wx.ALIGN_CENTER_VERTICAL, 5 )
        ctrlLibSizer.Add(self.ctrlLibTip, 0, wx.ALIGN_CENTER_VERTICAL, 5 )


        # Experimental Libraries text - GLOBAL
        expLibSizer = wx.BoxSizer( wx.HORIZONTAL )
        self.expLibLabel = wx.StaticText(self.globalPanel, wx.ID_ANY,
            u"Experimental Libraries:",  wx.DefaultPosition, (170,-1), 0)
        self.expLibLabel.Wrap( -1 )
        self.expLibText = wx.TextCtrl( self.globalPanel, wx.ID_ANY, "", wx.DefaultPosition,
            (-1,-1), 0 )
        self.expLibTip = pytransit.analysis.base.InfoIcon(self.globalPanel, wx.ID_ANY,
            tooltip="String of letters representing an identifier for the libraries the datasets \
            belong to. For example, if adding three datasets of different libraries, change the \
            string to 'ABC'. Set  of letters used must match those in Control datasets. Keep \
            empty or with all letters equal, e.g. 'AAA', to do regular resampling.")

        self.expLibText.Disable()
        expLibSizer.Add(self.expLibLabel, 0, wx.ALIGN_CENTER_VERTICAL, 5 )
        expLibSizer.Add(self.expLibText, 0, wx.ALIGN_CENTER_VERTICAL, 5 )
        expLibSizer.Add(self.expLibTip, 0, wx.ALIGN_CENTER_VERTICAL, 5 )


        globalSizerVT.Add( nTermSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )
        globalSizerVT.Add( cTermSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )
        globalSizerVT.Add( ctrlLibSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )
        globalSizerVT.Add( expLibSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )



        self.globalPanel.SetSizer( globalSizerVT )
        self.globalPanel.Layout()
        globalSizerVT.Fit( self.globalPanel )
        self.methodSizer.Add( self.globalPanel, 1, wx.ALIGN_CENTER_HORIZONTAL, 5 )


        #--------------------#

        self.optionsSizer.Add( self.methodSizer, 0, wx.EXPAND, 5 )

        self.optionsWindow.SetSizer( self.optionsSizer )
        self.optionsWindow.Layout()

        self.optionsWindow.Fit()

        bSizer1.Add( self.optionsWindow, 0, wx.ALL, 5 )

        #--------------------#

        self.SetSizer( bSizer1 )
        self.Layout()
        self.m_menubar1 = wx.MenuBar( 0 )
        self.fileMenuItem = wx.Menu()
        self.exportMenuItem = wx.Menu()
        self.selectedExportMenuItem = wx.Menu()

        # Selected datasets
        self.exportMenuItem.AppendSubMenu( self.selectedExportMenuItem, u"Selected Datasets" )

        self.fileMenuItem.AppendSubMenu( self.exportMenuItem, u"Export" )

        self.convertMenuItem = wx.Menu()
        self.annotationConvertPTToPTTMenu = wx.MenuItem( self.convertMenuItem, wx.ID_ANY, u"prot_table to PTT", wx.EmptyString, wx.ITEM_NORMAL )
        self.convertMenuItem.Append( self.annotationConvertPTToPTTMenu )

        self.annotationConvertPTToGFF3Menu = wx.MenuItem( self.convertMenuItem, wx.ID_ANY, u"prot_table to GFF3", wx.EmptyString, wx.ITEM_NORMAL )
        self.convertMenuItem.Append( self.annotationConvertPTToGFF3Menu )

        self.annotationConvertPTTToPT = wx.MenuItem( self.convertMenuItem, wx.ID_ANY, u"PTT to prot_table", wx.EmptyString, wx.ITEM_NORMAL )

        self.convertMenuItem.Append( self.annotationConvertPTTToPT )

        self.annotationConvertGFF3ToPT = wx.MenuItem( self.convertMenuItem, wx.ID_ANY, u"GFF3 to prot_table", wx.EmptyString, wx.ITEM_NORMAL )
        self.convertMenuItem.Append( self.annotationConvertGFF3ToPT )
        self.fileMenuItem.AppendSubMenu( self.convertMenuItem, u"Convert" )

        self.fileExitMenuItem = wx.MenuItem( self.fileMenuItem, wx.ID_ANY, u"&Exit", wx.EmptyString, wx.ITEM_NORMAL )
        self.fileMenuItem.Append( self.fileExitMenuItem )
        self.m_menubar1.Append( self.fileMenuItem, u"&File" )

        self.viewMenuItem = wx.Menu()
        self.scatterMenuItem = wx.MenuItem( self.viewMenuItem, wx.ID_ANY, u"&Scatter Plot", wx.EmptyString, wx.ITEM_NORMAL )

        self.viewMenuItem.Append( self.scatterMenuItem )

        self.trackMenuItem = wx.MenuItem( self.viewMenuItem, wx.ID_ANY, u"&Track View", wx.EmptyString, wx.ITEM_NORMAL )

        self.viewMenuItem.Append( self.trackMenuItem )
        self.qcMenuItem = wx.MenuItem( self.viewMenuItem, wx.ID_ANY, u"&Quality Control", wx.EmptyString, wx.ITEM_NORMAL )

        self.viewMenuItem.Append( self.qcMenuItem )
        self.m_menubar1.Append( self.viewMenuItem, u"&View" )

        #
        self.methodsMenuItem = wx.Menu()
        self.himar1MenuItem = wx.Menu()
        self.tn5MenuItem = wx.Menu()


        self.methodsMenuItem.AppendSubMenu(self.himar1MenuItem, "&Himar1 Methods")
        self.methodsMenuItem.AppendSubMenu(self.tn5MenuItem, "&Tn5 Methods")
        self.m_menubar1.Append( self.methodsMenuItem, u"&Analysis" )


        self.SetMenuBar( self.m_menubar1 )


        self.helpMenuItem = wx.Menu()
        self.documentationMenuItem = wx.MenuItem(self.helpMenuItem, wx.ID_ANY, u"&Documentation", wx.EmptyString, wx.ITEM_NORMAL)
        self.helpMenuItem.Append(self.documentationMenuItem)
        self.aboutMenuItem = wx.MenuItem(self.helpMenuItem, wx.ID_ANY, u"&About", wx.EmptyString, wx.ITEM_NORMAL)
        self.helpMenuItem.Append(self.aboutMenuItem)

        self.m_menubar1.Append( self.helpMenuItem, u"&Help" )


        self.statusBar = self.CreateStatusBar( 1, wx.STB_SIZEGRIP, wx.ID_ANY )




        self.Centre( wx.BOTH )

        # Connect Events

        self.annotationFilePicker.Bind( wx.EVT_BUTTON, self.annotationFileFunc )
        self.ctrlRemoveButton.Bind( wx.EVT_BUTTON, self.ctrlRemoveFunc )
        self.ctrlView.Bind( wx.EVT_BUTTON, self.allViewFunc )
        self.ctrlScatter.Bind( wx.EVT_BUTTON, self.scatterFunc )
        self.ctrlFilePicker.Bind( wx.EVT_BUTTON, self.loadCtrlFileFunc )
        self.expSizer.Bind( wx.EVT_BUTTON, self.expRemoveFunc )
        self.expView.Bind( wx.EVT_BUTTON, self.allViewFunc )
        self.expScatter.Bind( wx.EVT_BUTTON, self.scatterFunc )
        self.expFilePicker.Bind( wx.EVT_BUTTON, self.loadExpFileFunc )
        self.displayButton.Bind( wx.EVT_BUTTON, self.displayFileFunc )
        self.fileActionButton.Bind( wx.EVT_BUTTON, self.fileActionFunc )
        self.addFileButton.Bind( wx.EVT_BUTTON, self.addFileFunc )
        self.fileActionChoice.Bind( wx.EVT_CHOICE, self.fileActionFunc )
        self.list_files.Bind( wx.EVT_LIST_ITEM_SELECTED, self.fileSelected )

