#!/bin/bash

# Set the PBS info.
#PBS -N Predict1_DIRECTORY_STRING
#PBS -l nodes=1,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 'Predict1'  'Predict a Secondary Structure'  'DIRECTORY_STRING'  'EMAIL_TO'
DIRECTORY="DIRECTORY_STRING"
FULLCOMMAND="COMMAND_STRING"
FULLHTML="COMMAND_HTML_STRING"
PLOTBOUNDS="PLOT_BOUNDS_STRING"
SHAPEFILE="SHAPE_FILE_STRING"

######################################################################
# Do the partition function calculation.
######################################################################

COMMAND=`echo $FULLCOMMAND | cut -d ';' -f '1'`
HTMLCOMMAND=`echo $FULLHTML | cut -d ';' -f '1'`

# Run the commands that create plot files.
writeStatus "Running partition..."
runTool partition $COMMAND 
writeStatus -d "Running ProbabilityPlot..."
runTool ProbabilityPlot partition.pfs partition.ps $PLOTBOUNDS  
runTool ProbabilityPlot partition.pfs partition.svg $PLOTBOUNDS --svg 
#writeStatus -d "Generating pdf..."
#runTool ps2pdf partition.ps partition.pdf  
#runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=partition.jpeg partition.ps 
writeStatus -d

# If no errors occurred in results files generation, create a results page using a templated HTML file.
# Place the proper interface name, results directory, and command line in the results page.
if [[ ! -s errors.txt ]]; then

   copyTemplate ResultsPagePlots  Results.html
   INTERFACEDESC=`grep -r --after-context=1 partition/partition.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@partition/partition.html@g' Results.html 
   sed -i 's@INTERFACE_NAME@partition@g' Results.html 
   sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/partition@g" Results.html 
   sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/partition.html\">partition</a> $HTMLCOMMAND@g" Results.html 
   sed -i 's@partition/ResultsPages@Predict1/ResultsPages@g' Results.html
   sed -i 's@src="partition.svg"@src="partition/partition.svg"@g' Results.html
   sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/partition.pfs@getFile=Predict1/ResultsPages/$DIRECTORY/partition/partition.pfs@g" Results.html
fi

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

######################################################################
# Do the Fold calculation and annotate results with probability data.
######################################################################

# 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 commands that create comprehensive CT, PS, and PDF files. 
writeStatus "Running Fold..."
runTool Fold $COMMAND   
writeStatus -d "Drawing Structures (Combined)..."
runTool draw Fold.ct Fold.ps -p partition/partition.pfs  
runTool ps2pdf Fold.ps Fold.pdf
writeStatus -d

# 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 Fold.ps | wc -l`
   writeStatus "Drawing Structures (Individual)..."
   if (( $NUMSTRUCTURES == 1 )); then
      #runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=Fold.jpeg Fold.ps 
      runTool draw Fold.ct Fold.svg -p partition/partition.pfs -n 1 --svg 
   else
      if [[ ! -s errors.txt ]]; then
         SEQLENGTH=`head -n 1 Fold.ct | awk '{print $1}'`
	 let SEQLENGTH++;
         awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 Fold.ct
      fi
      typeset -i i END; 
      let END=$NUMSTRUCTURES; 
      let i=1; 
      while (( i <= END )); do 
	 runTool draw Fold.ct ${i}.ps -n $i -p partition/partition.pfs  
	 runTool ps2pdf ${i}.ps ${i}.pdf  
	 runTool draw Fold.ct ${i}.svg -n $i -p partition/partition.pfs --svg  
	 let i++; 
      done
   fi 
   writeStatus -d
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" Fold.svg
   then
      cp ../../../../Utilities/Pages/NoStructures.html Results.html
      rm -f Fold*
   else
      if (( $NUMSTRUCTURES == 1 )); then
         copyTemplate ResultsPageSingleCTSingleStructure  Results.html
      else
	 copyTemplate ResultsPageSingleCTManyStructures  Results.html
	 sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
	 rm -f extendedDivs.txt

