/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.datamodel;

import java.awt.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class Sequence implements SequenceI
{
  SequenceI datasetSequence;
  String name;
  private String sequence;
  String description;
  int start;
  int end;
  Vector pdbIds;
  String vamsasId;
  DBRefEntry[] dbrefs;

  /** This annotation is displayed below the alignment but the
   * positions are tied to the residues of this sequence */
  Vector annotation;

  /** DOCUMENT ME!! */
  public SequenceFeature[] sequenceFeatures;

  /** This array holds hidden sequences
   * of which this sequence is the representitive member of a group
   */
  SequenceGroup hiddenSequences;

  /**
   * Creates a new Sequence object.
   *
   * @param name DOCUMENT ME!
   * @param sequence DOCUMENT ME!
   * @param start DOCUMENT ME!
   * @param end DOCUMENT ME!
   */
  public Sequence(String name, String sequence, int start, int end)
  {
    this.name = name;
    this.sequence = sequence;
    this.start = start;
    this.end = end;

    parseId();

    checkValidRange();
  }

  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
      "[/][0-9]{1,}[-][0-9]{1,}$");
  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
      "[0-9]{1,}$");

  void parseId()
  {
    // Does sequence have the /start-end signiature?
    if (limitrx.search(name))
    {
      name = limitrx.left();
      endrx.search(limitrx.stringMatched());
      setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
          endrx.matchedFrom() - 1)));
      setEnd(Integer.parseInt(endrx.stringMatched()));
    }
  }

  void checkValidRange()
  {
    if (end < 1)
    {
      int endRes = 0;
      char ch;
      for (int j = 0; j < sequence.length(); j++)
      {
        ch = sequence.charAt(j);
        if (!jalview.util.Comparison.isGap( (ch)))
        {
          endRes++;
        }
      }
      if (endRes > 0)
      {
        endRes += start - 1;
      }

      this.end = endRes;
    }

  }

  /**
   * Creates a new Sequence object.
   *
   * @param name DOCUMENT ME!
   * @param sequence DOCUMENT ME!
   */
  public Sequence(String name, String sequence)
  {
    this(name, sequence, 1, -1);
  }

  /**
   * Creates a new Sequence object.
   *
   * @param seq DOCUMENT ME!
   */
  public Sequence(SequenceI seq)
  {
    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
  }

  /**
   * DOCUMENT ME!
   *
   * @param v DOCUMENT ME!
   */
  public void setSequenceFeatures(SequenceFeature[] features)
  {
    sequenceFeatures = features;
  }

  public synchronized void addSequenceFeature(SequenceFeature sf)
  {
    if (sequenceFeatures == null)
    {
      sequenceFeatures = new SequenceFeature[0];
    }

    for (int i = 0; i < sequenceFeatures.length; i++)
    {
      if (sequenceFeatures[i].equals(sf))
      {
        return;
      }
    }

    SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
    System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
    temp[sequenceFeatures.length] = sf;

    sequenceFeatures = temp;
  }

  public void deleteFeature(SequenceFeature sf)
  {
    if(sequenceFeatures==null)
      return;

    int index=0;
    for (index = 0; index < sequenceFeatures.length; index++)
    {
      if (sequenceFeatures[index].equals(sf))
      {
        break;
      }
    }


    if(index==sequenceFeatures.length)
      return;

    int sfLength = sequenceFeatures.length;
    if(sfLength<2)
    {
      sequenceFeatures = null;
    }
    else
    {
      SequenceFeature[] temp = new SequenceFeature[sfLength-1];
      System.arraycopy(sequenceFeatures, 0, temp, 0, index);

      if(index<sfLength)
        System.arraycopy(sequenceFeatures,
                         index + 1,
                         temp,
                         index, sequenceFeatures.length - index -1);

      sequenceFeatures = temp;
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public SequenceFeature[] getSequenceFeatures()
  {
    return sequenceFeatures;
  }

  public void addPDBId(PDBEntry entry)
  {
    if (pdbIds == null)
      pdbIds = new Vector();

    pdbIds.addElement(entry);
  }

  /**
   * DOCUMENT ME!
   *
   * @param id DOCUMENT ME!
   */
  public void setPDBId(Vector id)
  {
    pdbIds = id;
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public Vector getPDBId()
  {
    return pdbIds;
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getDisplayId(boolean jvsuffix)
  {
    StringBuffer result = new StringBuffer(name);
    if (jvsuffix)
    {
      result.append("/" + start + "-" + end);
    }

    return result.toString();
  }

  /**
   * DOCUMENT ME!
   *
   * @param name DOCUMENT ME!
   */
  public void setName(String name)
  {
    this.name = name;
    this.parseId();
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getName()
  {
    return this.name;
  }

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

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public int getStart()
  {
    return this.start;
  }

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

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public int getEnd()
  {
    return this.end;
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public int getLength()
  {
    return this.sequence.length();
  }

  /**
   * DOCUMENT ME!
   *
   * @param seq DOCUMENT ME!
   */
  public void setSequence(String seq)
  {
    this.sequence = seq;
    checkValidRange();
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getSequence()
  {
    return this.sequence;
  }