        self.Bind( wx.EVT_MENU, self.annotationPT_to_PTT, id = self.annotationConvertPTToPTTMenu.GetId() )
        self.Bind( wx.EVT_MENU, self.annotationPT_to_GFF3, id = self.annotationConvertPTToGFF3Menu.GetId() )
        self.Bind( wx.EVT_MENU, self.annotationPTT_to_PT, id = self.annotationConvertPTTToPT.GetId() )
        self.Bind( wx.EVT_MENU, self.annotationGFF3_to_PT, id = self.annotationConvertGFF3ToPT.GetId() )
        self.Bind( wx.EVT_MENU, self.Exit, id = self.fileExitMenuItem.GetId() )
        self.Bind( wx.EVT_MENU, self.scatterFunc, id = self.scatterMenuItem.GetId() )
        self.Bind( wx.EVT_MENU, self.allViewFunc, id = self.trackMenuItem.GetId() )
        self.Bind( wx.EVT_MENU, self.qcFunc, id = self.qcMenuItem.GetId() )

        self.Bind( wx.EVT_MENU, self.aboutFunc, id = self.aboutMenuItem.GetId() )
        self.Bind( wx.EVT_MENU, self.documentationFunc, id = self.documentationMenuItem.GetId() )
        self.timer = wx.Timer(self)
        self.Bind(wx.EVT_TIMER, self.clearStatus, self.timer)



    def __del__( self ):
        pass


    # Virtual event handlers, overide them in your derived class
    def clearStatus(self, event):
        event.Skip()

    def onHimar1Checked(self, event):
        event.Skip()

    def onTn5Checked(self, event):
        event.Skip()

    def annotationFileFunc( self, event ):
        event.Skip()

    def ctrlRemoveFunc( self, event ):
        event.Skip()

    def allViewFunc( self, event ):
        event.Skip()

    def scatterFunc( self, event ):
        event.Skip()

    def loadCtrlFileFunc( self, event ):
        event.Skip()

    def expRemoveFunc( self, event ):
        event.Skip()

    def loadExpFileFunc( self, event ):
        event.Skip()

    def displayFileFunc( self, event ):
        event.Skip()

    def fileActionFunc( self, event ):
        event.Skip()

    def addFileFunc( self, event ):
        event.Skip()


    def MethodSelectFunc( self, event ):
        event.Skip()

#    def RunGumbelFunc( self, event ):
#        event.Skip()

    def RunBinomialFunc( self, event ):
        event.Skip()

    def LoessPrevFunc( self, event ):
        event.Skip()

    def RunHMMFunc( self, event ):
        event.Skip()


    def RunResamplingFunc( self, event ):
        event.Skip()


    def RunDEHMMFunc( self, event ):
        event.Skip()

    def ctrlToIGV( self, event ):
        event.Skip()

    def expToIGV( self, event ):
        event.Skip()

    def annotationPT_to_PTT( self, event ):
        event.Skip()

    def annotationPT_to_GFF3( self, event ):
        event.Skip()

    def annotationPTT_to_PT( self, event ):
        event.Skip()

    def annotationGFF3_to_PT( self, event ):
        event.Skip()

    def Exit( self, event ):
        event.Skip()


    def qcFunc( self, event ):
        event.Skip()

    def aboutFunc( self, event ):
        event.Skip()

    def documentationFunc( self, event ):
        event.Skip()


#!/usr/bin/env python

# Copyright 2015.
#   Michael A. DeJesus, Chaitra Ambadipudi, and  Thomas R. Ioerger.
#
#
#    This file is part of TRANSIT.
#
#    TRANSIT is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License.
#
#
#    TRANSIT is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with TRANSIT.  If not, see <http://www.gnu.org/licenses/>.


#inherit from the MainFrame created in wxFowmBuilder and create CalcFrame
class TnSeekFrame(MainFrame):
    #constructor
    def __init__(self,parent,DEBUG=False):
        #initialize parent class
        MainFrame.__init__(self,parent)

        self.SetIcon(images.transit_icon.GetIcon())

        self.workdir = os.getcwd()
        self.annotation = ""
        self.transposons = ["himar1", "tn5"]
        #import pkgutil
        #print [x for x in pkgutil.iter_modules(['transit/analysis'])]
        #print gumbel.Gumbel.__bases__

        self.logoImg.SetBitmap(images.transit_logo2.GetImage().ConvertToBitmap())
        self.versionLabel.SetLabel(pytransit.__version__)
        self.methodSizerText.Hide()

        self.index_ctrl = 0
        self.list_ctrl.InsertColumn(0, 'File', width=210)
        self.list_ctrl.InsertColumn(1, 'Total Reads', width=85)
        self.list_ctrl.InsertColumn(2, 'Density', width=85)
        self.list_ctrl.InsertColumn(3, 'Mean Count', width=90)
        self.list_ctrl.InsertColumn(4, 'Max Count', width=85)
        self.list_ctrl.InsertColumn(5, 'Full Path', width=403)


        self.index_exp = 0
        self.list_exp.InsertColumn(0, 'File', width=210)
        self.list_exp.InsertColumn(1, 'Total Reads', width=85)
        self.list_exp.InsertColumn(2, 'Density', width=85)
        self.list_exp.InsertColumn(3, 'Mean Count', width=90)
        self.list_exp.InsertColumn(4, 'Max Count', width=85)
        self.list_exp.InsertColumn(5, 'Full Path',width=403)


        self.index_file = 0
        self.list_files.InsertColumn(0, 'Name', width=350)
        self.list_files.InsertColumn(1, 'Type', width=100)
        self.list_files.InsertColumn(2, 'Date', width=230)
        self.list_files.InsertColumn(3, 'Full Path',width=403)


        self.verbose = True


        self.statusBar.SetStatusText("Welcome to TRANSIT")
        self.progress_count = 0
        pub.subscribe(self.setProgressRange, "progressrange")
        pub.subscribe(self.updateProgress, "progress")
        pub.subscribe(self.updateStatus, "status")
        pub.subscribe(self.addFile, "file")
        pub.subscribe(self.finishRun, "finish")
        pub.subscribe(self.saveHistogram, "histogram")

        #self.outputDirPicker.SetPath(os.path.dirname(os.path.realpath(__file__)))


        # Export Menu Items
        for name in export_methods:
            export_methods[name].gui.defineMenuItem(self, export_methods[name].label)
            tempMenuItem = export_methods[name].gui.menuitem
            self.selectedExportMenuItem.Append( tempMenuItem )

            self.Bind( wx.EVT_MENU, partial(self.ExportSelectFunc,  export_methods[name].label),
                tempMenuItem )




        # Method Panels

        methodChoiceChoices = [ "[Choose Method]"]
        for name in methods:
            methods[name].gui.definePanel(self)
            #methods[name].gui.panel.BackgroundColour = (0, 200, 20)
            self.methodSizer.Add(methods[name].gui.panel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
            methods[name].gui.Hide()

            if "himar1" in methods[name].transposons:
                tempMenuItem = wx.MenuItem( self.himar1MenuItem, wx.ID_ANY, methods[name].fullname(), wx.EmptyString, wx.ITEM_NORMAL )
                self.Bind( wx.EVT_MENU, partial(self.MethodSelectFunc,  methods[name].fullname()), tempMenuItem )

                self.himar1MenuItem.Append( tempMenuItem )

            if "tn5" in methods[name].transposons:
                tempMenuItem = wx.MenuItem( self.tn5MenuItem, wx.ID_ANY, methods[name].fullname(), wx.EmptyString, wx.ITEM_NORMAL )
                self.Bind( wx.EVT_MENU, partial(self.MethodSelectFunc, methods[name].fullname()), tempMenuItem )
                self.tn5MenuItem.Append( tempMenuItem )

