/*
* 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.io.*;

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;

    private AlignmentSorter() {
        try {
            jbInit();
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }

    public static void sortGroups(AlignmentI align) {
        Vector groups = align.getGroups();
        int nGroup = groups.size();

        float[] arr = new float[nGroup];
        Object[] s = new Object[nGroup];

        for (int i = 0; i < nGroup; i++) {
            arr[i] = ((SequenceGroup) groups.elementAt(i)).getSize();
            s[i] = groups.elementAt(i);
        }

        QuickSort.sort(arr, s);

        //  align..setGroups(newg);
    }

    /**
     * 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);
    }

    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);
        }
    }

    private static void setOrder(AlignmentI align, Vector tmp) {
        setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
    }

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

    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;
    }

    public static void sortByGroup(AlignmentI align) {
        Vector groups = align.getGroups();

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

        Vector seqs = new Vector();

        for (int i = 0; i < groups.size(); i++) {
            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);

            for (int j = 0; j < sg.getSize(); j++) {
                seqs.addElement(sg.getSequenceAt(j));
            }
        }

        // Deletions can happen so this check may fail

        /*
         if (seqs.size() != nSeq) {
          System.err.println("ERROR: tmp.size() != nseq in sortByGroups");
          if (seqs.size() < nSeq) {
            addStrays(align,seqs);
          }
        }
        */
        if (sortGroupAscending) {
            setOrder(align, seqs);
        } else {
            setReverseOrder(align,
                vectorSubsetToArray(seqs, align.getSequences()));
        }
    }

    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;
    }

    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {
        Vector seqs = new Vector();
        int i;
        int m;
        int p;
        boolean[] tmask = new boolean[m = mask.size()];

        for (i = 0; i < m; i++)
            tmask[i] = true;

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

            if (mask.contains(sq = tmp.elementAt(i))) {
                tmask[mask.indexOf(sq)] = false;
                seqs.addElement(sq);
                m--;
            }
        }

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

        return vectorToArray(seqs);
    }

    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 (tmp.size()<align.getHeight())
        //      addStrays(align, tmp);
        if (lastOrder == order) {
            sortOrderAscending = !sortOrderAscending;
        } else {
            sortOrderAscending = true;
        }

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

    public 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;
    }

    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()));
        }
    }

    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");
        }
    }

    public 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);
    }

    private void jbInit() throws Exception {
    }
}