/*
* 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 java.util.*;

/** Data structure to hold and manipulate a multiple sequence alignment
 */
public interface AlignmentI {

  public int         getHeight() ;
  public int         getWidth() ;
  public int         getMaxIdLength() ;

  public boolean isAligned();

  public Vector      getSequences();
  public SequenceI   getSequenceAt(int i);

  public void        addSequence(SequenceI seq) ;
  public void        setSequenceAt(int i,SequenceI seq);

  public void        deleteSequence(SequenceI s) ;
  public void        deleteSequence(int i) ;

  public SequenceI[] getColumns(int start, int end) ;
  public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;

  public void        deleteColumns(int start, int end) ;
  public void        deleteColumns(int seq1, int seq2, int start, int end) ;

  public void        insertColumns(SequenceI[] seqs, int pos) ;

  public SequenceI   findName(String name) ;
  public SequenceI   findbyDisplayId(String name);

  public int         findIndex(SequenceI s) ;

  // Modifying
  public void        trimLeft(int i) ;
  public void        trimRight(int i) ;

  public void        removeGaps() ;
  public Vector      removeRedundancy(float threshold, Vector sel) ;


  // Grouping methods
  public SequenceGroup findGroup(int i) ;
  public SequenceGroup findGroup(SequenceI s) ;
  public SequenceGroup [] findAllGroups(SequenceI s);
  public void          addToGroup(SequenceGroup g, SequenceI s) ;
  public void          removeFromGroup(SequenceGroup g,SequenceI s) ;
  public void          addGroup(SequenceGroup sg) ;
  public void          deleteGroup(SequenceGroup g) ;
  public Vector        getGroups();
  public void deleteAllGroups();

  public void          addSuperGroup(SuperGroup sg);
  public void          removeSuperGroup(SuperGroup sg);
  public SuperGroup    getSuperGroup(SequenceGroup sg);

  // Sorting
  public void          sortGroups() ;
  public void          sortByPID(SequenceI s) ;
  public void          sortByID() ;

  //Annotations
  public void addAnnotation(AlignmentAnnotation aa);
  public void deleteAnnotation(AlignmentAnnotation aa);
  public AlignmentAnnotation [] getAlignmentAnnotation();

  public void          setGapCharacter(char gc);
  public char          getGapCharacter();

  public Vector        getAAFrequency();
}