/*
 * 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.util.*;

import java.awt.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public interface SequenceI
{
    /**
     * DOCUMENT ME!
     *
     * @param name DOCUMENT ME!
     */
    public void setName(String name);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getName();


    /**
     * DOCUMENT ME!
     *
     * @param start DOCUMENT ME!
     */
    public void setStart(int start);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getStart();

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getDisplayId(boolean jvsuffix);

    /**
     * DOCUMENT ME!
     *
     * @param end DOCUMENT ME!
     */
    public void setEnd(int end);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getEnd();

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getLength();

    /**
     * DOCUMENT ME!
     *
     * @param sequence DOCUMENT ME!
     */
    public void setSequence(String sequence);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getSequence();

    /**
     * DOCUMENT ME!
     *
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getSequence(int start, int end);
    /**
     * create a new sequence object from start to end of this sequence
     * @param start int
     * @param end int
     * @return SequenceI
     */
    public SequenceI getSubSequence(int start, int end);
    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public char getCharAt(int i);

    /**
     * DOCUMENT ME!
     *
     * @param desc DOCUMENT ME!
     */
    public void setDescription(String desc);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getDescription();

    /**
     * DOCUMENT ME!
     *
     * @param pos DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int findIndex(int pos);

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int findPosition(int i);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int[] gapMap();

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     * @param j DOCUMENT ME!
     */
    public void deleteChars(int i, int j);

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     */
    public void deleteCharAt(int i);

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     * @param c DOCUMENT ME!
     */
    public void insertCharAt(int i, char c);


    /**
     * DOCUMENT ME!
     *
     * @param c DOCUMENT ME!
     */
    public void setColor(Color c);

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public Color getColor();

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

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

    /**
     * DOCUMENT ME!
     *
     * @param id DOCUMENT ME!
     */
    public void setPDBId(Vector ids);

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

    public void addPDBId(PDBEntry entry);

    public String getVamsasId();

    public void setVamsasId(String id);

    public void setDBRef(DBRefEntry[] dbs);

    public DBRefEntry [] getDBRef();

    public void addDBRef(DBRefEntry entry);

    public void addSequenceFeature(SequenceFeature sf);

    public void setDatasetSequence(SequenceI seq);

    public SequenceI getDatasetSequence();

    public AlignmentAnnotation [] getAnnotation();

    public void addAlignmentAnnotation(AlignmentAnnotation annotation);

    public SequenceGroup getHiddenSequences();

    public void addHiddenSequence(SequenceI seq);

    public void showHiddenSequence(SequenceI seq);

    public void changeCase(boolean toUpper, int start, int end);

    public void toggleCase(int start, int end);

  /**
   * getSubSequence from start to end of sequence
   * @param start first residue in subSequence
   * @return SequenceI
   */
  public SequenceI getSubSequence(int start);
  /**
   * remove all gaps in the sequence
   * @return number of gaps removed
   */
  public int removeGaps();
  /**
   * remove all gaps from start to end columns in sequence
   * @param start
   * @param end
   * @return number of gaps removed
   */
  public int removeGaps(int start, int end);

}