	 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

   INTERFACEDESC=`grep -r --after-context=1 Fold/Fold.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@Fold/Fold.html@g' Results.html 
   sed -i 's@INTERFACE_NAME@Fold@g' Results.html 
   sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/Fold@g" Results.html 
   sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/Fold.html\">Fold</a> $HTMLCOMMAND@g" Results.html
   sed -i 's@Fold/ResultsPages@Predict1/ResultsPages@g' Results.html
   sed -i 's@src="Fold.svg"@src="Fold/Fold.svg"@g' Results.html
   sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/Fold.ct@getFile=Predict1/ResultsPages/$DIRECTORY/Fold/Fold.ct@g" Results.html
fi

# Move all files created for this section into the Fold directory.
mkdir Fold;
mv *.ct Fold/;
mv *.ps Fold/;
mv *.pdf Fold/;
if (( $NUMSTRUCTURES == 1 )); then mv Fold.jpeg Fold/; fi
mv *.svg Fold/;
mv Results.html Fold/;

######################################################################
# If necessary, create another page of Fold results annotated with SHAPE data.
######################################################################

if [[ "$SHAPEFILE" != "false" ]]; then
   writeStatus "Annotating structures with SHAPE data..."
   # Run the commands that create comprehensive PS and PDF files.
   runTool draw Fold/Fold.ct Fold.ps -s $SHAPEFILE 
   runTool ps2pdf Fold.ps Fold.pdf 

   # If only one structure is present, create a JPEG and SVG file to be available to the user.
   # Otherwise, make 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 Fold.ps | wc -l`

       if (( $NUMSTRUCTURES == 1 )); then
	  runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=Fold.jpeg Fold.ps 
	  runTool draw Fold/Fold.ct Fold.svg -n 1 -s $SHAPEFILE --svg 
       else
	  typeset -i i END;
	  let END=$NUMSTRUCTURES;
	  let i=1;
	  while (( i <= END )); do
	     runTool draw Fold/Fold.ct ${i}.ps -n $i -s $SHAPEFILE 
	     runTool ps2pdf ${i}.ps ${i}.pdf 
	     runTool draw Fold/Fold.ct ${i}.svg -n $i -s $SHAPEFILE --svg 
	     let i++;
	  done
       fi
   fi
   writeStatus -d

   # 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" Fold.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
         rm -f Fold*
      else
	 if (( $NUMSTRUCTURES == 1 )); then
	     copyTemplate ResultsPageSingleCTSingleStructure  Results.html
	 else
	    copyTemplate ResultsPageSingleCTManyStructures  Results.html
	    sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
	    rm -f extendedDivs.txt

	    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@INTERFACE_NAME@Fold@g' Results.html
      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/Fold/SHAPE@g" Results.html
      sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/Fold.html\">Fold</a> $HTMLCOMMAND@g" Results.html
      sed -i 's@Fold/ResultsPages@Predict1/ResultsPages@g' Results.html
      sed -i 's@src="Fold.svg"@src="Fold/SHAPE/Fold.svg"@g' Results.html
      sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/Fold.ct@getFile=Predict1/ResultsPages/$DIRECTORY/Fold/SHAPE/Fold.ct@g" Results.html

      # Move all SHAPE-annotated files into the SHAPE directory.
      mkdir Fold/SHAPE;
      mv *.ps Fold/SHAPE/;
      mv *.pdf Fold/SHAPE/;
      if (( $NUMSTRUCTURES == 1 )); then mv Fold.jpeg Fold/SHAPE/; fi
      mv *.svg Fold/SHAPE/;
      mv Results.html Fold/SHAPE/;

      # Then, move all probability annotated files into the PFS directory and edit directory names accordingly.
      sed -i 's@Fold/@Fold/PFS/@g' Fold/Results.html
      sed -i 's@Fold"@Fold/PFS"@g' Fold/Results.html
      sed -i 's@Fold\&amp;@Fold/PFS\&amp;@g' Fold/Results.html
      mkdir Fold/PFS;
      mv Fold/*.ps Fold/PFS/;
      mv Fold/*.pdf Fold/PFS/;
      if (( $NUMSTRUCTURES == 1 )); then mv Fold/Fold.jpeg Fold/PFS/; fi
      mv Fold/*.svg Fold/PFS/;
      mv Fold/Results.html Fold/PFS/;

