#!/bin/bash

# Set the PBS info.
#PBS -N Predict3_DIRECTORY_STRING
#PBS -l nodes=1:ppn=4:long,walltime=48:00:00
#PBS -q batch
#PBS -j oe
cd $PBS_O_WORKDIR

source ../../../../Utilities/Scripts/RunScriptTools  || echo 'Internal Server error. Please contact the website administrator.' > errors.txt  #include common functions, including sendResultsEmail.
calcStarted 'Predict3'  'Predict a Secondary Structure Common to Three or More Sequences'  'DIRECTORY_STRING'  'EMAIL_TO'
DIRECTORY=DIRECTORY_STRING
FULLCOMMAND="COMMAND_STRING"
FULLHTML="COMMAND_HTML_STRING"
NUMSEQS=NUM_SEQS_STRING

######################################################################
# Do the multilign calculation.
######################################################################

# Create the unique script variables necessary for this calculation.
COMMAND=`echo $FULLCOMMAND | cut -d ';' -f '1'`
HTMLCOMMAND=`echo $FULLHTML | cut -d ';' -f '1'`

# Run the main calculation command.
runTool multilign-smp $COMMAND 

# 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${num};
   mv multilign${num}.ct seq${num}/multilign.ct
   cd seq${num}

   # Create the comprehensive PS and PDF files.
   runTool draw  multilign.ct multilign.ps 
   if [[ ! -s ../errors.txt ]]; then ps2pdf multilign.ps multilign.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 multilign.ps | wc -l`

      if (( $NUMSTRUCTURES == 1 )); then
	  if [[ ! -s ../errors.txt ]]; then gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=multilign.jpeg multilign.ps 1>/dev/null 2>>../errors.txt; fi
	  runTool draw  multilign.ct multilign.svg -n 1 --svg
      else
	  if [[ ! -s ../errors.txt ]]; then
	      SEQLENGTH=`head -n 1 multilign.ct | awk '{print $1}'`
	      let SEQLENGTH++;
	      awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 multilign.ct
	  fi
	  typeset -i i END; 
	  let END=$NUMSTRUCTURES; 
	  let i=1; 
	  while (( i <= END )); do 
	      runTool draw  multilign.ct ${i}.ps -n $i 
	      if [[ ! -s ../errors.txt ]]; then ps2pdf ${i}.ps ${i}.pdf 1>/dev/null 2>>../errors.txt; fi 
	      runTool draw  multilign.ct ${i}.svg -n $i --svg 
	      let i++; 
	  done
      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" multilign.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
	 rm -f multilign*
      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

# 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 multilign.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

    insertTextFile ALIGNMENT_TEXT multilign/multilign.ali Results.html 

    sed -i 's@ALIGNMENT_ROOT@multilign/multilign@g' Results.html
    sed -i 's@INTERFACE_PAGE@multilign/multilign.html@g' Results.html
    sed -i 's@INTERFACE_NAME@multilign@g' Results.html 
    sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY@g" Results.html
    sed -i "s@COMMAND_LINE@<a href=\"/Text/multilign.html\">multilign-smp</a> $HTMLCOMMAND@g" Results.html
    sed -i 's@multilign/ResultsPages@Predict3/ResultsPages@g' Results.html
    sed -i 's@/seq@/multilign/seq@g' Results.html
    sed -i 's@"/multilign@"multilign@g' Results.html
    sed -i 's@src="seq@src="multilign/seq@g' Results.html
    sed -i 's@/multilign.config@/multilign/multilign.config@g' Results.html
fi

# Move all files created for this section into the multilign directory.
mkdir multilign;
mv seq* multilign/;
mv multilign.config multilign/;
mv multilign.ali multilign/
mv Results.html multilign/;

######################################################################
# Do the TurboFold calculation.
######################################################################

# Create the unique script variables necessary for this calculation.
COMMAND=`echo $FULLCOMMAND | cut -d ';' -f '2'`
HTMLCOMMAND=`echo $FULLHTML | cut -d ';' -f '2'`

# Run the main calculation command.
runTool TurboFold-smp $COMMAND 

# 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${num};
   mv TurboFold${num}.ct seq${num}/TurboFold.ct
   cd seq${num}

