/**
 * SpeciesFile class
 * 
 * encapsulates info of a species file
 * ( many species )
 * 
 */

import java.util.Vector;
import java.util.StringTokenizer;
import java.io.*;
import java.text.DecimalFormat;

public class SpeciesFile
{

   /**
    * Description associated with this file
    */
   private String description;

   /**
    * Location of the html
    */
   private String directorySufix;

   /**
    * Data Sets within this file
    */
   private Vector datasets;


   public SpeciesFile()
   {
      datasets = new Vector();
      description = null;
      directorySufix = null;
   }

   /**
    * Add Species to this file
    * @param  data  array containing the original data file (kin.o02)
    * @return  true if data was well formed, false otherwise
    */
   public boolean addSpecies( byte data[] )
   {
      boolean retValue = true;
      boolean debugMac = false; 
      int start = 0;
      int end = 0;
      int k = 0;
      byte buffer[] = new byte[ 1024 ];

      final String speciesNamePrefix = "#          ";
      final String datasetSeparator = "time-dep. species concentrations";
      final String datasetNamePrefix = "data set";

      String str = "";
      String spname = null;
      String datasetName = null;
      String val = null;
      StringTokenizer st = null;

      Vector speciesname = null;
      Vector values = null;
      DatasetSpecies dataset = null;

      for( int i = 0; i < data.length; i++ ) {
         if( data[ i ] == 13 ) {
            // get rid of the \r that ms-dos files have
            continue;
         }

         if( data[ i ] == 10 ) {
            if( k <= 1 ) {
               k = 0;
               continue;
            }

            str = new String( buffer, 0, k );

            if( str.indexOf( datasetSeparator ) != -1 ) {
               dataset = new DatasetSpecies( datasetName );
               speciesname = dataset.getSpeciesname();
               values = dataset.getValues();
               datasets.addElement( dataset );
            }
            else if( str.indexOf( datasetNamePrefix ) != -1 ) {
               datasetName = str.substring( datasetNamePrefix.length() ).trim();
            }
            else if( str.startsWith( speciesNamePrefix ) ) {
               spname = str.substring( speciesNamePrefix.length() );
               if( speciesname != null ) {
                  speciesname.addElement( spname.trim() );
               }
               else {
                  System.err.println( "speciesname Vector is null" );
                  return false;
               }
            }
            else if( ! str.startsWith( "#" ) ) {
               st = new StringTokenizer( str );
               if( spname != null && st.countTokens() == 3 ) {
                  st.nextToken();
                  st.nextToken();
                  val = st.nextToken(); 
                  val = val.replace( 'D', 'E' );
                  if( values != null ) {
                     values.addElement( Double.valueOf( val ) );
                  }
                  else {
                     System.err.println( "values Vector is null" );
                     return false;
                  }
               }
            }

            k = 0;
         }
         else {
            // replace / with a _ to avoid problems with file naming
            buffer[ k ] = ( (byte) '/' ) == data[ i ]  ? (byte) '_' : data[ i ];
            k++;
            if( k >= 1023 ) {
               return false;
            }
         }
      }
      
      try {
         writeToLocation();
      }
      catch( Exception e ) {
         e.printStackTrace();
         return false;
      }

      return retValue;
   }

   /**
    * Writes data to a data file organized by columns
    */
   private void writeToLocation()
   throws IOException, InterruptedException
   {
      int numlines = 0;
      int status = 0;
      int dirno = 0;
      Process p = null;
      Runtime r = Runtime.getRuntime();

      Vector speciesname = null;
      Vector values = null;
      DatasetSpecies dataset = null;
      PrintStream htmlFile = null;

      Vector chmodFiles = new Vector();
      DecimalFormat threeDigits = new DecimalFormat( "000" );
      String base_directory = Environment.HTML_DIRECTORY;
      final String HTMLFILE = "index.html";

      String PSFILE = null;
      String GNUFILE = null;
      String directory = null;
      File tmpFile = null;
      int max = 0;
      Integer tmpInt = null;

      tmpFile = new File( base_directory );
      String files[] = tmpFile.list();

      for( int i = 0; files != null & i < files.length; i++ ) {
         try {
            tmpInt = Integer.valueOf( files[ i ] );
         }
         catch( NumberFormatException nfe ) {
            continue;
         }
         if( tmpInt.intValue() > dirno ) {
            dirno = tmpInt.intValue();
         }
      }
      dirno++;
      if( dirno == Integer.MAX_VALUE ) {
         throw new IOException( "Too many existent directories!"
         + "\n[" + directory + "]" );
      }
      directorySufix = threeDigits.format( dirno );
      directory = base_directory + directorySufix;
      tmpFile = new File( directory );
      tmpFile.mkdir();      

