#########################################
# This script is the standalone version
#   of contigViewer.
#   Brian Chan and Alexander Kozik     
#
#########################################

import sys, urllib
from Tkinter import *
from tkMessageBox import *
from tkFileDialog import *
from string import *
from math import log10
from math import fabs
import tkFont

# ====================================================
# global
g_interestListWin = 0        # these are for the interest win
g_interestListWin_open = 0
g_interestListIndex = 0
g_interestList_content = None

# ====================================================

class contigViewerUserInputWindow( Frame ):

	def __init__(self):

		# set up the main window
		Frame.__init__(self)
		root = self.root = self.master
		root.title("Blast Info Viewer")
		# root.geometry( "600x200" )
		myRow = 0    # keep track of the row number (for grid manager)

		# first row
		frame_1 = Frame(root)
		frame_1.pack(side = TOP, fill = X)
		self.input1_label = Label(frame_1, text="info file:", width=18)
		self.input1_label.pack(side = LEFT)
		self.input1_text = Entry(frame_1, name="input1_text", width=40)
		self.input1_text.pack(side = LEFT)
		self.input1_browse_btn = Button(frame_1, text="Browse", command=self.getInputFile1)
		self.input1_browse_btn.pack(side = LEFT)
		self.input1_load_btn = Button(frame_1, text="Load", command=self.loadInputFile1)
		self.input1_load_btn.pack(side = LEFT)
		self.input1_text.insert(0, "x-let-ath-blastX.info2")

		# second row
		myRow = myRow + 1
		frame_2 = Frame(root)
		frame_2.pack(side = TOP, fill = X)
		self.input2_label = Label(frame_2, text="position file:", width=18)
		self.input2_label.pack(side = LEFT)
		self.input2_text = Entry(frame_2, name="input2_text", width=40)
		self.input2_text.pack(side = LEFT)
		self.input2_browse_btn = Button(frame_2, text="Browse", command=self.getInputFile2)
		self.input2_browse_btn.pack(side = LEFT)
		self.input2_load_btn = Button(frame_2, text="Load", command=self.loadInputFile2)
		self.input2_load_btn.pack(side = LEFT)
		self.input2_text.insert(0, "x-ath_NCBI_genes.coords.nr")

		# third row
		myRow = myRow + 1
		frame_3 = Frame(root)
		frame_3.pack(side = TOP, fill = X)
		self.input3_label = Label(frame_3, text="seq tab file:", width=18)
		self.input3_label.pack(side = LEFT)
		self.input3_text = Entry(frame_3, name="input3_text", width=40)
		self.input3_text.pack(side = LEFT)
		self.input3_browse_btn = Button(frame_3, text="Browse", command=self.getInputFile3)
		self.input3_browse_btn.pack(side = LEFT)
		self.input3_load_btn = Button(frame_3, text="Load", command=self.loadInputFile3)
		self.input3_load_btn.pack(side = LEFT)
		self.input3_text.insert(0, "x-lettuce_assembly.tab")

		# load both
		myRow = myRow + 1
		frame_23 = Frame(root)
		frame_23.pack(side = TOP, fill = X)
		self.loadAll_btn = Button(frame_23, text="Load All", command=self.loadInputFiles, width=12, bg="orange")
		self.loadAll_btn.pack(side = LEFT)
		self.status_label = Label(frame_23, text=".....")
		self.status_label.pack(side = LEFT)

		# forth row
		myRow = myRow + 1
		frame_4 = Frame(root)
		frame_4.pack(side = TOP, fill = X)
		self.queryID_label = Label(frame_4, text="Query ID:", width=18)
		self.queryID_label.pack(side = LEFT)
		self.queryID_text = Entry(frame_4, name="queryID_text", bg="lightgreen")
		self.queryID_text.pack(side = LEFT)
		self.queryID_btn = Button(frame_4, text="Search", command=self.searchQueryID)
		self.queryID_btn.pack(side = LEFT)
		self.queryID_text.bind("<Return>", self.searchQueryID)
		self.queryID_text.insert(0, "QG_CA_Contig1258")