        #progress
        self.progressPanel = wx.Panel( self.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
        progressSizer = wx.BoxSizer( wx.VERTICAL )

        self.progressLabel = wx.StaticText( self.progressPanel, wx.ID_ANY, u"Progress", wx.DefaultPosition, wx.DefaultSize, 0 )
        self.progressLabel.Wrap( -1 )
        progressSizer.Add( self.progressLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )

        self.progress = wx.Gauge( self.progressPanel, wx.ID_ANY, 20, wx.DefaultPosition, wx.DefaultSize, wx.GA_HORIZONTAL|wx.GA_SMOOTH )
        progressSizer.Add( self.progress, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )


        #self.progressPanel.BackgroundColour = (0, 0, 250)
        self.progressPanel.SetSizer( progressSizer )
        self.progressPanel.SetMaxSize(wx.Size(100, 100))
        self.progressPanel.Layout()

        #progressSizer.Fit( self.progressPanel )
        self.methodSizer.Add( self.progressPanel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )

        #self.methodSizer.Add( self.globalLabel, 1, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
        #self.methodSizer.Hide()
        self.progress.SetRange(50)
        #########

        self.optionsWindow.Fit()

        self.HideProgressSection()
        self.HideGlobalOptions()

        self.DEBUG = DEBUG
        if self.DEBUG:
            ctrlData = ["glycerol_H37Rv_rep1.wig", "glycerol_H37Rv_rep2.wig"]
            for dataset in ctrlData:
                try:
                    path = os.path.dirname(os.path.realpath(__file__))
                    path = os.path.join(os.path.dirname('/pacific/home/mdejesus/transit/src/transit.py'), "pytransit/data", dataset)
                    transit_tools.transit_message("Adding Ctrl File: " + path)
                    self.loadCtrlFile(path)
                except Exception as e:
                    print "Error:", str(e)

            expData = ["cholesterol_H37Rv_rep1.wig", "cholesterol_H37Rv_rep2.wig", "cholesterol_H37Rv_rep3.wig"]
            for dataset in expData:
                try:
                    path = os.path.join(os.path.dirname('/pacific/home/mdejesus/transit/src/transit.py'), "pytransit/data", dataset)
                    transit_tools.transit_message("Adding Exp File: " + path)
                    self.loadExpFile(path)
                except Exception as e:
                    print "Error:", str(e)

            try:
                self.annotation = os.path.join(os.path.dirname('/pacific/home/mdejesus/transit/src/transit.py'), "pytransit/genomes/H37Rv.prot_table")
                self.annotationFilePicker.SetLabel(transit_tools.basename(self.annotation))
                transit_tools.transit_message("Annotation File Selected: %s" % self.annotation)
            except Exception as e:
                print "Error:", str(e)

#

    def Exit(self, event):
        """Exit Menu Item"""
        if self.verbose:
            transit_tools.transit_message("Exiting Transit")
        self.Close()

#

    def updateProgress(self, msg):
        """"""
        method, count = msg
        self.progress_count = count
        try:
            self.progress.SetValue(self.progress_count)
        except:
            pass

#

    def setProgressRange(self, msg):
        """"""
        count = msg
        try:
            self.progress.SetRange(count)
        except:
            pass

#

    def updateStatus(self, msg, time=-1):
        """"""
        if type(msg) == type("A"):
            text = msg
        else:
            method, text, time = msg
        if time > 0:
            self.timer.Start(time)
        self.statusBar.SetStatusText(text)

#

    def clearStatus(self, event):
        self.statusBar.SetStatusText("")
        self.timer.Stop()

#

    def saveHistogram(self, msg):
        data, orf, path, delta = msg

        n, bins, patches = plt.hist(data, density=1, facecolor='c', alpha=0.75, bins=100)
        plt.xlabel('Delta Sum')
        plt.ylabel('Probability')
        plt.title('%s - Histogram of Delta Sum' % orf)
        plt.axvline(delta, color='r', linestyle='dashed', linewidth=3)
        plt.grid(True)
        genePath = os.path.join(path, orf +".png")
        plt.savefig(genePath)
        plt.clf()

#

    def addFile(self, data):
        fullpath = data["path"]
        name = transit_tools.basename(fullpath)
        type = data["type"]
        date = data["date"]
        self.list_files.InsertItem(self.index_file, name)
        self.list_files.SetItem(self.index_file, 1, "%s" % type)
        self.list_files.SetItem(self.index_file, 2, "%s" % (date))
        self.list_files.SetItem(self.index_file, 3, "%s" % (fullpath))
        self.index_file+=1

#

    def finishRun(self,msg):
        try:
            self.progress_count = 0
            self.progress.SetValue(self.progress_count)

        except Exception as e:
            transit_tools.transit_message("Error: %s" % e)
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)

#

    def ResetProgress(self):
        self.progress_count = 0

#

    def HideAllOptions(self):
        self.HideGlobalOptions()
        self.HideProgressSection()
        for name in methods:
            methods[name].gui.Hide()

#

    def HideGlobalOptions(self):
        self.globalLabel.Hide()
        self.HideGlobalCTerminus()
        self.HideGlobalNTerminus()
        self.HideGlobalLibraries()

#

    def HideGlobalCTerminus(self):
        self.globalCTerminusLabel.Hide()
        self.globalCTerminusText.Hide()
        self.globalCTerminusIcon.Hide()

#

    def HideGlobalNTerminus(self):
        self.globalNTerminusLabel.Hide()
        self.globalNTerminusText.Hide()
        self.globalNTerminusIcon.Hide()

#

    def HideGlobalLibraries(self):
        self.HideGlobalCtrlLibraries()
        self.HideGlobalExpLibraries()
#

    def HideGlobalCtrlLibraries(self):
        self.ctrlLibLabel.Hide()
        self.ctrlLibText.Hide()
        self.ctrlLibTip.Hide()

#

    def HideGlobalExpLibraries(self):
        self.expLibLabel.Hide()
        self.expLibText.Hide()
        self.expLibTip.Hide()

#

    def ShowGlobalOptions(self):
        self.globalLabel.Show()
        self.ShowGlobalCTerminus()
        self.ShowGlobalNTerminus()
        self.ShowGlobalLibraries()

#

    def ShowGlobalCTerminus(self):
        self.globalCTerminusLabel.Show()
        self.globalCTerminusText.Show()
        self.globalCTerminusIcon.Show()

#

    def ShowGlobalNTerminus(self):
        self.globalNTerminusText.Show()
        self.globalNTerminusLabel.Show()
        self.globalNTerminusIcon.Show()

    def ShowGlobalLibraries(self):
        self.ShowGlobalCtrlLibraries()
        self.ShowGlobalExpLibraries()

    def ShowGlobalCtrlLibraries(self):
        self.ctrlLibLabel.Show()
        self.ctrlLibText.Show()
        self.ctrlLibTip.Show()

    def ShowGlobalExpLibraries(self):
        self.expLibLabel.Show()
        self.expLibText.Show()
        self.expLibTip.Show()


#

    def HideProgressSection(self):
        self.progressLabel.Hide()
        self.progress.Hide()

#

    def ShowProgressSection(self):
        self.progressLabel.Show()
        self.progress.Show()

#

    def onHimar1Checked(self, event):
        if self.methodCheckBoxHimar1.GetValue():
            self.transposons.append("himar1")
        else:
            self.transposons.remove("himar1")
        self.filterMethodsByTransposon()

#

    def onTn5Checked(self, event):
        if self.methodCheckBoxTn5.GetValue():
            self.transposons.append("tn5")
        else:
            self.transposons.remove("tn5")
        self.filterMethodsByTransposon()