      # Correct any subdirectory assignments for files that weren't actually moved.
      awk '/CT/ { gsub(/PFS\//, "") }; { print }' Fold/PFS/Results.html > temp.out; mv temp.out Fold/PFS/Results.html;
      awk '/Fold.html/ { gsub(/PFS\//, "") }; { print }' Fold/PFS/Results.html > temp.out; mv temp.out Fold/PFS/Results.html;
      awk '/CT/ { gsub(/SHAPE\//, "") }; { print }' Fold/SHAPE/Results.html > temp.out; mv temp.out Fold/SHAPE/Results.html;
      awk '/Fold.html/ { gsub(/SHAPE\//, "") }; { print }' Fold/SHAPE/Results.html > temp.out; mv temp.out Fold/SHAPE/Results.html;

      # Put the two annotation results pages together into one big one reflecting the entire Fold section.
      copyTemplate ResultsPageManyAlignedStructures  Results.html
      sed -i '/results header starts/,/command line ends/d' Results.html

      sed -n "/results header starts/,/download links end/p" Fold/PFS/Results.html > combinedTemp.txt
      echo "<br/>" >> combinedTemp.txt
      sed "s@id=\"@id=\"1@g" combinedTemp.txt >> combined.txt
      sed -n "/image box starts/,/command line ends/p" Fold/SHAPE/Results.html > combinedTemp.txt
      echo "<br/>" >> 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
      mv Results.html Fold/;
   fi
fi

######################################################################
# Do the MaxExpect calculation.
######################################################################

# Create the unique script variables necessary for this calculation.
COMMAND=`echo $FULLCOMMAND | cut -d ';' -f '3'`
HTMLCOMMAND=`echo $FULLHTML | cut -d ';' -f '3'`

if [[ ! -s errors.txt ]]; then
   # Run the commands that create comprehensive CT, PS, and PDF files.
   writeStatus "Running MaxExpect..."
   runTool MaxExpect $COMMAND   
   writeStatus -d "Drawing MaxExpect Structures (Combined)..."
   runTool draw MaxExpect.ct MaxExpect.ps -p partition/partition.pfs  
   runTool ps2pdf MaxExpect.ps MaxExpect.pdf  
   writeStatus -d

   # 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 MaxExpect.ps | wc -l`
      writeStatus "Drawing MaxExpect structures (Individual)..."
      if (( $NUMSTRUCTURES == 1 )); then
         #runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=MaxExpect.jpeg MaxExpect.ps 
         runTool draw MaxExpect.ct MaxExpect.svg -n 1 -p partition/partition.pfs --svg 
      else
         if [[ ! -s errors.txt ]]; then
            SEQLENGTH=`head -n 1 MaxExpect.ct | awk '{print $1}'`
   	 let SEQLENGTH++;
            awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 MaxExpect.ct
         fi
         typeset -i i END; 
         let END=$NUMSTRUCTURES; 
         let i=1; 
         while (( i <= END )); do 
   	 runTool draw MaxExpect.ct ${i}.ps -n $i -p partition/partition.pfs  
   	 #runTool ps2pdf ${i}.ps ${i}.pdf  
   	 runTool draw MaxExpect.ct ${i}.svg -n $i -p partition/partition.pfs --svg  
   	 let i++; 
         done
      fi 
      writeStatus -d
   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" MaxExpect.svg
      then
         cp ../../../../Utilities/Pages/NoStructures.html Results.html
         rm -f MaxExpect*
      else
         if (( $NUMSTRUCTURES == 1 )); then
            copyTemplate ResultsPageSingleCTSingleStructure  Results.html
         else
   	 copyTemplate ResultsPageSingleCTManyStructures  Results.html
   	 sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
   	 rm -f extendedDivs.txt