		# fifth row
		myRow = myRow + 1
		frame_5 = Frame(root)
		frame_5.pack(side = TOP, fill = X)
		self.subjectID_label = Label(frame_5, text="Subject ID:", width=18)
		self.subjectID_label.pack(side = LEFT)
		self.subjectID_text = Entry(frame_5, name="subjectID_text")
		self.subjectID_text.pack(side = LEFT)
		self.subjectID_btn = Button(frame_5, text="Search", command=self.searchSubjectID)
		self.subjectID_btn.pack(side = LEFT)
		self.subjectID_text.bind("<Return>", self.searchSubjectID)
		self.subjectID_text.insert(0, "At2g45260")

		# sixth row
		myRow = myRow + 1
		frame_6 = Frame(root)
		frame_6.pack(side = TOP, fill = X)
		self.hitN_label = Label(frame_6, text="Hit N:", width=18)
		self.hitN_label.pack(side = LEFT)
		self.hitN_text = Entry(frame_6, name="hit_N")
		self.hitN_text.pack(side = LEFT)
		self.hitN_text.insert(0, "1")

		# make menu
		self.makemenu()

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

	def getInputFile1(self):
		filename = askopenfilename()
		if filename == "":
			return
		self.input1_text.delete(0, END)
		self.input1_text.insert(0, filename)

	def getInputFile2(self):
		filename = askopenfilename()
		if filename == "":
			return
		self.input2_text.delete(0, END)
		self.input2_text.insert(0, filename)

	def getInputFile3(self):
		filename = askopenfilename()
		if filename == "":
			return
		self.input3_text.delete(0, END)
		self.input3_text.insert(0, filename)

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

	def loadInputFiles(self):
		self.status_label.configure(text="start loading file 1...")
		self.root.update()
		self.loadInputFile1()
		self.status_label.configure(text="start loading file 2...")
		self.root.update()
		self.loadInputFile2()
		self.status_label.configure(text="start loading file 3...")
		self.root.update()
		self.loadInputFile3()
		self.status_label.configure(text="finish loading...")
		"""
		q_id = 'QG_CA_Contig1'
		print q_id
		print self.QID_data[q_id]
		print "---------"
		"""

	def loadInputFile1(self):
		# clear old data
		self.QID1_data = {}
		self.SID1_data = {}
		self.QID2_data = {}
		self.SID2_data = {}
		self.QID3_data = {}
		self.SID3_data = {}
		# get raw data
		infoData = self.getData( self.input1_text.get() )
		delimiter = "\t"
		for line in infoData:
			if find(line, "no_hits_found") != -1:
				continue
			cells = split(line, delimiter)
			hit_num = int(cells[7])
			# if hit_num != 1:
			if hit_num == 1:
				# up to here, they are all lines with hit_num = 1
				queryID = cells[0]
				subjectID = cells[1]
				query_first = int(cells[9])
				query_last = int(cells[10])
				subject_first = int(cells[11])
				subject_last = int(cells[12])
				len_q_str, len_s_str = split(cells[13], "/")
				len_q = int(len_q_str)
				len_s = int(len_s_str)
				data = [subjectID, query_first, query_last, subject_first, subject_last, len_q, len_s]
				self.QID1_data[queryID] = data
				if self.SID1_data.has_key(subjectID):
					self.SID1_data[subjectID].append(queryID)
				else:
					self.SID1_data[subjectID] = [queryID]

			if hit_num == 2:
				# up to here, they are all lines with hit_num = 2
				queryID = cells[0]
				subjectID = cells[1]
				query_first = int(cells[9])
				query_last = int(cells[10])
				subject_first = int(cells[11])
				subject_last = int(cells[12])
				len_q_str, len_s_str = split(cells[13], "/")
				len_q = int(len_q_str)
				len_s = int(len_s_str)
				data = [subjectID, query_first, query_last, subject_first, subject_last, len_q, len_s]
				self.QID2_data[queryID] = data
				if self.SID2_data.has_key(subjectID):
					self.SID2_data[subjectID].append(queryID)
				else:
					self.SID2_data[subjectID] = [queryID]

