/*
* 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();
}