  /**
   * DOCUMENT ME!
   *
   * @param start DOCUMENT ME!
   * @param end DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getSequence(int start, int end)
  {
    // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
    if (start >= sequence.length())
    {
      return "";
    }

    if (end >= sequence.length())
    {
      end = sequence.length();
    }

    return this.sequence.substring(start, end);
  }

  /**
   * make a new Sequence object from start to end (including gaps) over this seqeunce
   * @param start int
   * @param end int
   * @return SequenceI
   */
  public SequenceI getSubSequence(int start, int end)
  {
    if (start < 0)
      start = 0;
    String seq = getSequence(start, end);
    if (seq == "")
      return null;
    int nstart = findPosition(start);
    int nend = findPosition(end) - 1;
    // JBPNote - this is an incomplete copy.
    SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
    nseq.setDescription(description);
    nseq.setDatasetSequence(getDatasetSequence());
    return nseq;
  }

  /**
   * DOCUMENT ME!
   *
   * @param i DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public char getCharAt(int i)
  {
    if (i < sequence.length())
    {
      return sequence.charAt(i);
    }
    else
    {
      return ' ';
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param desc DOCUMENT ME!
   */
  public void setDescription(String desc)
  {
    this.description = desc;
  }

  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getDescription()
  {
    return this.description;
  }

  /**
   * DOCUMENT ME!
   *
   * @param pos DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public int findIndex(int pos)
  {
    // returns the alignment position for a residue
    int j = start;
    int i = 0;

    while ( (i < sequence.length()) && (j <= end) && (j <= pos))
    {
      if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
      {
        j++;
      }

      i++;
    }

    if ( (j == end) && (j < pos))
    {
      return end + 1;
    }
    else
    {
      return i;
    }
  }

  /**
   * Returns the sequence position for an alignment position
   *
   * @param i column index in alignment (from 1)
   *
   * @return residue number for residue (left of and) nearest ith column
   */
  public int findPosition(int i)
  {
    int j = 0;
    int pos = start;
    int seqlen = sequence.length();
    while ( (j < i) && (j < seqlen))
    {
      if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
      {
        pos++;
      }

      j++;
    }

    return pos;
  }

  /**
   * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
   *
   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
   */
  public int[] gapMap()
  {
    String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
        GapChars, sequence);
    int[] map = new int[seq.length()];
    int j = 0;
    int p = 0;

    while (j < sequence.length())
    {
      if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
      {
        map[p++] = j;
      }

      j++;
    }

    return map;
  }

  /**
   * DOCUMENT ME!
   *
   * @param i DOCUMENT ME!
   */
  public void deleteCharAt(int i)
  {
    if (i >= sequence.length())
    {
      return;
    }

    sequence = sequence.substring(0, i) + sequence.substring(i + 1);
  }

  /**
   * DOCUMENT ME!
   *
   * @param i DOCUMENT ME!
   * @param j DOCUMENT ME!
   */
  public void deleteChars(int i, int j)
  {
    if (i >= sequence.length())
    {
      return;
    }

    if (j >= sequence.length())
    {
      sequence = sequence.substring(0, i);
    }
    else
    {
      sequence = sequence.substring(0, i) + sequence.substring(j);
    }
  }

  /**
   * DOCUMENT ME!
   *
   * @param i DOCUMENT ME!
   * @param c DOCUMENT ME!
   * @param chop DOCUMENT ME!
   */
  public void insertCharAt(int i, int length, char c)
  {
    StringBuffer tmp;

    if (i >= sequence.length())
    {
      tmp = new StringBuffer(sequence);
    }
    else
      tmp = new StringBuffer(sequence.substring(0, i));

    while (length > 0)
    {
      tmp.append(c);
      length--;
    }

    if (i < sequence.length())
    {
      tmp.append(sequence.substring(i));
    }

    sequence = tmp.toString();
  }

  public void insertCharAt(int i, char c)
  {
    insertCharAt(i, 1, c);
  }

  public String getVamsasId()
  {
    return vamsasId;
  }

  public void setVamsasId(String id)
  {
    vamsasId = id;
  }

  public void setDBRef(DBRefEntry[] dbref)
  {
    dbrefs = dbref;
  }

  public DBRefEntry[] getDBRef()
  {
    return dbrefs;
  }

  public void addDBRef(DBRefEntry entry)
  {
    if (dbrefs == null)
      dbrefs = new DBRefEntry[0];

    int i, iSize = dbrefs.length;

    for(i=0; i<iSize; i++)
      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
      && dbrefs[i].getSource().equals(entry.getSource())
      && dbrefs[i].getVersion().equals(entry.getVersion()))
      {
        return;
      }

    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
    System.arraycopy(dbrefs, 0, temp, 0, iSize);
    temp[temp.length - 1] = entry;

    dbrefs = temp;
  }

  public void setDatasetSequence(SequenceI seq)
  {
    datasetSequence = seq;
  }

  public SequenceI getDatasetSequence()
  {
    return datasetSequence;
  }

  public AlignmentAnnotation[] getAnnotation()
  {
    if (annotation == null)
      return null;

    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
    for (int r = 0; r < ret.length; r++)
      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);

    return ret;
  }

  public void addAlignmentAnnotation(AlignmentAnnotation annotation)
  {
    if (this.annotation == null)
      this.annotation = new Vector();

    this.annotation.addElement(annotation);
  }

  public SequenceGroup getHiddenSequences()
  {
    return hiddenSequences;
  }

  public void addHiddenSequence(SequenceI seq)
  {
    if (hiddenSequences == null)
    {
      hiddenSequences = new SequenceGroup();
    }
    hiddenSequences.addSequence(seq, false);
  }

  public void showHiddenSequence(SequenceI seq)
  {
    hiddenSequences.deleteSequence(seq, false);
    if (hiddenSequences.getSize(false) < 1)
    {
      hiddenSequences = null;
    }
  }
}