			if hit_num == 3:
				# up to here, they are all lines with hit_num = 3
				queryID = cells[0]
				subjectID = cells[1]
				query_first = int(cells[9])
				query_last = int(cells[10])
				subject_first = int(cells[11])
				subject_last = int(cells[12])
				len_q_str, len_s_str = split(cells[13], "/")
				len_q = int(len_q_str)
				len_s = int(len_s_str)
				data = [subjectID, query_first, query_last, subject_first, subject_last, len_q, len_s]
				self.QID3_data[queryID] = data
				if self.SID3_data.has_key(subjectID):
					self.SID3_data[subjectID].append(queryID)
				else:
					self.SID3_data[subjectID] = [queryID]


	def loadInputFile2(self):
		# clear old data
		self.GI_data = {}
		# get raw data
		posData = self.getData( self.input2_text.get() )
		delimiter = "\t"
		for line in posData:
			line = strip(line)
			cells = split(line, delimiter)
			fr = cells[3]
			# gi_id = cells[4]
			gi_id = cells[0]
			ie = cells[5]
			data = [fr, ie]
			self.GI_data[gi_id] = data

	def loadInputFile3(self):
		# clear old data
		self.seq_data = {}
		# get raw data
		seqData = self.getData( self.input3_text.get() )
		delimiter = "\t"
		for line in seqData:
			line = strip(line)
			cells = split(line, delimiter)
			seqName = cells[0]
			seqBody = cells[2]
			self.seq_data[seqName] = seqBody

	def getData(self, filename):
		if filename:
			all_lines = open(filename, 'r').readlines()
		else:
			showinfo('Error', 'file is corrupted')
		return all_lines

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

	def searchQueryID(self, o=None):

		which_hit = self.hitN_text.get()
		print which_hit

		queryID = self.queryID_text.get()

		if which_hit == "1":
			if not self.QID1_data.has_key(queryID):
				showinfo('Error', 'No such query ID: ' + str(queryID))
				return
			infoData = self.QID1_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)

		if which_hit == "2":
			if not self.QID2_data.has_key(queryID):
				showinfo('Error', 'No such query ID: ' + str(queryID))
				return
			infoData = self.QID2_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)

		if which_hit == "3":
			if not self.QID3_data.has_key(queryID):
				showinfo('Error', 'No such query ID: ' + str(queryID))
				return
			infoData = self.QID3_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)


	def searchSubjectID(self, o=None):

		which_hit = self.hitN_text.get()
		print which_hit

		subjectID = self.subjectID_text.get()

		if which_hit == "1":
			if self.SID1_data.has_key(subjectID):
				queryID_list = self.SID1_data[subjectID]
			else:
				showinfo('Error', 'No such subject ID: ' + str(subjectID))
				return
			print queryID_list
			queryID = queryID_list[0]
			infoData = self.QID_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			# eventually make this another select box
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)

		if which_hit == "2":
			if self.SID2_data.has_key(subjectID):
				queryID_list = self.SID2_data[subjectID]
			else:
				showinfo('Error', 'No such subject ID: ' + str(subjectID))
				return
			print queryID_list
			queryID = queryID_list[0]
			infoData = self.QID_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			# eventually make this another select box
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)

		if which_hit == "3":
			if self.SID3_data.has_key(subjectID):
				queryID_list = self.SID3_data[subjectID]
			else:
				showinfo('Error', 'No such subject ID: ' + str(subjectID))
				return
			print queryID_list
			queryID = queryID_list[0]
			infoData = self.QID_data[queryID]
			subjectID = infoData[0]
			posData = self.GI_data[subjectID]
			seqBody = self.seq_data[queryID]
			# eventually make this another select box
			self.plotGraph(queryID, infoData, posData, seqBody, which_hit)

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

	def makemenu(self):
		self.menubar = Menu(self.master)
		self.master.config(menu=self.menubar)

