#!/bin/bash
binDir=$(cd `dirname $0`; pwd)
export CLASSPATH=$binDir/../../software/VARNAv3-93.jar:$CLASSPATH
export PATH=$binDir/../../software/kentUtils:$PATH
export PATH=$binDir/../../software/scour:$PATH
seqDir=$1
species=$2
drawType=$3
ppid=$4
seqId=`basename $seqDir`
outDir=$seqDir/secondary_structure

sleep 2

cd $outDir
logFile=draw_${drawType}.log
colorMapFile=$outDir/${seqId}_${drawType}.txt
svgFile=${seqId}_${drawType}.svg
pngFile=$outDir/${seqId}_${drawType}.png

mypid=`ps -ef | grep -w $ppid | grep "fr.orsay.lri.varna.applications.VARNAcmd" | grep "naview" | awk '{print $2}'`

for((i=1;i<=100;i++));do
	sleep 3
	err=`grep "Exception" $logFile`
	finish=`grep "^Output file" $logFile`

	if [ -n "$err" ];then

########## run the alternative method ###########
	        rnafoldResultFile=seq_struct.dbn
		colorMapFile=${seqId}_${drawType}.txt
	        colorMap=`cat $colorMapFile`
	        max=2
		min=-2
		if [ $drawType == entropy ]; then
			max=1
			min=0
		fi

	# run
		java -Djava.awt.headless=true fr.orsay.lri.varna.applications.VARNAcmd  -colorMapMax $max  -colorMapMin $min -i $outDir/seq_struct.dbn -colorMap "$colorMap" -o $svgFile

                kill -9 $mypid
		rm -rf $logFile
		break
	
	elif [ -n "$finish" ];then
		rm -rf $logFile
		break
	fi
done