/*
 * 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 jalview.schemes.*;

import java.awt.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class SequenceGroup
{
    String groupName;
    Conservation conserve;
    Vector aaFrequency;
    boolean displayBoxes;
    boolean displayText;
    boolean colourText;

    /** DOCUMENT ME!! */
    public Vector sequences = new Vector();
    int width = -1;

    /** DOCUMENT ME!! */
    public ColourSchemeI cs;
    int startRes = 0;
    int endRes = 0;
    Color outlineColour = Color.black;

    /**
     * Creates a new SequenceGroup object.
     */
    public SequenceGroup()
    {
        groupName = "Group";
        this.displayBoxes = true;
        this.displayText = true;
        this.colourText = false;
        cs = null;
    }

    /**
     * Creates a new SequenceGroup object.
     *
     * @param sequences DOCUMENT ME!
     * @param groupName DOCUMENT ME!
     * @param scheme DOCUMENT ME!
     * @param displayBoxes DOCUMENT ME!
     * @param displayText DOCUMENT ME!
     * @param colourText DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     */
    public SequenceGroup(Vector sequences, String groupName,
        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
        boolean colourText, int start, int end)
    {
        this.sequences = sequences;
        this.groupName = groupName;
        this.displayBoxes = displayBoxes;
        this.displayText = displayText;
        this.colourText = colourText;
        this.cs = scheme;
        startRes = start;
        endRes = end;
        recalcConservation();
    }

    /**
     * Creates a new SequenceGroup object.
     *
     * @param groupName DOCUMENT ME!
     * @param scheme DOCUMENT ME!
     * @param displayBoxes DOCUMENT ME!
     * @param displayText DOCUMENT ME!
     * @param colourText DOCUMENT ME!
     * @param start DOCUMENT ME!
     * @param end DOCUMENT ME!
     */
    public SequenceGroup(String groupName, ColourSchemeI scheme,
        boolean displayBoxes, boolean displayText, boolean colourText,
        int start, int end)
    {
        this.groupName = groupName;
        this.displayBoxes = displayBoxes;
        this.displayText = displayText;
        this.colourText = colourText;
        this.cs = scheme;
        startRes = start;
        endRes = end;
    }

    /**
     * DOCUMENT ME!
     *
     * @param col DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public boolean adjustForRemoveLeft(int col)
    {
        // return value is true if the group still exists
        if (startRes >= col)
        {
            startRes = startRes - col;
        }

        if (endRes >= col)
        {
            endRes = endRes - col;

            if (startRes > endRes)
            {
                startRes = 0;
            }
        }
        else
        {
            // must delete this group!!
            return false;
        }

        return true;
    }

    /**
     * DOCUMENT ME!
     *
     * @param col DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public boolean adjustForRemoveRight(int col)
    {
        if (startRes > col)
        {
            // delete this group
            return false;
        }

        if (endRes >= col)
        {
            endRes = col;
        }

        return true;
    }

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

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

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public Conservation getConservation()
    {
        return conserve;
    }

    /**
     * DOCUMENT ME!
     *
     * @param c DOCUMENT ME!
     */
    public void setConservation(Conservation c)
    {
        conserve = c;
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param recalc DOCUMENT ME!
     */
    public void addSequence(SequenceI s, boolean recalc)
    {
        if (!sequences.contains(s))
        {
            sequences.addElement(s);
        }

        if (recalc)
        {
            recalcConservation();
        }
    }

    /**
     * DOCUMENT ME!
     */
    public void recalcConservation()
    {
        if(cs == null)
          return;

        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));


        if (cs instanceof ClustalxColourScheme)
        {
            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
        }


        if (cs.conservationApplied())
        {
            Conservation c = new Conservation(groupName,
                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
            c.calculate();
            c.verdict(false, 25);


            cs.setConservation(c);

            if (cs instanceof ClustalxColourScheme)
            {
                ((ClustalxColourScheme) cs).resetClustalX(sequences,
                    getWidth());
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param recalc DOCUMENT ME!
     */
    public void addOrRemove(SequenceI s, boolean recalc)
    {
        if (sequences.contains(s))
        {
            deleteSequence(s, recalc);
        }
        else
        {
            addSequence(s, recalc);
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param recalc DOCUMENT ME!
     */
    public void deleteSequence(SequenceI s, boolean recalc)
    {
        sequences.removeElement(s);

        if (recalc)
        {
            recalcConservation();
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getStartRes()
    {
        return startRes;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getEndRes()
    {
        return endRes;
    }

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     */
    public void setStartRes(int i)
    {
        startRes = i;
    }

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     */
    public void setEndRes(int i)
    {
        endRes = i;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getSize()
    {
        return sequences.size();
    }

    /**
     * DOCUMENT ME!
     *
     * @param i DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public SequenceI getSequenceAt(int i)
    {
        return (SequenceI) sequences.elementAt(i);
    }

    /**
     * DOCUMENT ME!
     *
     * @param state DOCUMENT ME!
     */
    public void setColourText(boolean state)
    {
        colourText = state;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public boolean getColourText()
    {
        return colourText;
    }

    /**
     * DOCUMENT ME!
     *
     * @param state DOCUMENT ME!
     */
    public void setDisplayText(boolean state)
    {
        displayText = state;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public boolean getDisplayText()
    {
        return displayText;
    }

    /**
     * DOCUMENT ME!
     *
     * @param state DOCUMENT ME!
     */
    public void setDisplayBoxes(boolean state)
    {
        displayBoxes = state;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public boolean getDisplayBoxes()
    {
        return displayBoxes;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getWidth()
    {
        // MC This needs to get reset when characters are inserted and deleted
        if (sequences.size() > 0)
        {
            width = ((SequenceI) sequences.elementAt(0)).getLength();
        }

        for (int i = 1; i < sequences.size(); i++)
        {
            SequenceI seq = (SequenceI) sequences.elementAt(i);

            if (seq.getLength() > width)
            {
                width = seq.getLength();
            }
        }

        return width;
    }

    /**
     * DOCUMENT ME!
     *
     * @param c DOCUMENT ME!
     */
    public void setOutlineColour(Color c)
    {
        outlineColour = c;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public Color getOutlineColour()
    {
        return outlineColour;
    }

    /**
     *
     * returns the sequences in the group ordered by the ordering given by al
     *
     * @param al Alignment
     * @return SequenceI[]
     */
    public SequenceI[] getSequencesInOrder(AlignmentI al)
    {
        int sz = sequences.size();
        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
        SequenceI[] seqs = new SequenceI[sz];

        for (int i = 0; i < sz; i++)
        {
            SequenceI seq = (SequenceI) sequences.elementAt(i);
            int index = al.findIndex(seq);
            orderedSeqs.put(index + "", seq);
        }

        int index = 0;

        for (int i = 0; i < al.getHeight(); i++)
        {
            if (orderedSeqs.containsKey(i + ""))
            {
                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
            }
        }

        return seqs;
    }
}