      //do {
      //   dirno++;
      //   directorySufix = threeDigits.format( dirno );
      //   directory = base_directory + directorySufix;
      //   tmpFile = new File( directory );
      //   status = tmpFile.mkdir() ? 0 : 1;
      //} while( status != 0 && dirno < Environment.MAX_DIRECTORIES );
      //if( dirno >= Environment.MAX_DIRECTORIES ) {
      //   throw new IOException( "Too many existent directories!" 
      //   + "\n[" + directory + "]" );
      //}
	
      // write out each of the datasets

      for( int i = 0; i < datasets.size(); i++ ) {

         PSFILE = "all_vs_time_" + i + ".ps";
         GNUFILE = "toplot_" + i + ".gnufile";
         dataset = (DatasetSpecies) datasets.elementAt( i );
         speciesname = dataset.getSpeciesname();
         values = dataset.getValues();

         if( speciesname.size() == 0 ) {
            throw new IOException( "ERROR, dataset " + i + " has no species" );
         }
         numlines = values.size() / speciesname.size();
         if( numlines == 0 ) {
            throw new IOException( "ERROR, dataset " + i + " numlines is 0!" );
         }

         PrintStream fileColumns = new PrintStream( new FileOutputStream( 
         new File( directory + File.separator 
         + Environment.COLUMNS_DATA + i ) ) );
	
         String out = null;
         for( int lc = 0; lc < numlines; lc++ ) {
            out = "";
            for( int sp = 0; sp < speciesname.size(); sp++ ) {
               out += ( (Double) values.elementAt( lc + numlines * sp ) 
                      ).toString() + " ";
            }
            fileColumns.println( out );
         }
         fileColumns.close();

         PrintStream gnuFile = new PrintStream( new FileOutputStream( 
         new File( directory + File.separator + GNUFILE ) ) );

         // create first a postcript with all species vs. time
         gnuFile.println( "cd '" + directory + "'" );
         gnuFile.println( "set terminal postscript" );
         gnuFile.println( "set nokey" );
         gnuFile.println( "set output '" + PSFILE + "'" );
         gnuFile.println( "set xlabel 'time'" );

         String spname = null;
         for( int sp = 0; sp < speciesname.size(); sp++ ) {
            spname = (String) speciesname.elementAt( sp );
            gnuFile.println( "set title '" + spname + " vs. time'" );
            gnuFile.println( "set ylabel '" + spname + "'" );
            gnuFile.println( "plot '" + Environment.COLUMNS_DATA + i
            + "' using 0:" + ( sp + 1 ) );
         }
         gnuFile.println( "quit" );
         gnuFile.close();

         String[] command = { Environment.GNUPLOT, directory + File.separator 
         + GNUFILE };
         r = Runtime.getRuntime();
         p = r.exec( command );
         p.waitFor();
         
         // create all plots and thumbnails
         final String SCRIPT = "convert_" + i + ".sh";
         PrintStream scriptFile = new PrintStream( new FileOutputStream( 
         new File( directory + File.separator + SCRIPT ) ) );
         PrintStream t_gnuFile = new PrintStream( new FileOutputStream( 
         new File( directory + File.separator + "t_" + GNUFILE ) ) );

         String plotName = null;
         t_gnuFile.println( "cd '" + directory + "'" );
         t_gnuFile.println( "set terminal pbm" );
         t_gnuFile.println( "set nokey" );
         scriptFile.println( "cd '" + directory + "'" );
     
         // do one iteration for thumbnails, other for the (big) images
         for( int iter = 0; iter < 2; iter++ ) {
            for( int each_sp = 0; each_sp < speciesname.size(); each_sp++ ) {
               spname = (String) speciesname.elementAt( each_sp );
               if( iter == 0 ) {
                  t_gnuFile.println( "set size 0.15, 0.10" );
                  t_gnuFile.println( "set noxtics" );
                  t_gnuFile.println( "set noytics" );
                  t_gnuFile.println( "set xlabel ''" );
                  t_gnuFile.println( "set ylabel ''" );
                  t_gnuFile.println( "set title  ''" );
                  plotName = "t_" + spname + "__time_" + i;
               }
               else {
                  t_gnuFile.println( "set size 0.8, 0.8" );
                  t_gnuFile.println( "set xtics" );
                  t_gnuFile.println( "set ytics" );
                  t_gnuFile.println( "set ylabel '" + spname + "'" );
                  t_gnuFile.println( "set xlabel 'time'" );
                  t_gnuFile.println( "set title  '" + spname + " vs. time'" );
                  plotName = spname + "__time_" + i;
               }
               t_gnuFile.println( "set output '" + plotName + ".pbm'" );
               t_gnuFile.println( "plot '" + Environment.COLUMNS_DATA + i
               + "' using 0:" + ( each_sp + 1 ) );
               scriptFile.println( Environment.PBM2GIF + " < '" + plotName 
               + ".pbm' > '" + plotName + ".gif'" );
               chmodFiles.addElement( plotName + ".gif" );
               scriptFile.println( "rm '" + plotName + ".pbm'" );
            }
         }
         t_gnuFile.println( "quit" );
         t_gnuFile.close();
         scriptFile.close();
      
