/*
 * Jalview - A Sequence Alignment Editor and Viewer (2.11.2.6)
 * Copyright (C) 2023 The Jalview Authors
 * 
 * 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/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;

import com.stevesoft.pat.Regex;

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 = Double.valueOf(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(seqs[i].getName() + " 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;
  }
}
