from rpy import *

## R handles the plotting for us. All we need to do is to make the R code.
## This first function plots the overlap for all the helices in the TM bundle
def Plot( table1, title1, xaxis1, yaxis1, psplotfilename, modes, bundle, suffix, names, legendposWeight=5.5):
#Aug07: legendposWeight argument added to allow different placement of legend for kinkvectors(which have more text)
#this could possible by calcualted from the size if names
	
	#for i in range(0, len(bundle)):
	#	print table1[i][130]

	lower = 0
	for i in range(0, len(bundle)):
		if table1[i][len(modes)-7] < len(bundle)*0.04:
			lower += 1

	if lower < (len(bundle) / 2):
		x = len(modes)-(min(len(modes),len(modes)/legendposWeight))#len(modes)-(min(len(modes),len(modes)/5.5))
		y = 0.036*len(bundle)
	else:
		x = 0
		y = 1
		
	if suffix == 'pdf':
		r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE)
		#r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE,paper='a4')
		
	#if suffix == 'png':
		#r.bitmap(psplotfilename+suffix, res=100 )
		#r.png(psplotfilename+suffix, res=100 )
		#r.jpeg(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE,paper='a4')
		
	r.par(mfrow=r.c(1,1))

	if title1[0:2] == 'Cu':
		r.plot(table1[0], type='n', xlab=xaxis1, ylab=yaxis1, main=title1, ylim=r.c(0,1) )
	else:
		r.plot(table1[0], type='n', xlab=xaxis1, ylab=yaxis1, main=title1 )

	color_dict = dict()
	line_dict = dict()

	for name in names:
		color_dict[name] = ''
		line_dict[name] = ''
		
	co = []
	li = []
	c=1
	j=1

	for i in range(0,len(table1)):
		if ( i%7 == 0 ):
			j=j+1

		helix_id = bundle[i]
		name = names[helix_id]

		if name != '':
			if color_dict[name] != '':
				
				color = color_dict[name]
				line = line_dict[name]
			else:
				color_dict[name] = c	
				line_dict[name] = j
				color = c
				line = j
				j+=1
				c+=1

		else:
			color = c
			line = j
			j+=1
			c+=1
						
		r.lines(table1[i], col=color,type='l', lty=line, lwd=0.9)
		co.append(color)
		li.append(line)

		
	new_bundle = []

	#
	#Aug07:
	#when plotting of kinvectors is done there should be no '' names
	#make sure that the naming convetion of helices for kinkvectors is kept consistent with this.
	#we might want to move all naming responsibilities out of plotR
	#/
	for i in range(len(bundle)):
		helix_id = bundle[i]
		name = names[helix_id]

		if name == '':
			new_bundle.append('Helix ' + str(helix_id))
		else:
			new_bundle.append('Helix ' + str(name))

	r.legend(x,y, r.c(new_bundle), col=r.c(co), lty=r.c(li) )
	
	r.dev_off()
	r.graphics_off()

	os.system('convert -size 120x120 ./'+ psplotfilename+suffix + ' ./' + psplotfilename+'png')
	os.system('convert ./'+ psplotfilename+'png' + ' -resize 120x120 ./' + psplotfilename+'THUMB.png')
	os.system('convert ./'+ psplotfilename+'THUMB.png'+ ' -sharpen 10 ./'+ psplotfilename+'THUMB.png')
	
	## if suffix == 'pdf':
## 		os.system('gv '+ psplotfilename+suffix)
## 	if suffix == 'png':
## 		os.system('display '+ psplotfilename+suffix)

	return

def sort_by_value(d):
    """ Returns the keys of dictionary d sorted by their values """
    items=d.items()
    backitems=[ [v[1],v[0]] for v in items]
    backitems.sort()
    backitems.reverse()
    return [ int(backitems[i][1]) for i in range(0,len(backitems)) ]
        

