X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=cc4c46930ebce044e4178c5b2a56e69ab32c8dca;hb=45715055c536e1c31020b8ab7ce30b2e28f3aafd;hp=bb554262f5674bcedb5382c9b978602e7077d93c;hpb=a4a68a8b10217312efe5f2ea4746f1cfc9da155d;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bb55426..cc4c469 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,27 +1,39 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+import jalview.util.QuickSort;
+
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Routines for manipulating the order of a multiple sequence alignment TODO:
@@ -40,6 +52,10 @@ import jalview.util.*;
  */
 public class AlignmentSorter
 {
+  /**
+   * todo: refactor searches to follow a basic pattern: (search property, last
+   * search state, current sort direction)
+   */
   static boolean sortIdAscending = true;
 
   static int lastGroupHash = 0;
@@ -50,7 +66,7 @@ public class AlignmentSorter
 
   static boolean sortOrderAscending = true;
 
-  static NJTree lastTree = null;
+  static TreeModel lastTree = null;
 
   static boolean sortTreeAscending = true;
 
@@ -59,56 +75,45 @@ public class AlignmentSorter
    */
   private static String lastSortByScore;
 
+  private static boolean sortByScoreAscending = true;
+
   /**
    * compact representation of last arguments to SortByFeatureScore
    */
   private static String lastSortByFeatureScore;
 
+  private static boolean sortByFeatureScoreAscending = true;
+
   private static boolean sortLengthAscending;
 
   /**
-   * Sort by Percentage Identity w.r.t. s
+   * Sorts sequences in the alignment by Percentage Identity with the given
+   * reference sequence, sorting the highest identity to the top
    * 
    * @param align
-   *                AlignmentI
+   *          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 
+   *          SequenceI
    * @param end
    */
-  public static void sortByPID(AlignmentI align, SequenceI s,
-          SequenceI[] tosort,int start, int end)
+  public static void sortByPID(AlignmentI align, SequenceI s)
   {
     int nSeq = align.getHeight();
 
     float[] scores = new float[nSeq];
     SequenceI[] seqs = new SequenceI[nSeq];
+    String refSeq = s.getSequenceAsString();
 
+    SimilarityParams pidParams = new SimilarityParams(true, true, true,
+            true);
     for (int i = 0; i < nSeq; i++)
     {
-      scores[i] = Comparison.PID(align.getSequenceAt(i)
-              .getSequenceAsString(), s.getSequenceAsString());
+      scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i)
+              .getSequenceAsString(), refSeq, pidParams);
       seqs[i] = align.getSequenceAt(i);
     }
 
-    QuickSort.sort(scores, 0, scores.length - 1, seqs);
+    QuickSort.sort(scores, seqs);
 
     setReverseOrder(align, seqs);
   }
@@ -117,9 +122,9 @@ public class AlignmentSorter
    * Reverse the order of the sort
    * 
    * @param align
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -137,11 +142,15 @@ public class AlignmentSorter
     }
 
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    for (int i = 0; i < len; i++)
+    List<SequenceI> asq;
+    synchronized (asq = align.getSequences())
     {
-      // SequenceI tmp = seqs[i];
-      align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
-      align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+      for (int i = 0; i < len; i++)
+      {
+        // SequenceI tmp = seqs[i];
+        asq.set(i, seqs[nSeq - i - 1]);
+        asq.set(nSeq - i - 1, seqs[i]);
+      }
     }
   }
 
@@ -149,11 +158,11 @@ public class AlignmentSorter
    * Sets the Alignment object with the given sequences
    * 
    * @param align
-   *                Alignment object to be updated
+   *          Alignment object to be updated
    * @param tmp
-   *                sequences as a vector
+   *          sequences as a vector
    */
-  private static void setOrder(AlignmentI align, Vector tmp)
+  private static void setOrder(AlignmentI align, List<SequenceI> tmp)
   {
     setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
   }
@@ -162,38 +171,40 @@ public class AlignmentSorter
    * Sets the Alignment object with the given sequences
    * 
    * @param align
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqs
-   *                sequences as an array
+   *          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++)
+    List<SequenceI> algn;
+    synchronized (algn = align.getSequences())
     {
-      if (algn.contains(seqs[i]))
+      List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+      for (int i = 0; i < seqs.length; i++)
       {
-        tmp.addElement(seqs[i]);
+        if (algn.contains(seqs[i]))
+        {
+          tmp.add(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));
+      algn.clear();
+      // User may have hidden seqs, then clicked undo or redo
+      for (int i = 0; i < tmp.size(); i++)
+      {
+        algn.add(tmp.get(i));
+      }
     }
-
   }
 