   	 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

      INTERFACEDESC=`grep -r --after-context=1 MaxExpect.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@MaxExpect/MaxExpect.html@g' Results.html 
      sed -i 's@INTERFACE_NAME@MaxExpect@g' Results.html 
      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/MaxExpect@g" Results.html 
      sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/MaxExpect.html\">MaxExpect</a> $HTMLCOMMAND@g" Results.html
      sed -i 's@MaxExpect/ResultsPages@Predict1/ResultsPages@g' Results.html
      sed -i 's@src="MaxExpect.svg"@src="MaxExpect/MaxExpect.svg"@g' Results.html
      sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/MaxExpect.ct@getFile=Predict1/ResultsPages/$DIRECTORY/MaxExpect/MaxExpect.ct@g" Results.html
   fi

   # Move all files created for this section into the MaxExpect directory.
   mkdir MaxExpect;
   mv *.ct MaxExpect/;
   mv *.ps MaxExpect/;
   mv *.pdf MaxExpect/;
   if (( $NUMSTRUCTURES == 1 )); then mv MaxExpect.jpeg MaxExpect/; fi
   mv *.svg MaxExpect/;
   mv Results.html MaxExpect/;

fi #from top of max-expect

######################################################################
# If necessary, create another page of MaxExpect results annotated with SHAPE data.
######################################################################

if [[ ! -s errors.txt && "$SHAPEFILE" != "false" ]]; then
   writeStatus "Annotating MaxExpect structures with SHAPE data..."
   # Run the commands that create comprehensive PS and PDF files.
   runTool draw MaxExpect/MaxExpect.ct MaxExpect.ps -s $SHAPEFILE 
   runTool ps2pdf MaxExpect.ps MaxExpect.pdf 

   # If only one structure is present, create a JPEG and SVG file to be available to the user.
   # Otherwise, make 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 MaxExpect.ps | wc -l`

       if (( $NUMSTRUCTURES == 1 )); then
	  #runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=MaxExpect.jpeg MaxExpect.ps 
	  runTool draw MaxExpect/MaxExpect.ct MaxExpect.svg -n 1 -s $SHAPEFILE --svg 
       else
	  typeset -i i END;
	  let END=$NUMSTRUCTURES;
	  let i=1;
	  while (( i <= END )); do
	     runTool draw MaxExpect/MaxExpect.ct ${i}.ps -n $i -s $SHAPEFILE 
	     #runTool ps2pdf ${i}.ps ${i}.pdf 
	     runTool draw MaxExpect/MaxExpect.ct ${i}.svg -n $i -s $SHAPEFILE --svg 
	     let i++;
	  done
       fi
   fi
   writeStatus -d

   # 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" MaxExpect.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
         rm -f MaxExpect*
      else
	 if (( $NUMSTRUCTURES == 1 )); then
	     copyTemplate ResultsPageSingleCTSingleStructure  Results.html
	 else
	    copyTemplate ResultsPageSingleCTManyStructures  Results.html
	    sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
	    rm -f extendedDivs.txt

	    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@INTERFACE_NAME@MaxExpect@g' Results.html
      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/MaxExpect/SHAPE@g" Results.html
      sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/MaxExpect.html\">MaxExpect</a> $HTMLCOMMAND@g" Results.html
      sed -i 's@MaxExpect/ResultsPages@Predict1/ResultsPages@g' Results.html
      sed -i 's@src="MaxExpect.svg"@src="MaxExpect/SHAPE/MaxExpect.svg"@g' Results.html
      sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/MaxExpect.ct@getFile=Predict1/ResultsPages/$DIRECTORY/MaxExpect/SHAPE/MaxExpect.ct@g" Results.html

      # Move all SHAPE-annotated files into the SHAPE directory.
      mkdir MaxExpect/SHAPE;
      mv *.ps MaxExpect/SHAPE/;
      mv *.pdf MaxExpect/SHAPE/;
      if (( $NUMSTRUCTURES == 1 )); then mv MaxExpect.jpeg MaxExpect/SHAPE/; fi
      mv *.svg MaxExpect/SHAPE/;
      mv Results.html MaxExpect/SHAPE/;