#

    def filterMethodsByTransposon(self):
        newmethods = {}
        fullmethods = pytransit.analysis.methods
        goodTn = False
        for method in fullmethods:
            goodTn = False
            for tn in self.transposons:
                if tn in fullmethods[method].transposons:
                    goodTn = True
            if goodTn:
                newmethods[method] = fullmethods[method]

        methodChoiceChoices = [ "[Choose Method]"]
        for name in newmethods:
            methodChoiceChoices.append(methods[name].fullname())
        self.methodChoice.SetItems(methodChoiceChoices)
        self.methodChoice.SetSelection( 0 )

#

    def SaveFile(self, DIR=None, FILE="", WC=u'Common output extensions (*.txt,*.dat,*.out)|*.txt;*.dat;*.out;|\nAll files (*.*)|*.*"'):
        """
        Create and show the Save FileDialog
        """
        path = ""

        if not DIR:
            DIR = os.getcwd()

        dlg = wx.FileDialog(
            self, message="Save file as ...",
            defaultDir=DIR,
            defaultFile=FILE, wildcard=WC, style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT
            )
        if dlg.ShowModal() == wx.ID_OK:
            path = dlg.GetPath()
            if self.verbose:
                transit_tools.transit_message("You chose the following output filename: %s" % path)
        dlg.Destroy()
        return path

#

    def OpenFile(self, DIR=".", FILE="", WC=""):
        """
        Create and show the Open FileDialog
        """
        path = ""
        dlg = wx.FileDialog(
            self, message="Save file as ...",
            defaultDir=DIR,
            defaultFile=FILE, wildcard=WC, style=wx.FD_OPEN
            )
        if dlg.ShowModal() == wx.ID_OK:
            path = dlg.GetPath()
            if self.verbose:
                transit_tools.transit_message("You chose the following file: %s" % path)
        dlg.Destroy()
        return path

#

    def ctrlSelected(self, col=5):
        selected_ctrl = []
        current = -1
        while True:
            next = self.list_ctrl.GetNextSelected(current)
            if next == -1:
                break
            path = self.list_ctrl.GetItem(next, col).GetText()
            selected_ctrl.append(path)
            current = next
        return selected_ctrl

#

    def expSelected(self, col=5):
        selected_exp = []
        current = -1
        while True:
            next = self.list_exp.GetNextSelected(current)
            if next == -1:
                break
            path = self.list_exp.GetItem(next, col).GetText()
            selected_exp.append(path)
            current = next
        return selected_exp

#

    def allSelected(self, col=5):
        selected_all = self.ctrlSelected(col) + self.expSelected(col)
        return selected_all

#

    def ctrlAll(self, col=5):
        all_ctrl = []
        for i in range(self.list_ctrl.GetItemCount()):
            all_ctrl.append(self.list_ctrl.GetItem(i, col).GetText())
        return all_ctrl

#

    def expAll(self, col=5):
        all_exp = []
        for i in range(self.list_exp.GetItemCount()):
            all_exp.append(self.list_exp.GetItem(i, col).GetText())
        return all_exp

#

    def loadCtrlFile(self, fullpath):
        name = transit_tools.basename(fullpath)
        (density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
        self.list_ctrl.InsertItem(self.index_ctrl, name)
        self.list_ctrl.SetItem(self.index_ctrl, 1, "%1.1f" % (totalrd))
        self.list_ctrl.SetItem(self.index_ctrl, 2, "%2.1f" % (density*100))
        self.list_ctrl.SetItem(self.index_ctrl, 3, "%1.1f" % (meanrd))
        self.list_ctrl.SetItem(self.index_ctrl, 4, "%d" % (maxrd))
        self.list_ctrl.SetItem(self.index_ctrl, 5, "%s" % (fullpath))

        self.list_ctrl.Select(self.index_ctrl)
        self.index_ctrl+=1
        try:
            self.ctrlLibText.SetValue(self.ctrlLibText.GetValue()+"A")
        except Exception as e:
            transit_tools.transit_message("Error Modifying Ctrl Lib String: %s" % e)
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)


#

    def loadExpFile(self, fullpath):
        name = transit_tools.basename(fullpath)
        (density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
        self.list_exp.InsertItem(self.index_exp, name)
        self.list_exp.SetItem(self.index_exp, 1, "%1.1f" % (totalrd))
        self.list_exp.SetItem(self.index_exp, 2, "%2.1f" % (density*100))
        self.list_exp.SetItem(self.index_exp, 3, "%1.1f" % (meanrd))
        self.list_exp.SetItem(self.index_exp, 4, "%d" % (maxrd))
        self.list_exp.SetItem(self.index_exp, 5, "%s" % (fullpath))
        self.list_exp.Select(self.index_exp)
        self.index_exp+=1

        try:
            self.expLibText.SetValue(self.expLibText.GetValue()+"A")
        except Exception as e:
            transit_tools.transit_message("Error Modifying Ctrl Lib String: %s" % e)
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)


#

    def loadCtrlFileFunc(self, event):
        self.statusBar.SetStatusText("Loading Control Dataset(s)...")
        try:

            dlg = wx.FileDialog(
                self, message="Choose a file",
                defaultDir=self.workdir,
                defaultFile="",
                wildcard=u"Read Files (*.wig)|*.wig;|\nRead Files (*.txt)|*.txt;|\nRead Files (*.dat)|*.dat;|\nAll files (*.*)|*.*",
                style=wx.FD_OPEN | wx.FD_MULTIPLE | wx.FD_CHANGE_DIR
                )
            if dlg.ShowModal() == wx.ID_OK:
                paths = dlg.GetPaths()
                print "You chose the following Control file(s):"
                for fullpath in paths:
                    print "\t%s" % fullpath
                    self.loadCtrlFile(fullpath)
            dlg.Destroy()
        except Exception as e:
            transit_tools.transit_message("Error: %s" % e)
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)
        self.statusBar.SetStatusText("")

#

    def loadExpFileFunc(self, event):
        self.statusBar.SetStatusText("Loading Experimental Dataset(s)...")
        try:

            dlg = wx.FileDialog(
                self, message="Choose a file",
                defaultDir=self.workdir,
                defaultFile="",
                wildcard=u"Read Files (*.wig)|*.wig;|\nRead Files (*.txt)|*.txt;|\nRead Files (*.dat)|*.dat;|\nAll files (*.*)|*.*",
                style=wx.FD_OPEN | wx.FD_MULTIPLE | wx.FD_CHANGE_DIR
                )
            if dlg.ShowModal() == wx.ID_OK:
                paths = dlg.GetPaths()
                print "You chose the following Experimental file(s):"
                for fullpath in paths:
                    print "\t%s" % fullpath
                    self.loadExpFile(fullpath)
            dlg.Destroy()
        except Exception as e:
            transit_tools.transit_message("Error: %s" % e)
            print "PATH", fullpath
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)

        self.statusBar.SetStatusText("")

#

    def ctrlRemoveFunc(self, event):
        next = self.list_ctrl.GetNextSelected(-1)
        while next != -1:
            if self.verbose:
                transit_tools.transit_message("Removing control item (%d): %s" % (next, self.list_ctrl.GetItem(next, 0).GetText()))

            # Update library string after removing wig file
            updated_lib_text = self.ctrlLibText.GetValue()
            updated_lib_text = updated_lib_text[:next] + updated_lib_text[(next+1):]
            self.ctrlLibText.SetValue(updated_lib_text)

            # Delete and Get next selected
            self.list_ctrl.DeleteItem(next)
            next = self.list_ctrl.GetNextSelected(-1)
            self.index_ctrl-=1

#

    def expRemoveFunc(self, event):
        next = self.list_exp.GetNextSelected(-1)
        while next != -1:
            if self.verbose:
                transit_tools.transit_message("Removing experimental item (%d): %s" % (next, self.list_exp.GetItem(next, 0).GetText()))

