#!/bin/bash

# Set the PBS info.
#PBS -N dynalign_DIRECTORY_STRING
#PBS -l nodes=1:ppn=4:walltime=48:00:00
#PBS -q long
#PBS -j oe
#cd $PBS_O_WORKDIR

# Create the unique script variables necessary for this calculation.
COMMAND="COMMAND_STRING"
DIRECTORY=DIRECTORY_STRING
EMAIL="EMAIL_STRING"
HTMLCOMMAND="COMMAND_HTML_STRING"
NUMSEQS=2

# Export the data path and run the main calculation command.
source ../../../../Utilities/Scripts/RunScriptTools  || echo 'Internal Server error. Please contact the website administrator.' > errors.txt  #include common functions, including sendResultsEmail.
calcStarted 'dynalign'  'Dynalign'  'DIRECTORY_STRING'  'EMAIL_TO'
writeStatus "Running dynalign..."
runTool dynalign-smp $COMMAND 

writeStatus -d "Drawing Structures...\n"
# For each input sequence, create its results files and individual HTML page in a separate subfolder.
typeset -i i SEQS;
let SEQS=NUMSEQS;
let num=1;
while (( num <= SEQS )); do

   # Make the next subfolder and move the relevant files into it.
   # Then move to the subfolder.
   mkdir seq${num};
   mv dynalign${num}.fasta seq${num}/dynalign.fasta
   mv dynalign${num}.ct seq${num}/dynalign.ct
   cd seq${num}

   # Create the comprehensive PS and PDF files.
   writeStatus "  Drawing Sequence $num Structures (Combined)..."
   runTool draw dynalign.ct dynalign.ps
   writeStatus -d
   #if [[ ! -s ../errors.txt ]]; then ps2pdf dynalign.ps dynalign.pdf 1>/dev/null 2>>../errors.txt; fi

   # If only one structure is present, create a JPEG and SVG file to be available to the user.
   # Otherwise, split the CT file into individual structures and make CT, PS, PDF, and SVG files for each structure.
   # Individual JPEG files are not created because they take too long and occupy too much space; they are made only if and when the user requests them.
   NUMSTRUCTURES=0
   if [[ ! -s ../errors.txt ]]; then
      NUMSTRUCTURES=`grep -r showpage dynalign.ps | wc -l`

      if (( $NUMSTRUCTURES == 1 )); then
    	  #if [[ ! -s ../errors.txt ]]; then gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=dynalign.jpeg dynalign.ps 1>/dev/null 2>>../errors.txt; fi
    	  runTool draw dynalign.ct dynalign.svg -n 1 --svg
       else
    	  if [[ ! -s ../errors.txt ]]; then
    	      SEQLENGTH=`head -n 1 dynalign.ct | awk '{print $1}'`
    	      let SEQLENGTH++;
    	      awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 dynalign.ct
    	  fi
    	  typeset -i i END; 
    	  let END=$NUMSTRUCTURES; 
    	  let i=1; 
   	  writeStatus "  Drawing Structures:"
        while (( i <= END )); do 
           (( $i != 1 && $i % 5 == 1 )) && writeStatus "\n  Drawing Structures:"
           writeStatus "  $num.$i"
           runTool draw dynalign.ct ${i}.ps -n $i
   	     #if [[ ! -s ../errors.txt ]]; then ps2pdf ${i}.ps ${i}.pdf 1>/dev/null 2>>../errors.txt; fi 
   	     runTool draw dynalign.ct ${i}.svg -n $i --svg
   	     let i++; 
   	  done
        writeStatus "  \ndone.\n"
      fi 
   fi 

   # If no errors occurred in results files generation, create a results page using a templated HTML file.
   # If no structures were generated, use a static notification HTML page as the results page.
   # If only one structure was generated, place it in a specialized static HTML page.
   # If multiple structures were generated, place it in a dynamic, expandable HTML page.
   # If one or more structures were made, place the proper interface name, results directory, and command line in the results page.
   if [[ ! -s ../errors.txt ]]; then

      if grep -Fqs "contains no pairs" dynalign.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
	 rm -f dynalign*
      else
	  if (( $NUMSTRUCTURES == 1 )); then
	      copyTemplate ResultsPageSingleCTSingleStructure  Results.html
	  else
	      copyTemplate ResultsPageSingleCTManyStructures  Results.html
	      sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html

	      awk '/download structure 1 links/,/structure 1 links end here -->/{print}' ../../../../../Utilities/Templates/ResultsPageSingleCTManyStructures.html > individualDiv.txt
	      typeset -i i END;
	      let END=$NUMSTRUCTURES;
	      let i=1;
	      while (( i <= END )); do
		  sed "s/1/$i/g" individualDiv.txt >> extendedDivs.txt
		  let i++;
	      done

	      sed -i '/download structure 1 links/,/structure 1 links end here -->/d' Results.html
	      sed -i "N;/Download Individual Structures/r extendedDivs.txt" Results.html
	  fi
      fi

      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/seq${num}@g" Results.html
   fi

   # If an error did occur in results file generation, create an error page using a templated HTML file, delete all generated files, and break out of the loop.
   if [[ -s ../errors.txt ]]; then
       #copyTemplate Error  ../Results.html 
       #sed -i "N;/errorText/r ../errors.txt" ../Results.html
       rm -f  ../Results.html 
       cd ..
       rm -rf seq*
       break
   fi

   # Move back to the main directory and increment the loop.
   cd ..
   let num++;
done
writeStatus "Done Drawing Structures.\n"

# If an error results page was not already made, put the results pages together into one big one.
if [[ ! -s Results.html ]]; then
    copyTemplate ResultsPageManyAlignedStructures  Results.html
    sed -i '/image box starts/,/command line ends/d' Results.html

    let num=1;
    while (( num <= SEQS )); do
       echo "<h3 class=\"centerClass\">Structures derived from sequence $num:</h3>" > combinedTemp.txt
       sed -n "/image box starts here/,/download links end here/p" seq$num/Results.html >> combinedTemp.txt
       echo "<br/>" >> combinedTemp.txt
       sed "s@id=\"@id=\"$num@g" combinedTemp.txt >> combined.txt
       sed -i "s@src=\"INTERFACE_NAME.svg\"@src=\"seq${num}/INTERFACE_NAME.svg\"@g" combined.txt
       let num++;
    done

    sed -i "N;/alignment file ends here/r combined.txt" Results.html
    rm -f combined*.txt

    INTERFACEDESC=`grep -r --after-context=1 dynalign.html ../../../../index.html | tail -n 1 | cut -d '>' -f 2 | cut -d '<' -f 1`
    sed -i "s@Results</h1>@Results<br/><span style=\"font-weight: normal; color: black;\">($INTERFACEDESC)</span></h1>@g" Results.html

    sed -i 's@ALIGNMENT_ROOT@dynalign@g' Results.html
    sed -i 's@INTERFACE_PAGE@dynalign/dynalign.html@g' Results.html
    sed -i 's@INTERFACE_NAME@dynalign@g' Results.html 
    sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY@g" Results.html
    sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/dynalign.html\">dynalign-smp</a> $HTMLCOMMAND@g" Results.html
fi

######################################################################
# Perform end-of-calculation tasks
######################################################################
calcCompleted #send results email, notify web client, etc