		# add file pulldown menu
		file = Menu(self.menubar, tearoff=0)
		file.add_command(label='Quit', command=self.quit)
		self.menubar.add_cascade(label='File', underline=0, menu=file)

		# add help pulldown menu
		help = Menu(self.menubar, tearoff=0)
		help.add_command(label='About', command=self.openAboutWin)
		self.menubar.add_cascade(label='Help', underline=0, menu=help)

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

	def quit(self):
		if askyesno('Really quit?', 'Are you sure you want to quit?'):
			Frame.quit(self)

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

	def openAboutWin(self):
		s = """

In the sequence window, the top bar is the arabidopsis, the bottom 
bar is the lettuce. 

"""
		showinfo('About:', s)

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

	def plotGraph(self, queryID, infoData, posData, seqBody, which_hit):

		# generate picture
		cv = contigViewerClass(queryID, infoData, posData, which_hit)
		cv.generatePicture()
		tv = textViewerClass(queryID, infoData, seqBody, which_hit)
		tv.displayText()

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

# ===================================================

class textViewerClass( Frame ):

	def __init__(self, queryID, infoData, seqBody, which_hit):
		self.queryID = queryID
		self.seqBody = seqBody
		self.subjectID = infoData[0]
		self.query_first = infoData[1]
		self.query_last = infoData[2]
		self.subject_first = infoData[3]
		self.subject_last = infoData[4]
		self.len_q = infoData[5]
		self.len_s = infoData[6]
		self.hitN = which_hit

	def displayText(self):
		# setup up a new window and a new picture
		self.textWin = Toplevel()
		self.textWin.title( "Query ID: " + str(self.queryID) + " Hit_N: " + self.hitN)

		maxX = 100
		maxY = 10
		frame_1 = Frame(self.textWin)
		frame_1.pack(side = TOP, fill = BOTH, expand = True)
		myFont = tkFont.Font(family="Courier", size="10")
		self.content = Text(frame_1, width=maxX, height=maxY, wrap=NONE, font=myFont)
		self.content.pack(side = LEFT, fill = BOTH, expand = True)

		# set up a scrollable bar
		vertical_scrollbar = Scrollbar(frame_1, orient=VERTICAL, command=self.content.yview)
		vertical_scrollbar.pack(side = LEFT, fill = Y)
		vertical_scrollbar.width = 10
		self.content.config(yscrollcommand=vertical_scrollbar.set)

		# insert the seq name and body
		self.content.insert("0.1", ">" + str(self.queryID) + "\n")
		row = 0
		count = 0
		size = len(self.seqBody)
		while count < size:
			end = 0
			row += 1
			if count+maxX < size:
				self.content.insert(END, self.seqBody[count:count+maxX] + "\n")
				count = row * maxX
				end = maxX
			else:
				self.content.insert(END, self.seqBody[count:] + "\n")
				end = size - count
				count = size
			"""
			print row
			print count
			print end
			print "------"
			"""
			# add tag
			for i in range(end):
				index = (row-1)*maxX+i+1
				if (index >= self.query_first and index <= self.query_last) or  (index <= self.query_first and index >= self.query_last):
					index_str = str(row+1) + "." + str(i)
					self.content.tag_add("alignment", index_str)
					#print index_str
			#print "============="
		self.content.tag_config("alignment", background = "yellow")
		#print self.seqBody 
		

# ===================================================


class contigViewerClass( Frame ):

	def __init__(self, queryID, infoData, posData, which_hit):

		# init this class
		self.queryID = queryID
		self.subjectID = infoData[0]
		self.query_first = infoData[1]
		self.query_last = infoData[2]
		self.subject_first = infoData[3]
		self.subject_last = infoData[4]
		self.len_q = infoData[5]
		self.len_s = infoData[6]
		self.hitN = which_hit
		print infoData
		print posData