            # Update library string after removing wig file
            updated_lib_text = self.expLibText.GetValue()
            updated_lib_text = updated_lib_text[:next] + updated_lib_text[(next+1):]
            self.expLibText.SetValue(updated_lib_text)

            # Delete and Get next selected
            self.list_exp.DeleteItem(next)
            next = self.list_exp.GetNextSelected(-1)
            self.index_exp-=1

#

    def allViewFunc(self, event, gene=""):

        annotationpath = self.annotation
        datasets = self.ctrlSelected() + self.expSelected()

        if datasets and annotationpath:
            if self.verbose:
                transit_tools.transit_message("Visualizing counts for: %s" % ", ".join([transit_tools.fetch_name(d) for d in datasets]))
            viewWindow = trash.TrashFrame(self, datasets, annotationpath, gene=gene)
            viewWindow.Show()
        elif not datasets:
            transit_tools.ShowError("Error: No datasets selected.")
            return
        else:
            transit_tools.ShowError("Error: No annotation file selected.")
            return

#

    def ctrlViewFunc(self, event, gene=""):
        annotationpath = self.annotation
        datasets = self.ctrlSelected()
        if datasets and annotationpath:
            if self.verbose:
                transit_tools.transit_message("Visualizing counts for: %s" % ", ".join([transit_tools.fetch_name(d) for d in datasets]))
            viewWindow = trash.TrashFrame(self, datasets, annotationpath, gene)
            viewWindow.Show()
        elif not datasets:
            if self.verbose:
                transit_tools.transit_message("No datasets selected to visualize!")
        else:
            if self.verbose:
                transit_tools.transit_message("No annotation file selected")

#

    def expViewFunc(self, event, gene=""):
        annotationpath = self.annotation
        datasets = self.expSelected()
        if datasets and annotationpath:
            if self.verbose:
                transit_tools.transit_message("Visualizing counts for: %s" % ", ".join([transit_tools.fetch_name(d) for d in datasets]))
            viewWindow = trash.TrashFrame(self, datasets, annotationpath, gene)
            viewWindow.Show()
        elif not datasets:
            if self.verbose:
                transit_tools.transit_message("No datasets selected to visualize!")
        else:
            if self.verbose:
                transit_tools.transit_message("No annotation file selected")

#

    def scatterFunc(self, event):
        """ """
        #annotationpath = self.annotation
        datasets = self.ctrlSelected() + self.expSelected()
        if len(datasets) == 2:
            if self.verbose:
                transit_tools.transit_message("Showing scatter plot for: %s" % ", ".join([transit_tools.fetch_name(d) for d in datasets]))
            (data, position) = tnseq_tools.get_data(datasets)
            X = data[0,:]
            Y = data[1,:]

            plt.plot(X,Y, "bo")
            plt.title('Scatter plot - Reads at TA sites')
            plt.xlabel(transit_tools.fetch_name(datasets[0]))
            plt.ylabel(transit_tools.fetch_name(datasets[1]))
            plt.show()
        else:
            transit_tools.ShowError(MSG="Please make sure only two datasets are selected (across control and experimental datasets).")

#

    def qcFunc(self, event):
        datasets = self.allSelected()
        nfiles = len(datasets)

        if nfiles == 0:
            transit_tools.transit_message("You must select atleast one dataset control or experimental dataset.")
            transit_tools.ShowError(MSG="You must select atleast one dataset control or experimental dataset.")

        elif nfiles >= 1:
            transit_tools.transit_message("Displaying results: %s" % datasets[0])
            try:
                qcWindow = qcDisplay.qcFrame(self, datasets)
                qcWindow.Show()
            except Exception as e:
                transit_tools.transit_message("Error occured displaying file: %s" % str(e))
                traceback.print_exc()

#

    def aboutFunc(self, event):
        description = """TRANSIT is a tool for analysing TnSeq data. It provides an easy to use graphical interface and access to several different analysis methods that allow the user to determine essentiality within a single condition as well as between two conditions.


If you need to cite this tool, please use the following reference:

DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT - a Software Tool for Himar1 TnSeq Analysis. PLOS Computational Biology, 11(10):e1004401


"""


        licence = """
TRANSIT is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License.


TRANSIT is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with TRANSIT.  If not, see <http://www.gnu.org/licenses/>.
        """



        info = wx.adv.AboutDialogInfo()
        info.SetIcon(images.transit_logo2.GetIcon())
        #images.transit_logo2.GetImage().ConvertToBitmap()
        info.SetName('TRANSIT')
        info.SetVersion(pytransit.__version__)
        info.SetDescription(description)
        info.SetCopyright('(C) 2015\n Michael A. DeJesus\nThomas R. Ioerger')
        info.SetWebSite('http://saclab.tamu.edu/essentiality/transit/')
        info.SetLicence(licence)
        info.AddDeveloper('Michael A. DeJesus')
        info.AddDeveloper('Thomas R. Ioerger')
        info.AddDeveloper('Chaitra Ambadipudi')
        info.AddDeveloper('Richard Baker')
        info.AddDeveloper('Christopher Sassetti')
        info.AddDeveloper('Eric Nelson')
        wx.adv.AboutBox(info)
#

    def documentationFunc(self, event):

        filepath = "http://saclab.tamu.edu/essentiality/transit/transit.html"
        output = ""
        error = ""
        try:
            if sys.platform.startswith('darwin'):
                OS = "OSX"
                #subprocess.call(('open', filepath))
                args = ["open", filepath]
                output,error = subprocess.Popen(args,stdout = subprocess.PIPE, stderr= subprocess.PIPE).communicate()
            elif os.name == 'nt':
                OS = "Windows"
                os.startfile(filepath)
            elif os.name == 'posix':
                OS = "Linux"
                args = ["xdg-open", filepath]
                output,error = subprocess.Popen(args,stdout = subprocess.PIPE, stderr= subprocess.PIPE).communicate()
                if "not found" in error:
                    args = ["exo-open", filepath]
                    output,error = subprocess.Popen(args,stdout = subprocess.PIPE, stderr= subprocess.PIPE).communicate()

        except Exception as e:
            error_text = """Error occurred opening documentation URL.\nYour browser or OS may not be configured correctly."""
            transit_tools.ShowError(MSG=error_text)
            traceback.print_exc()

#

    def annotationFileFunc(self, event):

        wc = u"Known Annotation Formats (*.prot_table,*.gff3,*.gff)|*.prot_table;*.gff3;*.gff;|\nProt Table (*.prot_table)|*.prot_table;|\nGFF3 (*.gff,*.gff3)|*.gff;*.gff3;|\nAll files (*.*)|*.*"
        self.annotation = self.OpenFile(DIR=self.workdir, FILE="", WC=wc)
        if self.annotation:
            self.annotationFilePicker.SetLabel(transit_tools.basename(self.annotation))
            if self.verbose:
                transit_tools.transit_message("Annotation File Selected: %s" % self.annotation)
        else:
            self.annotationFilePicker.SetLabel("[Click to add Annotation File (.prot_table or .gff3)]")

#
    def MethodSelectFunc(self, selected_name, test=""):
        #X = self.methodChoice.GetCurrentSelection()
        #selected_name = self.methodChoice.GetString(X)

        #If empty is selected
        if selected_name == "[Choose Method]":
            self.HideAllOptions()
            self.methodInfoText.SetLabel(u"Instructions")
            self.methodInstructions.Show()
            self.methodInstructions.SetLabel(self.instructions_text)
            self.methodInstructions.Wrap(method_wrap_width)
            self.methodShortText.Hide()
            self.methodLongText.Hide()
            self.methodTnText.Hide()
            self.methodDescText.Hide()

            self.method_choice = ""
        else:
            self.ShowGlobalOptions()
            self.methodSizerText.Show()

