/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
 */
/**
 * PredFile.java
 * JalviewX / Vamsas Project
 * JPred.seq.concise reader
 */
package jalview.io;

import java.io.*;
import java.util.*;

import jalview.datamodel.*;

/**
 * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
 * line is either a sequence (QUERY), a sequence profile (align;), or jnet
 * prediction annotation (anything else). Automagic translation happens for
 * annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
 * or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
 * differentiated from symbolic by being parseable into a float vector. They are
 * put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
 * data parsed by this object into annotation on an alignment. It is
 * automatically called but can be used to transfer the annotation onto a
 * sequence in another alignment (and insert gaps where necessary)
 * 
 * @author jprocter
 * @version $Revision$
 */
public class JPredFile extends AlignFile
{
  Vector ids;

  Vector conf;

  Hashtable Scores; // Hash of names and score vectors

  Hashtable Symscores; // indexes of symbol annotation properties in sequenceI

  // vector

  private int QuerySeqPosition;

  /**
   * Creates a new JPredFile object.
   * 
   * @param inFile
   *          DOCUMENT ME!
   * @param type
   *          DOCUMENT ME!
   * 
   * @throws IOException
   *           DOCUMENT ME!
   */
  public JPredFile(String inFile, String type) throws IOException
  {
    super(inFile, type);
  }

  public JPredFile(FileParse source) throws IOException
  {
    super(source);
  }

  /**
   * DOCUMENT ME!
   * 
   * @param QuerySeqPosition
   *          DOCUMENT ME!
   */
  public void setQuerySeqPosition(int QuerySeqPosition)
  {
    this.QuerySeqPosition = QuerySeqPosition;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public int getQuerySeqPosition()
  {
    return QuerySeqPosition;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public Hashtable getScores()
  {
    return Scores;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public Hashtable getSymscores()
  {
    return Symscores;
  }

  /**
   * DOCUMENT ME!
   */
  public void initData()
  {
    super.initData();
    Scores = new Hashtable();
    ids = null;
    conf = null;
  }

  /**
   * parse a JPred concise file into a sequence-alignment like object.
   */
  public void parse() throws IOException
  {
    // JBPNote log.System.out.println("all read in ");
    String line;
    QuerySeqPosition = -1;
    noSeqs = 0;

    Vector seq_entries = new Vector();
    Vector ids = new Vector();
    Hashtable Symscores = new Hashtable();

    while ((line = nextLine()) != null)
    {
      // Concise format allows no comments or non comma-formatted data
      StringTokenizer str = new StringTokenizer(line, ":");
      String id = "";

      if (!str.hasMoreTokens())
      {
        continue;
      }

      id = str.nextToken();

      String seqsym = str.nextToken();
      StringTokenizer symbols = new StringTokenizer(seqsym, ",");

      // decide if we have more than just alphanumeric symbols
      int numSymbols = symbols.countTokens();

      if (numSymbols == 0)
      {
        continue;
      }

      if (seqsym.length() != (2 * numSymbols))
      {
        // Set of scalars for some property
        if (Scores.containsKey(id))
        {
          int i = 1;

          while (Scores.containsKey(id + "_" + i))
          {
            i++;
          }

          id = id + "_" + i;
        }

        Vector scores = new Vector();

        // Typecheck from first entry
        int i = 0;
        String ascore = "dead";

        try
        {
          // store elements as floats...
          while (symbols.hasMoreTokens())
          {
            ascore = symbols.nextToken();

            Float score = new Float(ascore);
            scores.addElement((Object) score);
          }

          Scores.put(id, scores);
        } catch (Exception e)
        {
          // or just keep them as strings
          i = scores.size();

          for (int j = 0; j < i; j++)
          {
            scores.setElementAt(
                    (Object) ((Float) scores.elementAt(j)).toString(), j);
          }

          scores.addElement((Object) ascore);

          while (symbols.hasMoreTokens())
          {
            ascore = symbols.nextToken();
            scores.addElement((Object) ascore);
          }

