X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=bb554262f5674bcedb5382c9b978602e7077d93c;hb=50ae21686bb576ce02f2a83a1d53744b86290479;hp=64682c1f2433e0f2ba9fec3587dee3e5b9eaccd9;hpb=263b70c6c296776e942b7875023cafd293dee0b4;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 64682c1..bb55426 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,199 +1,895 @@
-package jalview.analysis;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-import jalview.io.*;
-
-import java.util.*;
-
-/** Data structure to hold and manipulate a multiple sequence alignment
- */
-public class AlignmentSorter {
-
-  private AlignmentSorter() {
-  }
-
-  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);
-
-    Vector newg = new Vector(nGroup);
-
-    for (int i=nGroup-1; i >= 0; i--) {
-      newg.addElement(s[i]);
-    }
-
-    //    align.setGroups(newg);
-  }
-
-  /**    */
-  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.compare(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,vectorToArray(tmp));
-  }
-
-  private static void setOrder(AlignmentI align, SequenceI [] seqs) {
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    for (int i = 0; i < seqs.length; i++) {
-      align.getSequences().setElementAt(seqs[i],i);
-    }
-  }
-
-  /**    */
-  static boolean sortIdAscending = true;
-  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;
-  }
-
-  static boolean sortGroupAscending = true;
-  public static void sortByGroup(AlignmentI align) {
-    int    nSeq = align.getHeight();
-    Vector groups = align.getGroups();
-
-    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));
-      }
-    }
-
-    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, vectorToArray(seqs));
-
-    sortGroupAscending = ! sortGroupAscending;
-  }
-
-  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;
-  }
-
-  static boolean sortTreeAscending = true;
-  public static void sortByTree(AlignmentI align, NJTree tree) {
-    int    nSeq = align.getHeight();
-
-    Vector tmp = new Vector();
-
-    tmp = _sortByTree(tree.getTopNode(),tmp);
-
-    if (tmp.size() != nSeq) {
-      System.err.println("ERROR: tmp.size() != nseq in sortByTree");
-      if (tmp.size() < nSeq) {
-        addStrays(align,tmp);
-      }
-    }
-
-    if(sortTreeAscending)
-      setOrder(align,tmp);
-    else
-      setReverseOrder(align, vectorToArray(tmp));
-
-      sortTreeAscending = !sortTreeAscending;
-  }
-
-  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) {
-    if (node == null) {return tmp;}
-
-    SequenceNode left = (SequenceNode)node.left();
-    SequenceNode right = (SequenceNode)node.right();
-
-    if (left == null && right == null) {
-      if (node.element() instanceof SequenceI) {
-        tmp.addElement((SequenceI)node.element());
-        return tmp;
-      }
-    } else {
-      _sortByTree(left,tmp);
-      _sortByTree(right,tmp);
-    }
-    return tmp;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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;
+
+  /**
+   * last Annotation Label used by sortByScore
+   */
+  private static String lastSortByScore;
+
+  /**
+   * compact representation of last arguments to SortByFeatureScore
+   */
+  private static String lastSortByFeatureScore;
+
+  private static boolean sortLengthAscending;
+
+  /**
+   * 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)
+  {
+    sortByPID(align,s,tosort,0,-1);
+  }
+  /**
+   * Sort by Percentage Identity w.r.t. s
+   * 
+   * @param align
+   *                AlignmentI
+   * @param s
+   *                SequenceI
+   * @param tosort
+   *                sequences from align that are to be sorted.
+   * @param start   start column (0 for beginning 
+   * @param end
+   */
+  public static void sortByPID(AlignmentI align, SequenceI s,
+          SequenceI[] tosort,int start, int end)
+  {
+    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 by sequence length
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByLength(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    float[] length = new float[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+    
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      length[i] = (float) (seqs[i].getEnd()-seqs[i].getStart());
+    }
+
+    QuickSort.sort(length, seqs);
+
+    if (sortLengthAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortLengthAscending = !sortLengthAscending;
+  }
+
+  /**
+   * 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+1.0);
+        }
+      }
+    }
+
+    jalview.util.QuickSort.sort(scores, seqs);
+    if (lastSortByScore != scoreLabel)
+    {
+      lastSortByScore = scoreLabel;
+      setOrder(alignment, seqs);
+    }
+    else
+    {
+      setReverseOrder(alignment, seqs);
+    }
+  }
+  /**
+   * types of feature ordering:
+   * Sort by score : average score - or total score - over all features in region
+   * Sort by feature label text: (or if null - feature type text) - numerical or alphabetical
+   * Sort by feature density: based on counts - ignoring individual text or scores for each feature
+   */
+  public static String FEATURE_SCORE="average_score";
+  public static String FEATURE_LABEL="text";
+  public static String FEATURE_DENSITY="density";
+  
+  /**
+   * sort the alignment using the features on each sequence found between start and stop with the given featureLabel (and optional group qualifier) 
+   * @param featureLabel (may not be null)
+   * @param groupLabel (may be null)
+   * @param start (-1 to include non-positional features)
+   * @param stop (-1 to only sort on non-positional features)
+   * @param alignment - aligned sequences containing features
+   * @param method - one of the string constants FEATURE_SCORE, FEATURE_LABEL, FEATURE_DENSITY
+   */
+  public static void sortByFeature(String featureLabel, String groupLabel, int start, int stop, 
+          AlignmentI alignment, String method)
+  {
+    sortByFeature(featureLabel==null ? null : new String[] {featureLabel}, 
+            groupLabel==null ? null : new String[] {groupLabel}, start, stop, alignment, method);
+  }