            #Get selected Method and hide Others
            for name in methods:
                methods[name].gui.Hide()
                methods[name].gui.GlobalHide()
                methods[name].gui.GlobalDisable()

                if methods[name].fullname() == selected_name:
                    matched_name = name

            if matched_name in methods:
                name = matched_name
                self.methodInfoText.SetLabel("%s" % methods[name].long_name)

                self.methodTnText.Show()
                self.methodTnText.SetLabel(methods[name].getTransposonsText())
                self.methodTnText.Wrap(250)

                self.methodDescText.Show()
                self.methodDescText.SetLabel(methods[name].getDescriptionText())
                self.methodDescText.Wrap(250)
                self.methodInstructions.SetLabel(" ")
                methods[name].gui.Show()
                methods[name].gui.Show()
                methods[name].gui.GlobalEnable()
                self.statusBar.SetStatusText("[%s]" % methods[name].short_name)

            self.ShowProgressSection()
            self.method_choice = selected_name

        self.Layout()
        if self.verbose:
            transit_tools.transit_message("Selected Method: %s" % (selected_name))

#

    def ExportSelectFunc(self, selected_name, test=""):
        #X = self.methodChoice.GetCurrentSelection()
        #selected_name = self.methodChoice.GetString(X)

        if self.verbose:
            transit_tools.transit_message("Selected Export Method: %s" % (selected_name))

        for name in export_methods:
            if export_methods[name].label == selected_name:
                methodobj = export_methods[name].method
                try:
                    M = methodobj.fromGUI(self)
                    if M:
                        thread = threading.Thread(target=M.Run())
                        thread.setDaemon(True)
                        thread.start()
                except Exception as e:
                    transit_tools.transit_message("Error: %s" % str(e))
                    traceback.print_exc()

#

    def displayFileFunc(self, event):
        next = self.list_files.GetNextSelected(-1)
        if next > -1:
            dataset = self.list_files.GetItem(next, 3).GetText()
            if self.verbose:
                transit_tools.transit_message("Displaying results: %s" % self.list_files.GetItem(next, 0).GetText())

            try:
                #fileWindow = fileDisplay.FileFrame(self, dataset, self.list_files.GetItem(next, 1).GetText())
                fileWindow = fileDisplay.TransitGridFrame(self, dataset)
                fileWindow.Show()
            except Exception as e:
                transit_tools.transit_message("Error occurred displaying file: %s" % str(e))
                traceback.print_exc()

        else:
            if self.verbose:
                transit_tools.transit_message("No results selected to display!")

#

    def fileSelected(self,event):
        next = self.list_files.GetNextSelected(-1)
        if next > -1:
            dataset_path = self.list_files.GetItem(next, 3).GetText()
            dataset_name = self.list_files.GetItem(next, 0).GetText()
            dataset_type = self.list_files.GetItem(next, 1).GetText()
            self.updateGraphChoices(dataset_type)
        else:
            pass

#

    def updateGraphChoices(self, dataset_type):

        empty_action = "[Choose Action]"
        if dataset_type == "Gumbel":
            choices = [empty_action, "Plot Ranked Probability of Essentiality"]
        elif dataset_type == "Binomial":
            choices = [empty_action, "Plot Ranked Probability of Essentiality"]
        elif dataset_type == "HMM - Sites":
            choices = [empty_action]
        elif dataset_type == "HMM - Genes":
            choices = [empty_action]
        elif dataset_type == "Resampling":
            choices = [empty_action, "Create a Volcano Plot", "Plot Histogram of logFC of Gene Counts"]
        elif dataset_type == "DE-HMM - Sites":
            choices = [empty_action, "Recreate Sites File"]
        elif dataset_type == "DE-HMM - Segments":
            choices = [empty_action]
        else:
           choices = [empty_action]

        self.fileActionChoice.SetItems(choices)
        self.fileActionChoice.SetSelection(0)

#

    def fileActionFunc(self, event):
        # 0 - nothing
        # 1 - Volcano
        # 2 - Hist gene counts ratio

        plot_choice  = self.fileActionChoice.GetCurrentSelection()
        plot_name = self.fileActionChoice.GetString(plot_choice)
        if plot_name == "[Choose Action]":
                return
        next = self.list_files.GetNextSelected(-1)
        if next > -1:
            dataset_path = self.list_files.GetItem(next, 3).GetText()
            dataset_name = self.list_files.GetItem(next, 0).GetText()
            dataset_type = self.list_files.GetItem(next, 1).GetText()

            if self.verbose:
                transit_tools.transit_message("Performing the '%s' action on dataset '%s'" % (plot_name, dataset_name))

            if plot_name == "Create a Volcano Plot":
                self.graphVolcanoPlot(dataset_name, dataset_type, dataset_path)
            elif plot_name == "Plot Histogram of logFC of Gene Counts":
                self.graphGeneCounts(dataset_name, dataset_type, dataset_path)
            elif plot_name == "Plot Ranked Probability of Essentiality":
                self.graphRankedZbar(dataset_name, dataset_type, dataset_path)
            else:
                return

            self.fileActionChoice.SetSelection(0)

        else:
            transit_tools.ShowError(MSG="Please select a results file to plot!")

#

    def graphGeneCounts(self, dataset_name, dataset_type, dataset_path):
        try:
            if dataset_type == "Resampling":
                X = []
                for line in open(dataset_path):
                    if line.startswith("#"): continue
                    tmp = line.strip().split("\t")
                    try:
                        log2FC = float(tmp[-3])
                    except:
                        log2FC = 0
                    X.append(log2FC)

                n, bins, patches = plt.hist(X, density=1, facecolor='c', alpha=0.75, bins=100)
                plt.xlabel('log2 FC - Total Gene Counts')
                plt.ylabel('Probability')
                plt.title('Histogram of log2 Fold Change for Total Normalized Counts within Genes')
                plt.axvline(0, color='r', linestyle='dashed', linewidth=3)
                plt.grid(True)
                plt.show()
            else:
               transit_tools.ShowError(MSG="Need to select a 'Resampling' results file for this type of plot.")

        except Exception as e:
            transit_tools.transit_message("Error occurred creating plot: %s" % str(e))
            traceback.print_exc()

#

    def graphVolcanoPlot(self, dataset_name, dataset_type, dataset_path):
        try:
            if dataset_type == "Resampling":
                X = []; Y = []; header=[]; qval_list = []; bad = [];
                col_logFC = -6
                col_pval = -2
                col_qval = -1
                ii = 0
                for line in open(dataset_path):
                    if line.startswith("#"):
                        tmp = line.split("\t")
                        temp_col_logfc = [i for (i,x) in enumerate(tmp) if "logfc" in x.lower() or "log-fc" in x.lower() or "log2fc" in x.lower()]
                        temp_col_pval = [i for (i,x) in enumerate(tmp) if ("pval" in x.lower() or "p-val" in x.lower()) and "adj" not in x.lower()]
                        if temp_col_logfc:
                            col_logFC = temp_col_logfc[-1]
                        if temp_col_pval:
                            col_pval = temp_col_pval[-1]
                        continue


                    tmp = line.strip().split("\t")
                    try:
                        log10qval = -math.log(float(tmp[col_pval].strip()), 10)
                    except ValueError as e:
                        bad.append(ii)
                        log10qval = 0

                    log2FC = float(tmp[col_logFC])

                    qval_list.append((float(tmp[col_qval]), float(tmp[col_pval].strip())))
                    X.append(log2FC)
                    Y.append(log10qval)
                    ii+=1
                count = 0
                threshold = 0.00001
                backup_thresh = 0.00001
                qval_list.sort()
                for (q, p) in qval_list:
                    backup_thresh = p
                    if q > 0.05:
                        break
                    threshold = p
                    count+=1

                if threshold == 0:
                    threshold = backup_thresh
                for ii in bad:
                    Y[ii]  = max(Y)
                plt.plot(X,Y, "bo")
                plt.axhline(-math.log(threshold, 10), color='r', linestyle='dashed', linewidth=3)
                plt.xlabel("Log Fold Change (base 2)")
                plt.ylabel("-Log p-value (base 10)")
                plt.suptitle("Resampling - Volcano plot")
                plt.title("Adjusted threshold (red line): %1.8f" % threshold)
                plt.show()
            else:
               transit_tools.ShowError(MSG="Need to select a 'Resampling' results file for this type of plot.")