		# change direction
		self.dir_bottom_bar = "F"
		if self.query_first > self.query_last:
			self.query_first, self.query_last = self.query_last, self.query_first
			self.dir_bottom_bar = "R"
		if posData[0] == "forward":
			self.dir_top_bar = "F"
		else:
			self.dir_top_bar = "R"

		# store exons info
		positions = posData[1]
		exons_raw = split(positions, "|")
		self.introns = []
		self.exons = []
		for exon_raw in exons_raw:
			index1_str, index2_str = split(exon_raw, "-")
			index1, index2 = int(index1_str), int(index2_str)
			if self.dir_top_bar == "F":
				self.exons.append( [index1, index2] )
			elif self.dir_top_bar == "R":
				self.exons.append( [index2, index1] )
		if self.dir_top_bar == "R":
			self.exons.reverse()
		# store introns info
		if len(self.exons) > 1:
			numExons = len(self.exons)
			for ei in range(numExons-1):
				left_pair = self.exons[ei]
				right_pair = self.exons[ei+1]
				left = left_pair[1]
				right = right_pair[0]
				intron_size = right - left
				self.introns.append( intron_size )

		# constants for the graph
		self.graphChartSizeX = 1000    # the left part of the image (histogram)
		self.hSpace = 50      # horizontal empty space
		self.vSpace = 20      # vertical empty space
		  # actual graph chart sizeX
		self.adjustedGraphChartSizeX = self.graphChartSizeX - self.hSpace * 2
		self.barHeight = 10  # the height of the bar of seqs
		self.maxImageSizeX = self.graphChartSizeX   # total X pixels
		self.maxImageSizeY = 3*self.barHeight + 3*self.vSpace # total Y pixels
		self.maxGeneLen = 0  # end of contig  (not known yet)
		self.charSpace = 4     # the # of pixel to display a char (horizontally)

		# calculate the dimensions' parameters
		self.numOfBars = 2
		self.maxGeneLen = self.len_s

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

	def generatePicture(self):

		# setup up a new window and a new picture
		self.ViewerWin = Toplevel()
		self.ViewerWin.title( "Query ID: " + str(self.queryID) + " -- Subject ID: " + self.subjectID + " Hit_N: " + self.hitN)
		frame_1 = Frame(self.ViewerWin)
		frame_1.pack(side = TOP, fill = BOTH, expand = True)
		self.pic = Canvas(frame_1, width=self.maxImageSizeX, height=self.maxImageSizeY, bg='black')
		self.pic.pack(side = LEFT, fill = BOTH, expand = True)

		# set up a scrollable bar
		vertical_scrollbar = Scrollbar(frame_1, orient=VERTICAL, command=self.pic.yview)
		vertical_scrollbar.pack(side = LEFT, fill = Y)
		vertical_scrollbar.width = 10
		self.pic.config(yscrollcommand=vertical_scrollbar.set)
		self.pic.config(scrollregion=(0,0,self.maxImageSizeX,self.maxImageSizeY))

		# change the mouse icon for this canvas
		self.pic.config(cursor="crosshair")

		# plot it out ------------------------------------

		# draw the two seqs
		textcolor = 'white' # pick text color for each seq
		posY = self.vSpace + 0 *  (self.vSpace+self.barHeight)
		text_barHeight = self.barHeight   # height for the text
		# first bar ------------------------
		"""
		self.query_first = data[0]
		self.query_last = data[1]
		self.subject_first = data[2]
		self.subject_last = data[3]
		self.len_q = data[4]
		self.len_s = data[5]
		"""

		# place the longer seq bar
		barcolor = 'blue'
		start = 1.0
		end = self.len_s
		posX_start = self.hSpace + (start/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posX_end = self.hSpace + (end/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posY_start = posY
		posY_end = posY_start + self.barHeight
		self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)

		# place the shorter seq bar
		barcolor = 'yellow'
		start = self.subject_first * 1.0
		end = self.subject_last * 1.0
		posX_start = self.hSpace + (start/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posX_end = self.hSpace + (end/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posY_start = posY
		posY_end = posY_start + self.barHeight
		self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)