      # Then, move all probability annotated files into the PFS directory and edit directory names accordingly.
      sed -i 's@MaxExpect/@MaxExpect/PFS/@g' MaxExpect/Results.html
      sed -i 's@MaxExpect"@MaxExpect/PFS"@g' MaxExpect/Results.html
      sed -i 's@MaxExpect\&amp;@MaxExpect/PFS\&amp;@g' MaxExpect/Results.html
      mkdir MaxExpect/PFS;
      mv MaxExpect/*.ps MaxExpect/PFS/;
      mv MaxExpect/*.pdf MaxExpect/PFS/;
      if (( $NUMSTRUCTURES == 1 )); then mv MaxExpect/MaxExpect.jpeg MaxExpect/PFS/; fi
      mv MaxExpect/*.svg MaxExpect/PFS/;
      mv MaxExpect/Results.html MaxExpect/PFS/;

      # Correct any subdirectory assignments for files that weren't actually moved.
      awk '/CT/ { gsub(/PFS\//, "") }; { print }' MaxExpect/PFS/Results.html > temp.out; mv temp.out MaxExpect/PFS/Results.html;
      awk '/MaxExpect.html/ { gsub(/PFS\//, "") }; { print }' MaxExpect/PFS/Results.html > temp.out; mv temp.out MaxExpect/PFS/Results.html;
      awk '/CT/ { gsub(/SHAPE\//, "") }; { print }' MaxExpect/SHAPE/Results.html > temp.out; mv temp.out MaxExpect/SHAPE/Results.html;
      awk '/MaxExpect.html/ { gsub(/SHAPE\//, "") }; { print }' MaxExpect/SHAPE/Results.html > temp.out; mv temp.out MaxExpect/SHAPE/Results.html;

      # Put the two annotation results pages together into one big one reflecting the entire MaxExpect section.
      copyTemplate ResultsPageManyAlignedStructures  Results.html
      sed -i '/results header starts/,/command line ends/d' Results.html

      sed -n "/results header starts/,/download links end/p" MaxExpect/PFS/Results.html > combinedTemp.txt
      echo "<br/>" >> combinedTemp.txt
      sed "s@id=\"@id=\"1@g" combinedTemp.txt >> combined.txt
      sed -n "/image box starts/,/command line ends/p" MaxExpect/SHAPE/Results.html > combinedTemp.txt
      echo "<br/>" >> 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
      mv Results.html MaxExpect/;
   fi
fi

######################################################################
# Do the ProbKnot calculation.
######################################################################

# Create the unique script variables necessary for this calculation.
COMMAND=`echo $FULLCOMMAND | cut -d ';' -f '4'`
HTMLCOMMAND=`echo $FULLHTML | cut -d ';' -f '4'`

if [[ ! -s errors.txt ]]; then 
   # Run the commands that create comprehensive CT, PS, and PDF files.
   writeStatus "Running ProbKnot..."
   runTool ProbKnot $COMMAND   
   writeStatus -d "Drawing ProbKnot Structures (Combined)..."
   runTool draw ProbKnot.ct ProbKnot.ps -p partition/partition.pfs  
   runTool ps2pdf ProbKnot.ps ProbKnot.pdf  
   writeStatus -d

   # 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 ProbKnot.ps | wc -l`
      writeStatus "Drawing ProbKnot Structures (Individual)..."
      if (( $NUMSTRUCTURES == 1 )); then
         #runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=ProbKnot.jpeg ProbKnot.ps 
         runTool draw ProbKnot.ct ProbKnot.svg -n 1 -p partition/partition.pfs --svg 
      else
         if [[ ! -s errors.txt ]]; then
            SEQLENGTH=`head -n 1 ProbKnot.ct | awk '{print $1}'`
   	 let SEQLENGTH++;
            awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 ProbKnot.ct
         fi
         typeset -i i END; 
         let END=$NUMSTRUCTURES; 
         let i=1; 
         while (( i <= END )); do 
   	 runTool draw ProbKnot.ct ${i}.ps -n $i -p partition/partition.pfs  
   	 #runTool ps2pdf ${i}.ps ${i}.pdf  
   	 runTool draw ProbKnot.ct ${i}.svg -n $i -p partition/partition.pfs --svg  
   	 let i++; 
         done
      fi 
      writeStatus -d
   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" ProbKnot.svg
      then
         cp ../../../../Utilities/Pages/NoStructures.html Results.html
         rm -f ProbKnot*
      else
         if (( $NUMSTRUCTURES == 1 )); then
            copyTemplate ResultsPageSingleCTSingleStructure  Results.html
         else
   	 copyTemplate ResultsPageSingleCTManyStructures  Results.html
   	 sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
   	 rm -f extendedDivs.txt