   # Create the comprehensive PS and PDF files.
   runTool draw  TurboFold.ct TurboFold.ps 
   if [[ ! -s ../errors.txt ]]; then ps2pdf TurboFold.ps TurboFold.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 TurboFold.ps | wc -l`

      if (( $NUMSTRUCTURES == 1 )); then
	  if [[ ! -s ../errors.txt ]]; then gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=TurboFold.jpeg TurboFold.ps 1>/dev/null 2>>../errors.txt; fi
	  runTool draw  TurboFold.ct TurboFold.svg -n 1 --svg
      else
	  if [[ ! -s ../errors.txt ]]; then
	      SEQLENGTH=`head -n 1 TurboFold.ct | awk '{print $1}'`
	      let SEQLENGTH++;
	      awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 TurboFold.ct
	  fi
	  typeset -i i END; 
	  let END=$NUMSTRUCTURES; 
	  let i=1; 
	  while (( i <= END )); do 
	      runTool draw  TurboFold.ct ${i}.ps -n $i 
	      if [[ ! -s ../errors.txt ]]; then ps2pdf ${i}.ps ${i}.pdf 1>/dev/null 2>>../errors.txt; fi 
	      runTool draw  TurboFold.ct ${i}.svg -n $i --svg 
	      let i++; 
	  done
      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" TurboFold.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
	 rm -f TurboFold*
      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

# 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
    #sed -i '/alignment file starts/,/alignment file ends/d' Results.html
    rm -f combined*.txt

    INTERFACEDESC=`grep -r --after-context=1 TurboFold.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

    insertFileInTemplate ALIGNMENT_TEXT TurboFold.aln Results.html
    replaceInFile Results.html ALIGNMENT_ROOT.ali  TurboFold.aln

    sed -i 's@INTERFACE_PAGE@TurboFold/TurboFold.html@g' Results.html
    sed -i 's@INTERFACE_NAME@TurboFold@g' Results.html 
    sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY@g" Results.html
    sed -i "s@COMMAND_LINE@<a href=\"/Text/TurboFold.html\">TurboFold-smp</a> $HTMLCOMMAND@g" Results.html
    sed -i 's@TurboFold/ResultsPages@Predict3/ResultsPages@g' Results.html
    sed -i 's@/seq@/TurboFold/seq@g' Results.html
    sed -i 's@"/TurboFold@"TurboFold@g' Results.html
    sed -i 's@src="seq@src="TurboFold/seq@g' Results.html
    sed -i 's@/TurboFold.config@/TurboFold/TurboFold.config@g' Results.html
fi

# Move all files created for this section into the TurboFold directory.
mkdir TurboFold;
mv seq* TurboFold/;
mv TurboFold.config TurboFold/;
mv Results.html TurboFold/;

######################################################################
# Check for errors, then create the results page.
######################################################################

# 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 '/results header starts/,/command line ends/d' Results.html

    COMBINEDHEADER='
<!-- div for combined header starts here -->
<div id="combined_header">
    <h1 class="centerClass" style="background: none; border-bottom: none;">RNAstructure <a href="../../../../Servers/Predict3/Predict3.html">Predict a Secondary Structure Common to Three or More Sequences</a> Results</h1>
</div>
<!-- div for combined header ends here -->
'

    echo -e $COMBINEDHEADER > combined.txt
    sed -n "/results header starts/,/command line ends/p" multilign/Results.html > combinedTemp.txt
    echo "<br/>" >> combinedTemp.txt
    sed "s@id=\"@id=\"1@g" combinedTemp.txt >> combined.txt
    sed -n "/results header starts/,/command line ends/p" TurboFold/Results.html > combinedTemp.txt
    sed "s@id=\"@id=\"2@g" combinedTemp.txt >> combined.txt

    sed -i 'N;/id="main"/r combined.txt' Results.html
    rm -f combined*.txt

    sed -i 's@INTERFACE_PAGE@Predict3/Predict3.html@g' Results.html
    sed -i 's@INTERFACE_NAME@Predict a Secondary Structure Common to Three or More Sequences@g' Results.html
fi

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