		# place the start index
		start = self.subject_first
		posX = self.hSpace + (start*1.0/self.maxGeneLen)*self.adjustedGraphChartSizeX - self.charSpace * ( log10(start)+1 )
		self.pic.create_text(posX, text_barHeight, text=(str(start)+" aa"), fill=textcolor)

		# place the end index
		end = self.len_s
		posX = self.hSpace + (end/self.maxGeneLen)*self.adjustedGraphChartSizeX + self.charSpace * ( log10(end)+4 )
		self.pic.create_text(posX, text_barHeight, text=(str(end)+" aa"), fill=textcolor)

		# place position info
		middle = self.subject_last * 1.0
		posX = self.hSpace + (middle/self.maxGeneLen)*self.adjustedGraphChartSizeX - self.charSpace * ( log10(middle)+1 )
		self.pic.create_text(posX, text_barHeight, text=(str(int(middle))+" aa"), fill=textcolor)

		# place the direction
		dir = self.dir_top_bar
		posX = self.hSpace + self.adjustedGraphChartSizeX + self.charSpace * 3
		self.pic.create_text(posX, text_barHeight+self.barHeight*1.5, text=dir, fill=textcolor)


		# put introns and exons ------------------------
		print "exons: " + str(self.exons)
		print "introns: " + str(self.introns)

		exon_lens = []
		exon_sum = 0
		for exon_pair in self.exons:
			#diff = exon_pair[1] - exon_pair[0]
			diff = int( fabs(exon_pair[1]-exon_pair[0]) )
			exon_lens.append( diff )
			exon_sum += diff
		print "exon lens: " + str(exon_lens)
		print "exon sum: " + str(exon_sum)

		#== place exons
		curr_pos = 0
		if len(exon_lens) > 1:
			for exon_l in exon_lens:
				middle = curr_pos+(exon_l/2.0)
				posX = self.hSpace + (middle/exon_sum)*self.adjustedGraphChartSizeX
				self.pic.create_text(posX, text_barHeight+self.barHeight*2.5, text=str(exon_l), fill=textcolor)
				curr_pos += exon_l
		#== place introns
		#-- place vertical lines
		intronLineColor = "red"
		curr_pos = 0
		for intron_i in range( len(self.introns) ):
			pos = curr_pos + exon_lens[intron_i] * 1.0
			posX_start = self.hSpace + (pos/exon_sum)*self.adjustedGraphChartSizeX
			posX_end = posX_start+1
			posY_start = posY
			posY_end = posY_start + self.barHeight
			self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=intronLineColor)
			# draw triangle
			triangle_size = 10
			posX1 = posX_start
			posY1 = posY_end
			posX2 = posX1 - triangle_size
			posY2 = posY1 + triangle_size
			posX3 = posX1 + triangle_size
			posY3 = posY1 + triangle_size
			self.pic.create_line(posX1, posY1, posX2, posY2, fill=intronLineColor)
			self.pic.create_line(posX1, posY1, posX3, posY3, fill=intronLineColor)
			self.pic.create_line(posX2, posY2, posX3, posY3, fill=intronLineColor)
			# place intron value
			intron_val = self.introns[intron_i]
			posX = posX_start
			self.pic.create_text(posX, text_barHeight+self.barHeight*2.5+triangle_size+1, text=str(intron_val), fill=textcolor)

			# update curr pos
			curr_pos += exon_lens[intron_i] * 1.0


		# second bar ------------------------
		posY = self.vSpace + 1 *  (self.vSpace+self.barHeight) + self.barHeight
		text_barHeight = posY+self.barHeight*2.0   # height for the text

		# place the longer seq bar
		barcolor = 'blue'
		start = self.subject_first - self.query_first / 3.0 + 1
		if start < 1:
			start = 1.0
		end = self.subject_first + self.len_q / 3.0
		start_long, end_long = start, end
		if self.dir_bottom_bar == "R":
			middle = (self.subject_last + self.subject_first) / 2.0
			end_long = (middle-start) + middle
			start_long = middle - (end-middle)
		if start_long < 1.0:
			start_long = 1.0
		posX_start = self.hSpace + (start_long/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posX_end = self.hSpace + (end_long/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posY_start = posY
		posY_end = posY_start + self.barHeight
		self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)