   	 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

      INTERFACEDESC=`grep -r --after-context=1 ProbKnot.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@ProbKnot/ProbKnot.html@g' Results.html 
      sed -i 's@INTERFACE_NAME@ProbKnot@g' Results.html 
      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/ProbKnot@g" Results.html 
      sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/ProbKnot.html\">ProbKnot</a> $HTMLCOMMAND@g" Results.html
      sed -i 's@ProbKnot/ResultsPages@Predict1/ResultsPages@g' Results.html
      sed -i 's@src="ProbKnot.svg"@src="ProbKnot/ProbKnot.svg"@g' Results.html
      sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/ProbKnot.ct@getFile=Predict1/ResultsPages/$DIRECTORY/ProbKnot/ProbKnot.ct@g" Results.html
   fi

   # Move all files created for this section into the ProbKnot directory.
   mkdir ProbKnot;
   mv *.ct ProbKnot/;
   mv *.ps ProbKnot/;
   mv *.pdf ProbKnot/;
   if (( $NUMSTRUCTURES == 1 )); then mv ProbKnot.jpeg ProbKnot/; fi
   mv *.svg ProbKnot/;
   mv Results.html ProbKnot/;
fi # from top of ProbKnot

######################################################################
# If necessary, create another page of ProbKnot results annotated with SHAPE data.
######################################################################

if [[ ! -s errors.txt && "$SHAPEFILE" != "false" ]]; then
   writeStatus "Annotating ProbKnot Structures with SHAPE data..."
   # Run the commands that create comprehensive PS and PDF files.
   runTool draw ProbKnot/ProbKnot.ct ProbKnot.ps -s $SHAPEFILE 
   runTool ps2pdf ProbKnot.ps ProbKnot.pdf 

   # If only one structure is present, create a JPEG and SVG file to be available to the user.
   # Otherwise, make 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 ProbKnot.ps | wc -l`

       if (( $NUMSTRUCTURES == 1 )); then
	  #runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=ProbKnot.jpeg ProbKnot.ps 
	  runTool draw ProbKnot/ProbKnot.ct ProbKnot.svg -n 1 -s $SHAPEFILE --svg 
       else
	  typeset -i i END;
	  let END=$NUMSTRUCTURES;
	  let i=1;
	  while (( i <= END )); do
	     runTool draw ProbKnot/ProbKnot.ct ${i}.ps -n $i -s $SHAPEFILE 
	     #runTool ps2pdf ${i}.ps ${i}.pdf 
	     runTool draw ProbKnot/ProbKnot.ct ${i}.svg -n $i -s $SHAPEFILE --svg 
	     let i++;
	  done
       fi
   fi
   writeStatus -d

   writeStatus "Generating SHAPE-Annotated ProbKnot Results..."
   # 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" ProbKnot.svg
      then
	 cp ../../../../Utilities/Pages/NoStructures.html Results.html
         rm -f ProbKnot*
      else
	 if (( $NUMSTRUCTURES == 1 )); then
	    copyTemplate ResultsPageSingleCTSingleStructure  Results.html
	 else
	    copyTemplate ResultsPageSingleCTManyStructures  Results.html
	    sed -i "s@STRUCTURE_NUMBER@$END@g" Results.html
	    rm -f extendedDivs.txt

	    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@INTERFACE_NAME@ProbKnot@g' Results.html
      sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/ProbKnot/SHAPE@g" Results.html
      sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/ProbKnot.html\">ProbKnot</a> $HTMLCOMMAND@g" Results.html
      sed -i 's@ProbKnot/ResultsPages@Predict1/ResultsPages@g' Results.html
      sed -i 's@src="ProbKnot.svg"@src="ProbKnot/SHAPE/ProbKnot.svg"@g' Results.html
      sed -i "s@getFile=Predict1/ResultsPages/$DIRECTORY/ProbKnot.ct@getFile=Predict1/ResultsPages/$DIRECTORY/ProbKnot/SHAPE/ProbKnot.ct@g" Results.html

