/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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 jalview.analysis.*;
import java.awt.*;
import java.util.*;
import MCview.*;


public class Sequence implements SequenceI
{
  protected String name;
  protected String sequence;
  protected String description;
  protected int start;
  protected int end;
  protected String displayId;
  protected Color color = Color.white;
  String pdbId;

   public Vector sequenceFeatures = new Vector();
   public void setSequenceFeatures(Vector v)
   {
     sequenceFeatures = v;
   }

   public Vector getSequenceFeatures()
   {return sequenceFeatures; }

   public void setPDBId(String id)
   {
     pdbId = id;
   }
   public String getPDBId()
   {
     return pdbId;
   }


  public Sequence(String name, String sequence, int start, int end)
  {

    this.name     = name;
    this.sequence = sequence;
    this.start    = start;
    this.end      = end;

    setDisplayId();

  }

  public Sequence(String name,String sequence) {
    this(name,sequence,1,sequence.length());
  }
  public Sequence(SequenceI seq) {
    this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
  }
  public String getDisplayId() {
    return displayId;
  }
  public void setDisplayId() {
    displayId = name + "/" + start + "-" + end;
  }
  public void setName(String name) {
    this.name = name;
    setDisplayId();
  }
  public String getName() {
    return this.name;
  }
  public void setStart(int start) {
    this.start = start;
    setDisplayId();
  }
  public int getStart() {
    return this.start;
  }
  public void setEnd(int end) {
    this.end = end;
    setDisplayId();
  }
  public int getEnd() {
    return this.end;
  }
  public int getLength() {
    return this.sequence.length();
  }
  public void setSequence(String seq) {
    this.sequence = seq;
  }
  public String getSequence() {
    return this.sequence;
  }
  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);
  }

  public char getCharAt(int i) {
    if (i < sequence.length()) {
      return sequence.charAt(i);
    } else {
      return ' ';
    }
  }
  public void setDescription(String desc) {
    this.description = desc;
  }
  public String getDescription() {
    return this.description;
  }

  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) {

      char c = sequence.charAt(i);

      if (!jalview.util.Comparison.isGap((c)))
        j++;

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

  }

  public int findPosition(int i) {
    // Returns the sequence position for an alignment position
    int j   = 0;
    int pos = start;

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

      j++;
    }
    return pos;
  }

  public int[] gapMap() {
    // Returns an int array giving the position of each residue in the sequence in the alignment
    String seq = jalview.analysis.AlignSeq.extractGaps("-. ",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;
  }

  public void deleteCharAt(int i)
  {
    if (i>=sequence.length())
      return;
    sequence = sequence.substring(0,i) + sequence.substring(i+1);
  }

  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);
  }

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

  public void insertCharAt(int i,char c,boolean chop) {

    String tmp = new String(sequence);

    if (i < sequence.length()) {
      sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
    } else {
      // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
      char[] ch = new char[1+i-sequence.length()];
      for (int j=0, k=ch.length; j<k; j++)
        ch[j] = c;
      sequence = tmp + String.valueOf(ch);
    }

  }

  public void        setColor(Color c) {
    this.color = c;
  }

  public Color       getColor() {
    return color;
  }

}