		# place the left extention broken bar
		hSegment = self.hSpace / 8.0
		if (self.subject_first - self.query_first/3.0) < 0 or start_long <= 1.0:
			posX_start = hSegment*3.5
			posX_end = posX_start+hSegment
			self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)
			posX_start = hSegment*5
			posX_end = posX_start+hSegment
			self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)
			posX_start = hSegment*6.5
			posX_end = posX_start+hSegment
			self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)

		# decide start and end indexes
		start = self.subject_first * 1.0
		end = self.subject_last * 1.0
		if self.dir_bottom_bar == "F":
			start_str = self.query_first
			end_str = self.query_last
		else:
			end_str = self.query_first
			start_str = self.query_last
		# place the start index
		posX = self.hSpace + (start/self.maxGeneLen)*self.adjustedGraphChartSizeX - self.charSpace * ( log10(start)+1 )
		self.pic.create_text(posX, text_barHeight, text=(str(start_str)+" nt"), fill=textcolor)
		# place the end index
		posX = self.hSpace + (end/self.maxGeneLen)*self.adjustedGraphChartSizeX	+ self.charSpace * ( log10(end)+1 )
		self.pic.create_text(posX, text_barHeight, text=(str(end_str)+" nt"), fill=textcolor)

		# place the shorter seq bar
		barcolor = 'lightgreen'
		start = self.subject_first * 1.0
		end = self.subject_last * 1.0
		posX_start = self.hSpace + (start/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posX_end = self.hSpace + (end/self.maxGeneLen)*self.adjustedGraphChartSizeX
		posY_start = posY
		posY_end = posY_start + self.barHeight
		self.pic.create_rectangle(posX_start, posY_start, posX_end, posY_end, width=0, fill=barcolor)

		# place the direction
		dir = self.dir_bottom_bar
		posX = self.hSpace + self.adjustedGraphChartSizeX + self.charSpace * 3
		self.pic.create_text(posX, text_barHeight-self.barHeight*1.5, text=dir, fill=textcolor)



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


	def highlightTextWinGenes(self):
		L_str = self.CVLTR_L_text.get()        # left index
		LX_str = self.CVLTR_LX_text.get()      # left excluded index
		R_str = self.CVLTR_R_text.get()        # right index
		RX_str = self.CVLTR_RX_text.get()      # right excluded index
		doLeftFlag = 1   # indicate we should highlight the left one
		doRightFlag = 1   # indicate we should highlight the right one
		if L_str == "" or LX_str == "":   # no input yet, so quit
			doLeftFlag = 0
		if R_str == "" or RX_str == "":   # no input yet, so quit
			doRightFlag = 0
		# clear the old background color
		self.SeqTextWin_content.tag_delete('interested_tag')
		# draw the new background color
		if doLeftFlag == 1:
			L = int(L_str) + self.seqNameCharSpace
			LX = int(LX_str) + self.seqNameCharSpace
			for i in range(1, self.numOfBars+1):
				startingPos = "%d.%d" % (i, LX)
				endingPos = "%d.%d" % (i, L)
				self.SeqTextWin_content.tag_add('interested_tag', startingPos, endingPos)
		if doRightFlag == 1:
			R = int(R_str) + self.seqNameCharSpace
			RX = int(RX_str) + self.seqNameCharSpace
			for i in range(1, self.numOfBars+1):
				startingPos = "%d.%d" % (i, R)
				endingPos = "%d.%d" % (i, RX)
				self.SeqTextWin_content.tag_add('interested_tag', startingPos, endingPos)
		self.SeqTextWin_content.tag_config('interested_tag', background='yellow')

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



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




#########################################

def main():
	contigViewerUserInputWindow().mainloop()

if __name__ == "__main__":
	main()