/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.analysis;

import com.stevesoft.pat.Regex;

import jalview.datamodel.*;

public class ParseProperties
{
  /**
   * Methods for parsing free text properties on alignments and sequences. There
   * are a number of ways we might want to do this: arbitrary regex. and an
   * associated score name for the number that's extracted. Regex that provides
   * both score and name.
   * 
   * We may also want to : - modify description to remove parsed numbers (this
   * behaviour is dangerous since exporting the alignment would lose the
   * original form then) -
   * 
   */
  /**
   * The alignment being operated on
   */
  private AlignmentI al = null;

  /**
   * initialise a new property parser
   * 
   * @param al
   */
  public ParseProperties(AlignmentI al)
  {
    this.al = al;
  }

  public int getScoresFromDescription(String ScoreName,
          String ScoreDescriptions, String regex, boolean repeat)
  {
    return getScoresFromDescription(new String[]
    { ScoreName }, new String[]
    { ScoreDescriptions }, regex, repeat);
  }

  public int getScoresFromDescription(String[] ScoreNames,
          String[] ScoreDescriptions, String regex, boolean repeat)
  {
    return getScoresFromDescription(al.getSequencesArray(), ScoreNames,
            ScoreDescriptions, regex, repeat);
  }

  /**
   * Extract scores for sequences by applying regex to description string.
   * 
   * @param seqs
   *          seuqences to extract annotation from.
   * @param ScoreNames
   *          labels for each numeric field in regex match
   * @param ScoreDescriptions
   *          description for each numeric field in regex match
   * @param regex
   *          Regular Expression string for passing to
   *          <code>new com.stevesoft.patt.Regex(regex)</code>
   * @param repeat
   *          true means the regex will be applied multiple times along the
   *          description string of each sequence
   * @return total number of sequences that matched the regex
   */
  public int getScoresFromDescription(SequenceI[] seqs,
          String[] ScoreNames, String[] ScoreDescriptions, String regex,
          boolean repeat)
  {
    int count = 0;
    Regex pattern = new Regex(regex);
    if (pattern.numSubs() > ScoreNames.length)
    {
      // Check that we have enough labels and descriptions for any parsed
      // scores.
      int onamelen = ScoreNames.length;
      String[] tnames = new String[pattern.numSubs() + 1];
      System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
      String base = tnames[ScoreNames.length - 1];
      ScoreNames = tnames;
      String descrbase = ScoreDescriptions[onamelen - 1];
      if (descrbase == null)
        descrbase = "Score parsed from (" + regex + ")";
      tnames = new String[pattern.numSubs() + 1];
      System.arraycopy(ScoreDescriptions, 0, tnames, 0,
              ScoreDescriptions.length);
      ScoreDescriptions = tnames;
      for (int i = onamelen; i < ScoreNames.length; i++)
      {
        ScoreNames[i] = base + "_" + i;
        ScoreDescriptions[i] = descrbase + " (column " + i + ")";
      }
    }
    for (int i = 0; i < seqs.length; i++)
    {
      String descr = seqs[i].getDescription();
      if (descr == null)
        continue;
      int pos = 0;
      boolean added = false;
      int reps = 0;
      while ((repeat || pos == 0) && pattern.searchFrom(descr, pos))
      {
        pos = pattern.matchedTo();
        for (int cols = 0; cols < pattern.numSubs(); cols++)
        {
          String sstring = pattern.stringMatched(cols + 1);
          double score = Double.NaN;
          try
          {
            score = new Double(sstring).doubleValue();
          } catch (Exception e)
          {
            // don't try very hard to parse if regex was wrong.
            continue;
          }
          // add score to sequence annotation.
          AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols]
                  + ((reps > 0) ? "_" + reps : ""),
                  ScoreDescriptions[cols], null);
          an.setScore(score);
          System.out.println("Score: " + ScoreNames[cols] + "=" + score); // DEBUG
          an.setSequenceRef(seqs[i]);
          seqs[i].addAlignmentAnnotation(an);
          al.addAnnotation(an);
          added = true;
        }
        reps++; // repeated matches
      }
      if (added)
      {
        count++;
      }
    }
    return count;
  }

  public static void main(String argv[])
  {
    SequenceI[] seqs = new SequenceI[]
    { new Sequence("sq1", "THISISAPLACEHOLDER"),
        new Sequence("sq2", "THISISAPLACEHOLDER"),
        new Sequence("sq3", "THISISAPLACEHOLDER"),
        new Sequence("sq4", "THISISAPLACEHOLDER") };
    seqs[0].setDescription("1 mydescription1");
    seqs[1].setDescription("mydescription2");
    seqs[2].setDescription("2. 0.1 mydescription3");
    seqs[3].setDescription("3 0.01 mydescription4");
    // seqs[4].setDescription("5 mydescription5");
    Alignment al = new Alignment(seqs);
    ParseProperties pp = new ParseProperties(al);
    String regex = ".*([-0-9.+]+)";
    System.out.println("Matched "
            + pp.getScoresFromDescription("my Score",
                    "my Score Description", regex, true) + " for " + regex);
    regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
    System.out.println("Matched "
            + pp.getScoresFromDescription("my Score",
                    "my Score Description", regex, true) + " for " + regex);
    System.out.println("Finished.");
  }
}