         String[] plot2 = { Environment.GNUPLOT, directory + File.separator 
         + "t_" + GNUFILE };
         r = Runtime.getRuntime();
         p = r.exec( plot2 );
         p.waitFor();

         r = Runtime.getRuntime();
         p = r.exec( "chmod 755 " + directory + File.separator + SCRIPT );
         p.waitFor();

         r = Runtime.getRuntime();
         p = r.exec( directory + File.separator + SCRIPT );
         p.waitFor();

         // write out the html file
         if( i == 0 ) {
            htmlFile = new PrintStream( new FileOutputStream( 
            new File( directory + File.separator + HTMLFILE ) ) );
            htmlFile.println();
            htmlFile.println( "<html>" );
            htmlFile.println( "  <head>" );
            htmlFile.println( "    <title>Plots For '" + description 
            + "'</title>" );
            htmlFile.println( "  </head>" );
            htmlFile.println( "  <body>" );
            htmlFile.println( "  <h2>Plots For '" + description + "'</h2>" );
         }
      
         htmlFile.println( "<p>" );
         htmlFile.println( "  <table border>" );

         htmlFile.println( "    <tr>" );
         htmlFile.println( "      <th>" );
         htmlFile.println( "        <a href=\"" + PSFILE 
         + "\">all vs. time<br>" + "(postscript)</a></th>" );
         htmlFile.println( "      <td>time</td>" );
         htmlFile.println( "    </tr>" );

         for( int sp = 0; sp < speciesname.size(); sp++ ) {
            spname = (String) speciesname.elementAt( sp );
            htmlFile.println( "    <tr>" );
            htmlFile.println( "      <th>" + spname + "</th>" );
            htmlFile.println( "      <td><a href=\"" + spname + "__time_"
            + i + ".gif\">" );
            htmlFile.println( "        <img src=\"t_" + spname + "__time_"
            + i + ".gif\" " + "ALT=\"" + spname + " vs. time\"></a></td>" );
            htmlFile.println( "    </tr>" );
         }
         htmlFile.println( "  </table>" );
         htmlFile.println( "  <P>" );
         htmlFile.println( "  Plot especific species against each other<br>" );
         htmlFile.println( "  <form method=\"get\" action=\"" 
         + Environment.SERVLET_GNUPLOT + "\">" );
         htmlFile.println( "    <select name=\"yaxis\">" );
         for( int sp = 0; sp < speciesname.size(); sp++ ) {
            spname = (String) speciesname.elementAt( sp );
            htmlFile.println( "      <option value=\"" + ( sp + 1 ) + "." 
            + spname + "\">" + spname );
         }
         htmlFile.println( "    </select>" );
         htmlFile.println( "    <b>VS.</b>" );
         htmlFile.println( "    <select name=\"xaxis\">" );
         for( int sp = 0; sp < speciesname.size(); sp++ ) {
            spname = (String) speciesname.elementAt( sp );
            htmlFile.println( "      <option value=\"" + ( sp + 1 ) + "." 
            + spname + "\">" + spname );
         }
         htmlFile.println( "    </select>" );
         htmlFile.println( "    <INPUT TYPE=\"hidden\" NAME=\"dirno\" VALUE=\""
         + directorySufix + "\">" );
         htmlFile.println( "    <INPUT TYPE=\"hidden\" " 
         + "NAME=\"dataset\" VALUE=\"" + i + "\">" );
         htmlFile.println( "    <INPUT TYPE=\"submit\" VALUE=\"plot\">" );
         htmlFile.println( "  </form>" );

         chmodFiles.addElement( PSFILE ); 
      }

      htmlFile.println( "  <p><p>Go back to the <a href=\""
      + Environment.BASEURL + "\">Upload Page</a>" );

      htmlFile.println( "  </body>" );
      htmlFile.println( "</html>" );

      htmlFile.close();

      chmodFiles.addElement( "" );       // the actual directory
      chmodFiles.addElement( HTMLFILE ); 
      String tmp = null;
      r = Runtime.getRuntime();
      String chmod = "chmod 755 ";
      for( int i = 0; i < chmodFiles.size(); i++ ) {
         tmp = (String) chmodFiles.elementAt( i );
         chmod += directory + File.separator + tmp + " ";
      }
      p = r.exec( chmod );
      p.waitFor();
      p.destroy();
   }

   /**
    * Sets the description for this file
    * @paran  description  this file description
    */
   public void setDescription( String description )
   {
      this.description = description;
   }

   /**
    * Gets the description for this file
    * @return  this file description
    */
   public String getDescription()
   {
      return description;
   }

   /**
    * Gets the directorySufix
    */
   public String getDirectorySufix()
   {
      return directorySufix;
   }

}