#!/bin/bash

# Set the PBS info.
#PBS -N PredictBi_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 'PredictBi'  'Predict a Bimolecular Secondary Structure'  'DIRECTORY_STRING'  'EMAIL_TO'
DIRECTORY="DIRECTORY_STRING"
FULLCOMMAND="COMMAND_STRING"
FULLHTML="COMMAND_HTML_STRING"

######################################################################
# Do the bifold 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 commands that create comprehensive CT, PS, and PDF files. 
runTool bifold $COMMAND   
runTool draw bifold.ct bifold.ps  
runTool ps2pdf bifold.ps bifold.pdf  

# 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 bifold.ps | wc -l`

   if (( $NUMSTRUCTURES == 1 )); then
      runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=bifold.jpeg bifold.ps 
      runTool draw bifold.ct bifold.svg -n 1 --svg 
   else
      if [[ ! -s errors.txt ]]; then
         SEQLENGTH=`head -n 1 bifold.ct | awk '{print $1}'`
	 let SEQLENGTH++;
         awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 bifold.ct
      fi
      typeset -i i END; 
      let END=$NUMSTRUCTURES; 
      let i=1; 
      while (( i <= END )); do 
	 runTool draw bifold.ct ${i}.ps -n $i  
	 runTool ps2pdf ${i}.ps ${i}.pdf  
	 runTool draw bifold.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" bifold.svg
   then
      cp ../../../../Utilities/Pages/NoStructures.html Results.html
      rm -f bifold*
   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 bifold.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@bifold/bifold.html@g' Results.html 
   sed -i 's@INTERFACE_NAME@bifold@g' Results.html 
   sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/bifold@g" Results.html 
   sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/bifold.html\">bifold</a> $HTMLCOMMAND@g" Results.html
   sed -i 's@bifold/ResultsPages@PredictBi/ResultsPages@g' Results.html
   sed -i 's@src="bifold.svg"@src="bifold/bifold.svg"@g' Results.html
   sed -i "s@getFile=PredictBi/ResultsPages/$DIRECTORY/bifold.ct@getFile=PredictBi/ResultsPages/$DIRECTORY/bifold/bifold.ct@g" Results.html
fi

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

######################################################################
# Do the DuplexFold 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 commands that create comprehensive CT, PS, and PDF files.
runTool DuplexFold $COMMAND   
runTool draw DuplexFold.ct DuplexFold.ps  
runTool ps2pdf DuplexFold.ps DuplexFold.pdf  

# 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 DuplexFold.ps | wc -l`

   if (( $NUMSTRUCTURES == 1 )); then
      runTool gs -dNOPAUSE -dBATCH -q -r300 -dJPEGQ=100 -sDEVICE=jpeg -sOutputFile=DuplexFold.jpeg DuplexFold.ps 
      runTool draw DuplexFold.ct DuplexFold.svg -n 1 --svg 
   else
      if [[ ! -s errors.txt ]]; then
         SEQLENGTH=`head -n 1 DuplexFold.ct | awk '{print $1}'`
	 let SEQLENGTH++;
         awk '{print > (NR%"'"$SEQLENGTH"'"?i:i++)".ct";}' i=1 DuplexFold.ct
      fi
      typeset -i i END; 
      let END=$NUMSTRUCTURES; 
      let i=1; 
      while (( i <= END )); do 
	 runTool draw DuplexFold.ct ${i}.ps -n $i  
	 runTool ps2pdf ${i}.ps ${i}.pdf  
	 runTool draw DuplexFold.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" DuplexFold.svg
   then
      cp ../../../../Utilities/Pages/NoStructures.html Results.html
      rm -f DuplexFold*
   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 DuplexFold.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@DuplexFold/DuplexFold.html@g' Results.html 
   sed -i 's@INTERFACE_NAME@DuplexFold@g' Results.html 
   sed -i "s@FULL_RESULTS_DIRECTORY@ResultsPages/$DIRECTORY/DuplexFold@g" Results.html 
   sed -i "s@COMMAND_LINE@<a href=\"http://rna.urmc.rochester.edu/Text/DuplexFold.html\">DuplexFold</a> $HTMLCOMMAND@g" Results.html
   sed -i 's@DuplexFold/ResultsPages@PredictBi/ResultsPages@g' Results.html
   sed -i 's@src="DuplexFold.svg"@src="DuplexFold/DuplexFold.svg"@g' Results.html
   sed -i "s@getFile=PredictBi/ResultsPages/$DIRECTORY/DuplexFold.ct@getFile=PredictBi/ResultsPages/$DIRECTORY/DuplexFold/DuplexFold.ct@g" Results.html
fi

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

######################################################################
# 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/PredictBi/PredictBi.html">Predict a Bimolecular 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" bifold/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" DuplexFold/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@PredictBi/PredictBi.html@g' Results.html
    sed -i 's@INTERFACE_NAME@Predict a Bimolecular Secondary Structure@g' Results.html
fi

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