/*
* 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.analysis;

import jalview.datamodel.*;

import jalview.util.*;

import java.util.*;


/** Data structure to hold and manipulate a multiple sequence alignment
 */
public class AlignmentSorter
{
    static boolean sortIdAscending = true;
    static int lastGroupHash = 0;
    static boolean sortGroupAscending = true;
    static AlignmentOrder lastOrder = null;
    static boolean sortOrderAscending = true;
    static NJTree lastTree = null;
    static boolean sortTreeAscending = true;

    /**
     * Sort by Percentage Identity
     *
     * @param align AlignmentI
     * @param s SequenceI
     */
    public static void sortByPID(AlignmentI align, SequenceI s)
    {
        int nSeq = align.getHeight();

        float[] scores = new float[nSeq];
        SequenceI[] seqs = new SequenceI[nSeq];

        for (int i = 0; i < nSeq; i++)
        {
            scores[i] = Comparison.PID(align.getSequenceAt(i), s);
            seqs[i] = align.getSequenceAt(i);
        }

        QuickSort.sort(scores, 0, scores.length - 1, seqs);

        setReverseOrder(align, seqs);
    }

    /**
     * Reverse the order of the sort
     *
     * @param align DOCUMENT ME!
     * @param seqs DOCUMENT ME!
     */
    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
    {
        int nSeq = seqs.length;

        int len = 0;

        if ((nSeq % 2) == 0)
        {
            len = nSeq / 2;
        }
        else
        {
            len = (nSeq + 1) / 2;
        }

        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
        for (int i = 0; i < len; i++)
        {
            //SequenceI tmp = seqs[i];
            align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
            align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
        }
    }

    /**
     * Sets the Alignment object with the given sequences
     *
     * @param align Alignment object to be updated
     * @param tmp sequences as a vector
     */
    private static void setOrder(AlignmentI align, Vector tmp)
    {
        setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
    }

    /**
     * Sets the Alignment object with the given sequences
     *
     * @param align DOCUMENT ME!
     * @param seqs sequences as an array
     */
    private static void setOrder(AlignmentI align, SequenceI[] seqs)
    {
        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
        Vector algn = align.getSequences();

        for (int i = 0; i < seqs.length; i++)
        {
            algn.setElementAt(seqs[i], i);
        }
    }

    /**
     * Sorts by ID. Numbers are sorted before letters.
     *
     * @param align The alignment object to sort
     */
    public static void sortByID(AlignmentI align)
    {
        int nSeq = align.getHeight();

        String[] ids = new String[nSeq];
        SequenceI[] seqs = new SequenceI[nSeq];

        for (int i = 0; i < nSeq; i++)
        {
            ids[i] = align.getSequenceAt(i).getName();
            seqs[i] = align.getSequenceAt(i);
        }

        QuickSort.sort(ids, seqs);

        if (sortIdAscending)
        {
            setReverseOrder(align, seqs);
        }
        else
        {
            setOrder(align, seqs);
        }

        sortIdAscending = !sortIdAscending;
    }

    /**
     * Sorts the alignment by size of group.
     * <br>Maintains the order of sequences in each group
     * by order in given alignment object.
     *
     * @param align sorts the given alignment object by group
     */
    public static void sortByGroup(AlignmentI align)
    {
        //MAINTAINS ORIGNAL SEQUENCE ORDER,
        //ORDERS BY GROUP SIZE
        Vector groups = new Vector();

        if (groups.hashCode() != lastGroupHash)
        {
            sortGroupAscending = true;
            lastGroupHash = groups.hashCode();
        }
        else
        {
            sortGroupAscending = !sortGroupAscending;
        }

        //SORTS GROUPS BY SIZE
        //////////////////////
        for (int i = 0; i < align.getGroups().size(); i++)
        {
            SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);

            for (int j = 0; j < groups.size(); j++)
            {
                SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);

                if (sg.getSize() > sg2.getSize())
                {
                    groups.insertElementAt(sg, j);

                    break;
                }
            }

            if (!groups.contains(sg))
            {
                groups.addElement(sg);
            }
        }

        //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
        ///////////////////////////////////////////////
        Vector seqs = new Vector();

        for (int i = 0; i < groups.size(); i++)
        {
            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
            SequenceI[] orderedseqs = sg.getSequencesInOrder(align);

            for (int j = 0; j < orderedseqs.length; j++)
            {
                seqs.addElement(orderedseqs[j]);
            }
        }

        if (sortGroupAscending)
        {
            setOrder(align, seqs);
        }
        else
        {
            setReverseOrder(align,
                vectorSubsetToArray(seqs, align.getSequences()));
        }
    }

