#!/bin/bash

# Set the PBS info.
#PBS -N Predict2_DIRECTORY_STRING
#PBS -l nodes=1:ppn=4:long,walltime=24:00:00
#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 'Predict2'  'Predict a Secondary Structure Common to Two Sequences'  'DIRECTORY_STRING'  'EMAIL_TO'
DIRECTORY=DIRECTORY_STRING
FULLCOMMAND="COMMAND_STRING"
FULLHTML="COMMAND_HTML_STRING"
MODETYPE="MODE_TYPE_STRING"
NUMSEQS=2
OUTPUTTYPE=""

######################################################################
# Do the dynalign 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 dynalign-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${num};
   mv dynalign${num}.ct seq${num}/dynalign.ct
   cd seq${num}

   # Create the comprehensive PS and PDF files.
   runTool draw  dynalign.ct dynalign.ps 
   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; 
	  while (( i <= END )); do 
	      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
      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

# 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/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
    sed -i 's@dynalign/ResultsPages@Predict2/ResultsPages@g' Results.html
    sed -i 's@/seq@/dynalign/seq@g' Results.html
    sed -i 's@"/dynalign@"dynalign@g' Results.html
    sed -i 's@src="seq@src="dynalign/seq@g' Results.html
    sed -i 's@/dynalign.config@/dynalign/dynalign.config@g' Results.html
fi

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

######################################################################
# Do the PARTS 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 PARTS $COMMAND 

# Generate results files and create results pages depending on the calculation mode.
if [[ "$MODETYPE" == "pp" ]]; then
   OUTPUTTYPE="Plot"
   PLOTBOUNDS="PLOT_BOUNDS_STRING"

   # 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${num};
      mv PARTS${num}.txt seq${num}/PARTS.txt
      cd seq${num}

      # Create the plot files.
      runTool ProbabilityPlot  PARTS.txt PARTS.ps $PLOTBOUNDS --matrix
      runTool ps2pdf PARTS.ps PARTS.pdf  
      runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=PARTS.jpeg PARTS.ps 
      runTool ProbabilityPlot  PARTS.txt PARTS.svg $PLOTBOUNDS --matrix --svg

      # If no errors occurred in results files generation, create a results page using a templated HTML file.
      if [[ ! -s errors.txt ]]; then
	  copyTemplate ResultsPagePlots  Results.html
	  sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/seq${num}@g" Results.html
	  sed -i "s@PFS@Text@g" Results.html
	  sed -i "s@pfs@txt@g" Results.html
      fi

      # If an error did occur in results file generation, create an error page using a templated HTML file, break out of the loop.
      if [[ -s ../errors.txt ]]; then
         break
      fi

      # Move back to the main directory and increment the loop.
      cd ..
      let num++;
   done

   # Create the combined structure results page and set the alignment div invisible.
   copyTemplate ResultsPageManyAlignedStructures  Results.html
   sed -i 's@id="alignment" class="centerClass"@id="alignment" class="centerClass" style="display: none"@g' Results.html
else
   OUTPUTTYPE="Structures"

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

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

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

      # Move back to the main directory and increment the loop.
      cd ..
      let num++;
   done

   # Create the combined structure results page and set the alignment root in it.
   copyTemplate ResultsPageManyAlignedStructures  Results.html
   sed -i 's@ALIGNMENT_ROOT@PARTS/PARTS@g' Results.html
fi

# If an error results page was not already made, build the combined results page.
if [[ ! -s ../errors.txt ]]; then
   sed -i '/image box starts/,/command line ends/d' Results.html

   let num=1;
   while (( num <= SEQS )); do
      echo "<h3 class=\"centerClass\">$OUTPUTTYPE 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
fi

# Check for errors occurred in results files generation and initial results page generation.
# If none occurred, place the proper interface name and command line in the results page.
if [[ ! -s errors.txt ]]; then
   INTERFACEDESC=`grep -r --after-context=1 PARTS.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@INTERFACE_PAGE@PARTS/PARTS.html@g' Results.html 
   sed -i 's@INTERFACE_NAME@PARTS@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/PARTS.html\">PARTS</a> $HTMLCOMMAND@g" Results.html 
   sed -i 's@PARTS/ResultsPages@Predict2/ResultsPages@g' Results.html
   sed -i 's@/seq@/PARTS/seq@g' Results.html
   sed -i 's@"/PARTS@"PARTS@g' Results.html
   sed -i 's@src="seq@src="PARTS/seq@g' Results.html
   sed -i 's@/PARTS.config@/PARTS/PARTS.config@g' Results.html
fi

# Move all files created for this section into the PARTS directory.
mkdir PARTS;
mv seq* PARTS/;
mv PARTS.config PARTS/;
if [[ "$OUTPUTTYPE" == "Structures" ]]; then mv PARTS.ali PARTS/; fi
mv Results.html PARTS/;

######################################################################
# 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/Predict2/Predict2.html">Predict a Secondary Structure Common to Two 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" dynalign/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" PARTS/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@Predict2/Predict2.html@g' Results.html
    sed -i 's@INTERFACE_NAME@Predict a Secondary Structure Common to Two Sequences@g' Results.html
fi

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