+  private static boolean containsIgnoreCase(final String lab, final String[] labs)
+  {
+    if (labs==null)
+    {
+      return true;
+    }
+    if (lab==null)
+    {
+      return false;
+    }
+    for (int q=0;q<labs.length;q++)
+    {
+      if (labs[q]!=null && lab.equalsIgnoreCase(labs[q]))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+  public static void sortByFeature(String[] featureLabels, String[] groupLabels, int start, int stop, 
+          AlignmentI alignment, String method)
+  {
+    if (method!=FEATURE_SCORE && method!=FEATURE_LABEL && method!=FEATURE_DENSITY)
+    {
+      throw new Error("Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+    }
+    boolean ignoreScore=method!=FEATURE_SCORE;
+    StringBuffer scoreLabel = new StringBuffer();
+    scoreLabel.append(start+stop+method);
+    // This doesn't work yet - we'd like to have a canonical ordering that can be preserved from call to call
+    for (int i=0;featureLabels!=null && i<featureLabels.length; i++)
+    {
+      scoreLabel.append(featureLabels[i]==null ? "null" : featureLabels[i]);
+    }
+    for (int i=0;groupLabels!=null && i<groupLabels.length; i++)
+    {
+      scoreLabel.append(groupLabels[i]==null ? "null" : groupLabels[i]);
+    }
+    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];
+    int[] seqScores = new int[seqs.length];
+    Object[] feats = new Object[seqs.length];
+    double min = 0, max = 0;
+    for (int i = 0; i < seqs.length; i++)
+    {
+      SequenceFeature[] sf = seqs[i].getSequenceFeatures();
+      if (sf==null && seqs[i].getDatasetSequence()!=null)
+      {
+        sf = seqs[i].getDatasetSequence().getSequenceFeatures();
+      }
+      if (sf==null)
+      {
+        sf = new SequenceFeature[0];
+      } else {
+        SequenceFeature[] tmp = new SequenceFeature[sf.length];
+        for (int s=0; s<tmp.length;s++)
+        {
+          tmp[s] = sf[s];
+        }
+        sf = tmp;
+      }
+      int sstart = (start==-1) ? start : seqs[i].findPosition(start);
+      int sstop = (stop==-1) ? stop : seqs[i].findPosition(stop);
+      seqScores[i]=0;
+      scores[i]=0.0;
+      int n=sf.length;
+      for (int f=0;f<sf.length;f++)
+      {
+        // filter for selection criteria
+        if (
+        // ignore features outwith alignment start-stop positions.
+        (sf[f].end < sstart || sf[f].begin > sstop)
+                ||
+                // or ignore based on selection criteria
+                (featureLabels != null && !AlignmentSorter.containsIgnoreCase(sf[f].type, featureLabels))
+                || (groupLabels != null
+                        // problem here: we cannot eliminate null feature group features
+                        && (sf[f].getFeatureGroup() != null 
+                                && !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
+        {
+          // forget about this feature
+          sf[f] = null;
+          n--;
+        } else {
+          // or, also take a look at the scores if necessary.
+          if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+          {
+            if (seqScores[i]==0)
+            {
+              hasScores++;
+            }
+            seqScores[i]++;
+            hasScore[i] = true;
+            scores[i] += sf[f].getScore(); // take the first instance of this
+                                            // score.
+          }
+        }
+      }
+      SequenceFeature[] fs;
+      feats[i] = fs = new SequenceFeature[n];
+      if (n>0)
+      {
+        n=0;
+        for (int f=0;f<sf.length;f++)
+        {
+          if (sf[f]!=null)
+          {
+            ((SequenceFeature[]) feats[i])[n++] = sf[f];
+          }
+        }
+        if (method==FEATURE_LABEL)
+        {
+          // order the labels by alphabet
+          String[] labs = new String[fs.length];
+          for (int l=0;l<labs.length; l++)
+          {
+            labs[l] = (fs[l].getDescription()!=null ? fs[l].getDescription() : fs[l].getType());
+          }
+          jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+        }
+      }
+      if (hasScore[i])
+      {      
+        // compute average score
+        scores[i]/=seqScores[i];
+        // update the score bounds.
+        if (hasScores == 1)
+        {
+          max = min = scores[i];
+        }
+        else
+        {
+          if (max < scores[i])
+          {
+            max = scores[i];
+          }
+          if (min > scores[i])
+          {
+            min = scores[i];
+          }
+        }
+      }
+    }
+    
+    if (method==FEATURE_SCORE)
+    {
+      if (hasScores == 0)
+    {
+      return; // do nothing - no scores present to sort by.
+    }
+    // pad score matrix 
+    if (hasScores < seqs.length)
+    {
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (!hasScore[i])
+        {
+          scores[i] = (max + i);
+        } else {
+          int nf=(feats[i]==null) ? 0 :((SequenceFeature[]) feats[i]).length;
+          System.err.println("Sorting on Score: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
+        }
+      }
+    }
+
+    jalview.util.QuickSort.sort(scores, seqs);
+    }
+    else 
+      if (method==FEATURE_DENSITY)
+      {
+        
+        // break ties between equivalent numbers for adjacent sequences by adding 1/Nseq*i on the original order
+        double fr = 0.9/(1.0*seqs.length);
+        for (int i=0;i<seqs.length; i++)
+        {
+          double nf;
+          scores[i] = (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[]) feats[i]).length));
+          System.err.println("Sorting on Density: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
+        }
+        jalview.util.QuickSort.sort(scores, seqs);
+      }
+      else {
+        if (method==FEATURE_LABEL)
+        {
+          throw new Error("Not yet implemented.");
+        }
+      }
+    if (lastSortByFeatureScore ==null || scoreLabel.equals(lastSortByFeatureScore))
+    {
+      setOrder(alignment, seqs);
+    }
+    else
+    {
+      setReverseOrder(alignment, seqs);
+    }
+    lastSortByFeatureScore = scoreLabel.toString();
+  }
+
+}