## This function plots the overlap for the movement of the bundle. 
def Plot2(table1, title1, xaxis1, yaxis1, psplotfilename, modes, suffix):
	import operator
	
	best_mode = 0
	sec_mode = 0
	third_mode = 0

	new_table = []
	
	for key in range(len(table1)):
		value = table1[key]
		
		new_table.append( (value[1], key) )
	new_table.sort()
	#print new_table
	
	best_mode = new_table[len(new_table)-1][1]
	sec_mode = new_table[len(new_table)-2][1]
	third_mode = new_table[len(new_table)-3][1]
		
	value_1 = table1[best_mode][1]
	value_2 = table1[sec_mode][1]
	value_3 = table1[third_mode][1]

	#print best_mode
	#print sec_mode
	#print third_mode

	if suffix == 'pdf':
		r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE)
		#r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE,paper='a4')
	#if suffix == 'png':
	#	r.bitmap(psplotfilename+suffix, res=100 )
	
	#r.bitmap(psplotfilename, res=100 )
	#r.pdf(psplotfilename, horizontal=r.TRUE,onefile=r.TRUE,paper='a4')

	r.par(mfrow=r.c(1,1))
        r.plot(table1, type='l', xlab=xaxis1, ylab=yaxis1, main=title1 )

	r.text(best_mode+len(table1)/10, value_1, ' <-- mode ' + str(best_mode+1))
	r.text(sec_mode+len(table1)/10, value_2, ' <-- mode ' + str(sec_mode+1))
	r.text(third_mode+len(table1)/10, value_3, ' <-- mode ' + str(third_mode+1))
	#r.plot(best_mode, value_1, pch="+")
	#r.plot(sec_mode, value_2, pch="+")
	
	r.dev_off()
	r.graphics_off()

	
	#if suffix == 'png':
 	#	os.system('convert ./'+ psplotfilename+suffix + ' -resize 120x120 ./' + psplotfilename+'THUMB.'+suffix)
	#	os.system('convert ./'+ psplotfilename+'THUMB.'+suffix + ' -sharpen 10 ./'+ psplotfilename+'THUMB.'+suffix)

	os.system('convert -size 120x120 ./'+ psplotfilename+suffix + ' ./' + psplotfilename+'png')

	os.system('convert ./'+ psplotfilename+'png' + ' -resize 120x120 ./' + psplotfilename+'THUMB.png')
	os.system('convert ./'+ psplotfilename+'THUMB.png'+ ' -sharpen 10 ./'+ psplotfilename+'THUMB.png')
	
	return

## cumulative bundle rotation
def Plot3(table1, title1, xaxis1, yaxis1, psplotfilename, modes, suffix):

	if suffix == 'pdf':
		r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE)
		#r.pdf(psplotfilename+suffix, horizontal=r.TRUE,height=7, width=7, pointsize=10,onefile=r.FALSE,paper='a4')
	if suffix == 'png':
		r.bitmap(psplotfilename+suffix, res=100 )
	#r.bitmap(psplotfilename, res=100 )
	#r.pdf(psplotfilename, horizontal=r.TRUE,onefile=r.TRUE,paper='a4')

	r.par(mfrow=r.c(1,1))
        r.plot(table1, type='l', xlab=xaxis1, ylab=yaxis1, main=title1, ylim=r.c(0,1) )
	
	r.dev_off()
	r.graphics_off()

	
	#if suffix == 'png':
 	#	os.system('convert ./'+ psplotfilename+suffix + ' -resize 120x120 ./' + psplotfilename+ 'THUMB.'+suffix)
	#	os.system('convert ./'+ psplotfilename+'THUMB.'+suffix + ' -sharpen 10 ./'+ psplotfilename+'THUMB.'+suffix)

	os.system('convert -size 120x120 ./'+ psplotfilename+suffix + ' ./' + psplotfilename+'png')

	os.system('convert ./'+ psplotfilename+'png' + ' -resize 120x120 ./' + psplotfilename+'THUMB.png')
	os.system('convert ./'+ psplotfilename+'THUMB.png'+ ' -sharpen 10 ./'+ psplotfilename+'THUMB.png')

	return