    /**
     * Converts Vector to array.
     * java 1.18 does not have Vector.toArray()
     *
     * @param tmp Vector of SequenceI objects
     *
     * @return array of Sequence[]
     */
    private static SequenceI[] vectorToArray(Vector tmp)
    {
        SequenceI[] seqs = new SequenceI[tmp.size()];

        for (int i = 0; i < tmp.size(); i++)
        {
            seqs[i] = (SequenceI) tmp.elementAt(i);
        }

        return seqs;
    }

    /**
     * DOCUMENT ME!
     *
     * @param tmp DOCUMENT ME!
     * @param mask DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
    {
        Vector seqs = new Vector();
        int i;
        boolean[] tmask = new boolean[mask.size()];

        for (i = 0; i < mask.size(); i++)
            tmask[i] = true;

        for (i = 0; i < tmp.size(); i++)
        {
            Object sq = tmp.elementAt(i);

            if (mask.contains(sq) && tmask[mask.indexOf(sq)])
            {
                tmask[mask.indexOf(sq)] = false;
                seqs.addElement(sq);
            }
        }

        for (i = 0; i < tmask.length; i++)
            if (tmask[i])
            {
                seqs.addElement(mask.elementAt(i));
            }

        return vectorToArray(seqs);
    }

    /**
     * Sorts by a given AlignmentOrder object
     *
     * @param align Alignment to order
     * @param order specified order for alignment
     */
    public static void sortBy(AlignmentI align, AlignmentOrder order)
    {
        // Get an ordered vector of sequences which may also be present in align
        Vector tmp = order.getOrder();

        if (lastOrder == order)
        {
            sortOrderAscending = !sortOrderAscending;
        }
        else
        {
            sortOrderAscending = true;
        }

        if (sortOrderAscending)
        {
            setOrder(align, tmp);
        }
        else
        {
            setReverseOrder(align,
                vectorSubsetToArray(tmp, align.getSequences()));
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param align alignment to order
     * @param tree tree which has
     *
     * @return DOCUMENT ME!
     */
    private static Vector getOrderByTree(AlignmentI align, NJTree tree)
    {
        int nSeq = align.getHeight();

        Vector tmp = new Vector();

        tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());

        if (tmp.size() != nSeq)
        {
            // TODO: JBPNote - decide if this is always an error
            // (eg. not when a tree is associated to another alignment which has more
            //  sequences)
            if (tmp.size() < nSeq)
            {
                addStrays(align, tmp);
            }

            if (tmp.size() != nSeq)
            {
                System.err.println("ERROR: tmp.size()=" + tmp.size() +
                    " != nseq=" + nSeq + " in getOrderByTree");
            }
        }

        return tmp;
    }

    /**
     * Sorts the alignment by a given tree
     *
     * @param align alignment to order
     * @param tree tree which has
     */
    public static void sortByTree(AlignmentI align, NJTree tree)
    {
        Vector tmp = getOrderByTree(align, tree);

        // tmp should properly permute align with tree.
        if (lastTree != tree)
        {
            sortTreeAscending = true;
            lastTree = tree;
        }
        else
        {
            sortTreeAscending = !sortTreeAscending;
        }

        if (sortTreeAscending)
        {
            setOrder(align, tmp);
        }
        else
        {
            setReverseOrder(align,
                vectorSubsetToArray(tmp, align.getSequences()));
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param align DOCUMENT ME!
     * @param seqs DOCUMENT ME!
     */
    private static void addStrays(AlignmentI align, Vector seqs)
    {
        int nSeq = align.getHeight();

        for (int i = 0; i < nSeq; i++)
        {
            if (!seqs.contains(align.getSequenceAt(i)))
            {
                seqs.addElement(align.getSequenceAt(i));
            }
        }

        if (nSeq != seqs.size())
        {
            System.err.println(
                "ERROR: Size still not right even after addStrays");
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param node DOCUMENT ME!
     * @param tmp DOCUMENT ME!
     * @param seqset DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    private static Vector _sortByTree(SequenceNode node, Vector tmp,
        Vector seqset)
    {
        if (node == null)
        {
            return tmp;
        }

        SequenceNode left = (SequenceNode) node.left();
        SequenceNode right = (SequenceNode) node.right();

        if ((left == null) && (right == null))
        {
            if (!node.isPlaceholder() && (node.element() != null))
            {
                if (node.element() instanceof SequenceI)
                {
                    if (!tmp.contains(node.element()))
                    {
                        tmp.addElement((SequenceI) node.element());
                    }
                }
            }

            return tmp;
        }
        else
        {
            _sortByTree(left, tmp, seqset);
            _sortByTree(right, tmp, seqset);
        }

        return tmp;
    }

    // Ordering Objects
    // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
    //

    /**
     * recover the order of sequences given by the safe numbering scheme introducd
     * SeqsetUtils.uniquify.
     */
    public static void recoverOrder(SequenceI[] alignment)
    {
        float[] ids = new float[alignment.length];

        for (int i = 0; i < alignment.length; i++)
            ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();

        jalview.util.QuickSort.sort(ids, alignment);
    }
}