          Scores.put(id, scores);
        }
      }
      else if (id.equals("jnetconf"))
      {
        // log.debug System.out.println("here");
        id = "Prediction Confidence";
        this.conf = new Vector(numSymbols);

        for (int i = 0; i < numSymbols; i++)
        {
          conf.setElementAt(symbols.nextToken(), i);
        }
      }
      else
      {
        // Sequence or a prediction string (rendered as sequence)
        StringBuffer newseq = new StringBuffer();

        for (int i = 0; i < numSymbols; i++)
        {
          newseq.append(symbols.nextToken());
        }

        if (id.indexOf(";") > -1)
        {
          seq_entries.addElement(newseq);

          int i = 1;
          String name = id.substring(id.indexOf(";") + 1);

          while (ids.lastIndexOf(name) > -1)
          {
            name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
          }

          if (QuerySeqPosition == -1)
            QuerySeqPosition = ids.size();
          ids.addElement(name);
          noSeqs++;
        }
        else
        {
          if (id.equals("JNETPRED"))
          {
            id = "Predicted Secondary Structure";
          }

          seq_entries.addElement(newseq.toString());
          ids.addElement(id);
          Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
        }
      }
    }
    /*
     * leave it to the parser user to actually check this. if (noSeqs < 1) {
     * throw new IOException( "JpredFile Parser: No sequence in the
     * prediction!"); }
     */

    maxLength = seq_entries.elementAt(0).toString().length();

    for (int i = 0; i < ids.size(); i++)
    {
      // Add all sequence like objects
      Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
              seq_entries.elementAt(i).toString(), 1, seq_entries
                      .elementAt(i).toString().length());

      if (maxLength != seq_entries.elementAt(i).toString().length())
      {
        throw new IOException("JPredConcise: Entry ("
                + ids.elementAt(i).toString()
                + ") has an unexpected number of columns");
      }

      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
              .startsWith("align;")) && (QuerySeqPosition == -1))
      {
        QuerySeqPosition = seqs.size();
      }

      seqs.addElement(newSeq);
    }
    if (seqs.size() > 0 && QuerySeqPosition > -1)
    {
      // try to make annotation for a prediction only input (default if no
      // alignment is given and prediction contains a QUERY or align;sequence_id
      // line)
      Alignment tal = new Alignment(this.getSeqsAsArray());
      try
      {
        JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
                true);
      } catch (Exception e)
      {
        tal = null;
        IOException ex = new IOException(
                "Couldn't parse concise annotation for prediction profile.\n"
                        + e);
        e.printStackTrace(); // java 1.1 does not have :
                             // ex.setStackTrace(e.getStackTrace());
        throw ex;
      }
      this.annotations = new Vector();
      AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
      for (int aai = 0; aan != null && aai < aan.length; aai++)
      {
        annotations.addElement(aan[aai]);
      }
    }
  }

  /**
   * print
   * 
   * @return String
   */
  public String print()
  {
    return "Not Supported";
  }

  /**
   * DOCUMENT ME!
   * 
   * @param args
   *          DOCUMENT ME!
   */
  public static void main(String[] args)
  {
    try
    {
      JPredFile blc = new JPredFile(args[0], "File");

      for (int i = 0; i < blc.seqs.size(); i++)
      {
        System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
                + "\n"
                + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
                + "\n");
      }
    } catch (java.io.IOException e)
    {
      System.err.println("Exception " + e);
      // e.printStackTrace(); not java 1.1 compatible!
    }
  }

  Vector annotSeqs = null;

  /**
   * removeNonSequences
   */
  public void removeNonSequences()
  {
    if (annotSeqs != null)
    {
      return;
    }
    annotSeqs = new Vector();
    Vector newseqs = new Vector();
    int i = 0;
    int j = seqs.size();
    for (; i < QuerySeqPosition; i++)
    {
      annotSeqs.addElement(seqs.elementAt(i));
    }
    // check that no stray annotations have been added at the end.
    {
      SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
      if (sq.getName().toUpperCase().startsWith("JPRED"))
      {
        annotSeqs.addElement(sq);
        seqs.removeElementAt(--j);
      }
    }
    for (; i < j; i++)
    {
      newseqs.addElement(seqs.elementAt(i));
    }

    seqs.removeAllElements();
    seqs = newseqs;
  }
}

/*
 * StringBuffer out = new StringBuffer();
 * 
 * out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++)
 * { out.append(s[0].sequence.substring(i, i + 1) + " ");
 * out.append(s[1].sequence.substring(i, i + 1) + " ");
 * out.append(s[1].score[0].elementAt(i) + " ");
 * out.append(s[1].score[1].elementAt(i) + " ");
 * out.append(s[1].score[2].elementAt(i) + " ");
 * out.append(s[1].score[3].elementAt(i) + " ");
 * 
 * out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
 * 
 * public static void main(String[] args) { try { BLCFile blc = new
 * BLCFile(args[0], "File"); DrawableSequence[] s = new
 * DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++)
 * { s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String
 * out = BLCFile.print(s);
 * 
 * AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
 * System.out.println(out); } catch (java.io.IOException e) {
 * System.out.println("Exception " + e); } } }
 */