      # Move all SHAPE-annotated files into the SHAPE directory.
      mkdir ProbKnot/SHAPE;
      mv *.ps ProbKnot/SHAPE/;
      mv *.pdf ProbKnot/SHAPE/;
      if (( $NUMSTRUCTURES == 1 )); then mv ProbKnot.jpeg ProbKnot/SHAPE/; fi
      mv *.svg ProbKnot/SHAPE/;
      mv Results.html ProbKnot/SHAPE/;

      # Then, move all probability annotated files into the PFS directory and edit directory names accordingly.
      sed -i 's@ProbKnot/@ProbKnot/PFS/@g' ProbKnot/Results.html
      sed -i 's@ProbKnot"@ProbKnot/PFS"@g' ProbKnot/Results.html
      sed -i 's@ProbKnot\&amp;@ProbKnot/PFS\&amp;@g' ProbKnot/Results.html
      mkdir ProbKnot/PFS;
      mv ProbKnot/*.ps ProbKnot/PFS/;
      mv ProbKnot/*.pdf ProbKnot/PFS/;
      if (( $NUMSTRUCTURES == 1 )); then mv ProbKnot/ProbKnot.jpeg ProbKnot/PFS/; fi
      mv ProbKnot/*.svg ProbKnot/PFS/;
      mv ProbKnot/Results.html ProbKnot/PFS/;

      # Correct any subdirectory assignments for files that weren't actually moved.
      awk '/CT/ { gsub(/PFS\//, "") }; { print }' ProbKnot/PFS/Results.html > temp.out; mv temp.out ProbKnot/PFS/Results.html;
      awk '/ProbKnot.html/ { gsub(/PFS\//, "") }; { print }' ProbKnot/PFS/Results.html > temp.out; mv temp.out ProbKnot/PFS/Results.html;
      awk '/CT/ { gsub(/SHAPE\//, "") }; { print }' ProbKnot/SHAPE/Results.html > temp.out; mv temp.out ProbKnot/SHAPE/Results.html;
      awk '/ProbKnot.html/ { gsub(/SHAPE\//, "") }; { print }' ProbKnot/SHAPE/Results.html > temp.out; mv temp.out ProbKnot/SHAPE/Results.html;

      # Put the two annotation results pages together into one big one reflecting the entire ProbKnot section.
      copyTemplate ResultsPageManyAlignedStructures  Results.html
      sed -i '/results header starts/,/command line ends/d' Results.html

      sed -n "/results header starts/,/download links end/p" ProbKnot/PFS/Results.html > combinedTemp.txt
      echo "<br/>" >> combinedTemp.txt
      sed "s@id=\"@id=\"1@g" combinedTemp.txt >> combined.txt
      sed -n "/image box starts/,/command line ends/p" ProbKnot/SHAPE/Results.html > combinedTemp.txt
      echo "<br/>" >> 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
      mv Results.html ProbKnot/;
   fi
   writeStatus -d
fi


######################################################################
# 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/Predict1/Predict1.html">Predict a Secondary Structure</a> Results</h1>
</div>
<!-- div for combined header ends here -->
'

    echo -e $COMBINEDHEADER > combined.txt
    sed -n "/results header starts/,/command line ends/p" Fold/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" MaxExpect/Results.html > combinedTemp.txt
    echo "<br/>" >> combinedTemp.txt
    sed "s@id=\"@id=\"2@g" combinedTemp.txt >> combined.txt
    sed -n "/results header starts/,/command line ends/p" ProbKnot/Results.html > combinedTemp.txt
    echo "<br/>" >> combinedTemp.txt
    sed "s@id=\"@id=\"3@g" combinedTemp.txt >> combined.txt
    sed -n "/results header starts/,/command line ends/p" partition/Results.html > combinedTemp.txt
    sed "s@id=\"@id=\"4@g" combinedTemp.txt >> combined.txt

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

    sed -i 's@INTERFACE_PAGE@Predict1/Predict1.html@g' Results.html
    sed -i 's@INTERFACE_NAME@Predict a Secondary Structure@g' Results.html
fi

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