        except Exception as e:
            print "Error occurred creating plot:", str(e)

#

    def graphRankedZbar(self, dataset_name, dataset_type, dataset_path):
        try:
            X = []; Y = [];
            for line in open(dataset_path):
                if line.startswith("#"): continue
                tmp = line.strip().split("\t")
                try:
                    #log2FC = math.log(float(tmp[6])/float(tmp[5]),2)
                    zbar = float(tmp[-2])
                except:
                    zbar = 0
                if zbar >= 0:
                    Y.append(zbar)

            Y.sort()
            index=range(1,len(Y)+1)
            plt.plot(index,Y, "bo")
            plt.xlabel("Rank of Gene According to Probability of Essentiality")
            plt.ylabel("Probability of Essentiality")
            plt.title("Ranked Probability of Essentiality")
            plt.show()

        except Exception as e:
            print "Error occurred creating plot:", str(e)

#

    def LoessPrevFunc(self,event):
        datasets_selected = self.ctrlSelected() + self.expSelected()
        if not datasets_selected:
            transit_tools.ShowError(MSG="Need to select at least one control or experimental dataset.")
            return

        data, position = tnseq_tools.get_data(datasets_selected)
        (K,N) = data.shape
        window = 100
        for j in range(K):

            size = len(position)/window + 1
            x_w = numpy.zeros(size)
            y_w = numpy.zeros(size)
            for i in range(size):
                x_w[i] = window*i
                y_w[i] = sum(data[j][window*i:window*(i+1)])

            y_smooth = stat_tools.loess(x_w, y_w, h=10000)
            plt.plot(x_w, y_w, "g+")
            plt.plot(x_w, y_smooth, "b-")
            plt.xlabel("Genomic Position")
            plt.ylabel("Reads per 100 insertion sites")

            plt.title("LOESS Fit - %s" % transit_tools.basename(datasets_selected[j]) )
            plt.show()

#

    def addFileFunc(self, event):

        try:
            dlg = wx.FileDialog(
                self, message="Choose a file",
                defaultDir=self.workdir,
                defaultFile="",
                wildcard=u"Results Files (*.dat)|*.dat;|\nResults Files (*.txt)|*.txt;|\nAll files (*.*)|*.*",
                style=wx.FD_OPEN | wx.FD_MULTIPLE | wx.FD_CHANGE_DIR
                )
            if dlg.ShowModal() == wx.ID_OK:
                paths = dlg.GetPaths()
                print "You chose the following Results file(s):"
                for fullpath in paths:
                    print "\t%s" % fullpath
                    name = transit_tools.basename(fullpath)
                    line = open(fullpath).readline()
                    if line.startswith("#Gumbel"):
                        type = "Gumbel"
                    elif line.startswith("#Binomial"):
                        type = "Binomial"
                    elif line.startswith("#HMM - Sites"):
                        type = "HMM - Sites"
                    elif line.startswith("#HMM - Genes"):
                        type = "HMM - Genes"
                    elif line.startswith("#Resampling"):
                        type = "Resampling"
                    elif line.startswith("#DE-HMM - Sites"):
                        type = "DE-HMM - Sites"
                    elif line.startswith("#DE-HMM - Segments"):
                        type = "DE-HMM - Segments"
                    elif line.startswith("#GI"):
                        type = "GI"
                    else:
                        type = "Unknown"
                    data = {"path":fullpath, "type":type, "date": datetime.datetime.today().strftime("%B %d, %Y %I:%M%p")}
                    wx.CallAfter(pub.sendMessage, "file", data=data)
            dlg.Destroy()
        except Exception as e:
            transit_tools.transit_message("Error: %s" %  e)
            print "PATH", fullpath
            exc_type, exc_obj, exc_tb = sys.exc_info()
            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
            print(exc_type, fname, exc_tb.tb_lineno)

#

    def choseMethodsMenu(self, selected_name, event):
        if self.verbose:
            transit_tools.transit_message("Selected Method: %s" % (selected_name))
        self.MethodSelectFunc(selected_name)

#

    def chooseNormalization(self):

        norm_methods_choices = sorted(normmethods.keys())
        dlg = wx.SingleChoiceDialog(
                self, "Choose how to normalize read-counts accross datasets.", 'Normalization Choice',
                norm_methods_choices,
                wx.CHOICEDLG_STYLE
                )

        if dlg.ShowModal() == wx.ID_OK:
            transit_tools.transit_message("Selected the '%s' normalization method" % dlg.GetStringSelection())

        dlg.Destroy()
        return dlg.GetStringSelection()

#

    def annotationPT_to_GFF3(self, event):
        annotationpath = self.annotation
        defaultFile = transit_tools.fetch_name(annotationpath) + ".gff3"
        #defaultDir = os.path.dirname(os.path.realpath(__file__))
        defaultDir = os.getcwd()
        outputPath = self.SaveFile(defaultDir, defaultFile)

        ORGANISM = transit_tools.fetch_name(annotationpath)
        if not annotationpath:
            transit_tools.ShowError("Error: No annotation file selected.")

        elif outputPath:
            if self.verbose:
                transit_tools.transit_message("Converting annotation file from prot_table format to GFF3 format")
            year = time.localtime().tm_year
            month = time.localtime().tm_mon
            day = time.localtime().tm_mday

            output = open(outputPath, "w")
            output.write("##gff-version 3\n")
            output.write("##converted to IGV with TRANSIT.\n")
            output.write("##date %d-%d-%d\n" % (year, month, day))
            output.write("##Type DNA %s\n" % ORGANISM)

            for line in open(annotationpath):
                if line.startswith("#"): continue
                tmp = line.strip().split("\t")
                desc = tmp[0]; start = int(tmp[1]); end = int(tmp[2]); strand = tmp[3];
                length = tmp[4]; name = tmp[7]; orf = tmp[8];
                ID = name
                desc.replace("%", "%25").replace(";", "%3B").replace("=","%3D").replace(",","%2C")
                output.write("%s\tRefSeq\tgene\t%d\t%d\t.\t%s\t.\tID=%s;Name=%s;Alias=%s;locus_tag=%s;desc=%s\n" % (ORGANISM, start, end, strand, orf,ID, orf, orf,desc))

            output.close()
            if self.verbose:
                transit_tools.transit_message("Finished conversion")

#

    def annotationPT_to_PTT(self, event):

        annotationpath = self.annotation
        defaultFile = transit_tools.fetch_name(annotationpath) + ".ptt.table"
        #defaultDir = os.path.dirname(os.path.realpath(__file__))
        defaultDir = os.getcwd()

        datasets = self.ctrlSelected() + self.expSelected()
        if not annotationpath:
            transit_tools.ShowError("Error: No annotation file selected.")
        elif not datasets:
            transit_tools.ShowError("Error: Please add a .wig dataset, to determine TA sites.")
        else:

            outputPath = self.SaveFile(defaultDir, defaultFile)
            if not outputPath: return
            if self.verbose:
                transit_tools.transit_message("Converting annotation file from prot_table format to PTT format")
            (data, position) = tnseq_tools.get_data(datasets)
            orf2info = transit_tools.get_gene_info(annotationpath)
            hash = transit_tools.get_pos_hash(annotationpath)
            (orf2reads, orf2pos) = tnseq_tools.get_gene_reads(hash, data, position, orf2info)

            output = open(outputPath, "w")
            output.write("geneID\tstart\tend\tstrand\tTA coordinates\n")
            for line in open(annotationpath):
                if line.startswith("#"): continue
                tmp = line.strip().split("\t")
                orf = tmp[8]
                name = tmp[7]
                desc = tmp[0]
                start = int(tmp[1])
                end = int(tmp[2])
                strand = tmp[3]
                ta_str = "no TAs"
                if orf in orf2pos: ta_str = "\t".join([str(int(ta)) for ta in orf2pos[orf]])
                output.write("%s\t%s\t%s\t%s\t%s\n" % (orf, start, end, strand, ta_str))
            output.close()
            if self.verbose:
                transit_tools.transit_message("Finished conversion")

