X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=a3493f7d69363c7b7a274b84f3a44aaeb419e584;hb=cd5b2de469fb4c09242955cb4b74279e2da348d6;hp=7c2a554c952b11a1803b079f13089aea97734000;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 7c2a554..a3493f7 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,342 +1,560 @@
-/*
-* 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 {
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+/** 
+ * Routines for manipulating the order of a multiple sequence alignment
+ * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: refactor to allow a subset of selected sequences to be sorted within the context of a whole alignment.
+ * Sort method template is: SequenceI[] tobesorted, [ input data mapping to each tobesorted element to use ], Alignment context of tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie seuqence to be sorted w.r.t.])
+ * sortinplace implies that the sorted vector resulting from applying the operation to tobesorted should be mapped back to the original positions in alignment.
+ * Otherwise, normal behaviour is to re order alignment so that tobesorted is sorted and grouped together starting from the first tobesorted position in the alignment.
+ * e.g. (a,tb2,b,tb1,c,tb3 becomes a,tb1,tb2,tb3,b,c)
+ */
+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 static String lastSortByScore;
+
+  /**
+   * Sort by Percentage Identity w.r.t. s
+   *
+   * @param align AlignmentI
+   * @param s SequenceI
+   * @param tosort sequences from align that are to be sorted.
+   */
+  public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
+  {
+    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).getSequenceAsString(),
+                                 s.getSequenceAsString());
+      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
+   */
+  public static void setOrder(AlignmentI align, SequenceI[] seqs)
+  {
+    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+    Vector algn = align.getSequences();
+    Vector tmp = new Vector();
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (algn.contains(seqs[i]))
+      {
+        tmp.addElement(seqs[i]);
+      }
+    }
+
+    algn.removeAllElements();
+    //User may have hidden seqs, then clicked undo or redo
+    for (int i = 0; i < tmp.size(); i++)
+    {
+      algn.addElement(tmp.elementAt(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);
+  }
+  /**
+   * Sort sequence in order of increasing score attribute for annotation with a particular
+   * scoreLabel. Or reverse if same label was used previously
+   * @param scoreLabel exact label for sequence associated AlignmentAnnotation scores to use for sorting.
+   * @param alignment sequences to be sorted
+   */
+  public static void sortByAnnotationScore(String scoreLabel, AlignmentI alignment)
+  {
+    SequenceI[] seqs = alignment.getSequencesArray();
+    boolean[] hasScore = new boolean[seqs.length]; // per sequence score presence
+    int hasScores=0; // number of scores present on set
+    double[] scores = new double[seqs.length];
+    double min=0,max=0;
+    for (int i = 0; i < seqs.length; i++)
+    {
+      AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
+      if (scoreAnn!=null)
+      {
+        hasScores++;
+        hasScore[i] = true;
+        scores[i] = scoreAnn[0].getScore(); // take the first instance of this score.
+        if (hasScores==1)
+        {
+          max = min = scores[i];
+        } else
+        {
+          if (max<scores[i])
+          {
+            max = scores[i];
+          }
+          if (min>scores[i])
+          {
+            min = scores[i];
+          }
+        }
+      }
+      else
+      {
+        hasScore[i] = false;
+      }
+    }
+    if (hasScores==0)
+    {
+      return; // do nothing - no scores present to sort by.
+    }
+    if (hasScores<seqs.length)
+    {
+      for (int i=0; i<seqs.length;i++)
+      {
+        if (!hasScore[i])
+        {
+          scores[i] = (max+i);
+        }
+      }
+    }
+    
+    jalview.util.QuickSort.sort(scores, seqs);
+    if (lastSortByScore!=scoreLabel)
+    {
+      lastSortByScore = scoreLabel;
+      setOrder(alignment, seqs);
+    } else {
+      setReverseOrder(alignment, seqs);
+    }
+  }
+}