#

    def annotationPTT_to_PT(self, event):

        annotationpath = self.annotation
        defaultFile = transit_tools.fetch_name(annotationpath) + ".prot_table"
        #defaultDir = os.path.dirname(os.path.realpath(__file__))
        defaultDir = os.getcwd()

        datasets = self.ctrlSelected() + self.expSelected()
        if not annotationpath:
            transit_tools.ShowError("Error: No annotation file selected.")
        #elif not datasets:
        #    transit_tools.ShowError("Error: Please add a .wig dataset, to determine TA sites.")
        else:

            outputPath = self.SaveFile(defaultDir, defaultFile)
            if not outputPath: return
            if self.verbose:
                transit_tools.transit_message("Converting annotation file from PTT format to prot_table format")
            #(data, position) = tnseq_tools.get_data(datasets)
            #orf2info = transit_tools.get_gene_info(annotationpath)
            #hash = transit_tools.get_pos_hash(annotationpath)
            #(orf2reads, orf2pos) = tnseq_tools.get_gene_reads(hash, data, position, orf2info)


            output = open(outputPath, "w")
            #output.write("geneID\tstart\tend\tstrand\tTA coordinates\n")
            for line in open(annotationpath):
                if line.startswith("#"): continue
                if line.startswith("geneID"): continue
                tmp = line.strip().split("\t")
                orf = tmp[0]
                if orf == "intergenic": continue
                name = "-"
                desc = "-"
                start = int(tmp[1])
                end = int(tmp[2])
                length = ((end-start+1)/3)-1
                strand = tmp[3]
                someID = "-"
                someID2 = "-"
                COG = "-"
                output.write("%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n" % (desc, start, end, strand, length, someID, someID2, name, orf, COG))
            output.close()
            if self.verbose:
                transit_tools.transit_message("Finished conversion")

#

    def annotationGFF3_to_PT(self, event):

        annotationpath = self.annotation
        defaultFile = transit_tools.fetch_name(annotationpath) + ".prot_table"
        #defaultDir = os.path.dirname(os.path.realpath(__file__))
        defaultDir = os.getcwd()

        datasets = self.ctrlSelected() + self.expSelected()
        if not annotationpath:
            transit_tools.ShowError("Error: No annotation file selected.")
        else:
            outputPath = self.SaveFile(defaultDir, defaultFile)
            if not outputPath: return
            if self.verbose:
                transit_tools.transit_message("Converting annotation file from GFF3 format to prot_table format")


            output = open(outputPath, "w")
            for line in open(annotationpath):
                if line.startswith("#"): continue
                tmp = line.strip().split("\t")
                chr = tmp[0]
                type = tmp[2]
                start = int(tmp[3])
                end = int(tmp[4])
                length = ((end-start+1)/3)-1
                strand = tmp[6]
                features = dict([tuple(f.split("=")) for f in tmp[8].split(";")])
                if "ID" not in features: continue
                orf = features["ID"]
                name = features.get("Name", "-")
                if name == "-": name = features.get("name", "-")

                desc = features.get("Description", "-")
                if desc == "-": desc = features.get("description", "-")
                if desc == "-": desc = features.get("Desc", "-")
                if desc == "-": desc = features.get("desc", "-")

                someID = "-"
                someID2 = "-"
                COG = "-"
                output.write("%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n" % (desc, start, end, strand, length, someID, someID2, name, orf, COG))
            output.close()
            if self.verbose:
                transit_tools.transit_message("Finished conversion")

#

    def RunMethod(self, event):
        #FLORF
        #X = self.methodChoice.GetCurrentSelection()
        #selected_name = self.methodChoice.GetString(X)
        selected_name = self.method_choice
        for name in methods:
            if  methods[name].fullname() == selected_name:
                methodobj = methods[name].method
        try:
            M = methodobj.fromGUI(self)
            if M:
                thread = threading.Thread(target=M.Run())
                thread.setDaemon(True)
                thread.start()
        except Exception as e:
            transit_tools.transit_message("Error: %s" % str(e))
            traceback.print_exc()

#
"""
    def ExportMethod(self, event):
        #X = self.methodChoice.GetCurrentSelection()
        #selected_name = self.methodChoice.GetString(X)
        selected_name = self.export_choice
        for name in export_methods:
            if  export_methods[name].label == selected_name:
                methodobj = export_methods[name].method
        try:
            M = methodobj.fromGUI(self)
            if M:
                thread = threading.Thread(target=M.Run())
                thread.setDaemon(True)
                thread.start()
        except Exception as e:
            transit_tools.transit_message("Error: %s" % str(e))
            traceback.print_exc()
"""


class AssumeZerosDialog(wx.Dialog):

    def __init__(self, *args, **kw):

        self.ID_HIMAR1 = wx.NewId()
        self.ID_TN5 = wx.NewId()

        wx.Dialog.__init__(self, None, title="Dialog")

        self.ID_HIMAR1 = wx.NewId()
        self.ID_TN5 = wx.NewId()

        self.SetSize((500, 300))
        self.SetTitle("Warning:  Wig Files Do Not Include Empty Sites")

        mainSizer = wx.BoxSizer(wx.VERTICAL)
        self.SetSizer(mainSizer)

        warningText = """

One or more of your .wig files does not include any empty sites (i.e. sites with zero read-counts). The analysis methods in TRANSIT require knowing ALL possible insertion sites, even those without reads.

    Please indicate how you want to proceed:

    As Himar1: You will need to provide the DNA sequence (.fasta format) and TRANSIT will automatically determine empty TA sites.

    As Tn5: TRANSIT will assume all nucleotides are possible insertion sites. Those not included in the .wig file are assumed to be zero.
    """
        warningStaticBox = wx.StaticText(self, wx.ID_ANY, warningText, (-1,-1), (-1, -1), wx.ALL)
        warningStaticBox.Wrap(480)
        mainSizer.Add(warningStaticBox)

        button_sizer = wx.BoxSizer(wx.HORIZONTAL)
        himar1Button = wx.Button(self, self.ID_HIMAR1, label='Proceed as Himar1')
        tn5Button = wx.Button(self, self.ID_TN5, label='Proceed as Tn5')
        cancelButton = wx.Button(self, wx.ID_CANCEL, label='Cancel')


        button_sizer.Add(himar1Button, flag=wx.LEFT, border=5)
        button_sizer.Add(tn5Button, flag=wx.LEFT, border=5)
        button_sizer.Add(cancelButton, flag=wx.LEFT, border=5)

        mainSizer.Add(button_sizer,
            flag=wx.ALIGN_CENTER|wx.TOP|wx.BOTTOM, border=10)


        himar1Button.Bind(wx.EVT_BUTTON, self.OnClose)
        tn5Button.Bind(wx.EVT_BUTTON, self.OnClose)
        cancelButton.Bind(wx.EVT_BUTTON, self.OnClose)

#

    def OnClose(self, event):

        if self.IsModal():
            self.EndModal(event.EventObject.Id)
            self.Close()
        else:
            self.Close()