   /**
    * Sorts by ID. Numbers are sorted before letters.
    * 
    * @param align
-   *                The alignment object to sort
+   *          The alignment object to sort
    */
   public static void sortByID(AlignmentI align)
   {
@@ -221,11 +232,12 @@ public class AlignmentSorter
 
     sortIdAscending = !sortIdAscending;
   }
+
   /**
    * Sorts by sequence length
    * 
    * @param align
-   *                The alignment object to sort
+   *          The alignment object to sort
    */
   public static void sortByLength(AlignmentI align)
   {
@@ -233,11 +245,11 @@ public class AlignmentSorter
 
     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());
+      length[i] = (seqs[i].getEnd() - seqs[i].getStart());
     }
 
     QuickSort.sort(length, seqs);
@@ -260,13 +272,13 @@ public class AlignmentSorter
    * object.
    * 
    * @param align
-   *                sorts the given alignment object by group
+   *          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();
+    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -280,17 +292,15 @@ public class AlignmentSorter
 
     // SORTS GROUPS BY SIZE
     // ////////////////////
-    for (int i = 0; i < align.getGroups().size(); i++)
+    for (SequenceGroup sg : align.getGroups())
     {
-      SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
       for (int j = 0; j < groups.size(); j++)
       {
-        SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+        SequenceGroup sg2 = groups.get(j);
 
         if (sg.getSize() > sg2.getSize())
         {
-          groups.insertElementAt(sg, j);
+          groups.add(j, sg);
 
           break;
         }
@@ -298,22 +308,22 @@ public class AlignmentSorter
 
       if (!groups.contains(sg))
       {
-        groups.addElement(sg);
+        groups.add(sg);
       }
     }
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    Vector seqs = new Vector();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
 
     for (int i = 0; i < groups.size(); i++)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      SequenceGroup sg = groups.get(i);
       SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
 
       for (int j = 0; j < orderedseqs.length; j++)
       {
-        seqs.addElement(orderedseqs[j]);
+        seqs.add(orderedseqs[j]);
       }
     }
 
@@ -329,39 +339,25 @@ public class AlignmentSorter
   }
 
   /**
-   * Converts Vector to array. java 1.18 does not have Vector.toArray()
+   * Select sequences in order from tmp that is present in mask, and any
+   * remaining sequences in mask not in tmp
    * 
    * @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!
+   *          thread safe collection of sequences
    * @param mask
-   *                DOCUMENT ME!
+   *          thread safe collection of sequences
    * 
-   * @return DOCUMENT ME!
+   * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
    */
-  private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+  private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
+          List<SequenceI> mask)
   {
-    Vector seqs = new Vector();
-    int i;
+    // or?
+    // tmp2 = tmp.retainAll(mask);
+    // return tmp2.addAll(mask.removeAll(tmp2))
+
+    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
     for (i = 0; i < mask.size(); i++)
@@ -371,12 +367,12 @@ public class AlignmentSorter
 
     for (i = 0; i < tmp.size(); i++)
     {
-      Object sq = tmp.elementAt(i);
-
-      if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+      SequenceI sq = tmp.get(i);
+      idx = mask.indexOf(sq);
+      if (idx > -1 && tmask[idx])
       {
-        tmask[mask.indexOf(sq)] = false;
-        seqs.addElement(sq);
+        tmask[idx] = false;
+        seqs.add(sq);
       }
     }
 
@@ -384,25 +380,25 @@ public class AlignmentSorter
     {
       if (tmask[i])
       {
-        seqs.addElement(mask.elementAt(i));
+        seqs.add(mask.get(i));
       }
     }
 
-    return vectorToArray(seqs);
+    return seqs.toArray(new SequenceI[seqs.size()]);
   }
 
   /**
    * Sorts by a given AlignmentOrder object
    * 
    * @param align
-   *                Alignment to order
+   *          Alignment to order
    * @param order
-   *                specified order for alignment
+   *          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();
+    List<SequenceI> tmp = order.getOrder();
 
     if (lastOrder == order)
     {
@@ -427,17 +423,18 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param align
-   *                alignment to order
+   *          alignment to order
    * @param tree
-   *                tree which has
+   *          tree which has
    * 
    * @return DOCUMENT ME!
    */
-  private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+  private static List<SequenceI> getOrderByTree(AlignmentI align,
+          TreeModel tree)
   {
     int nSeq = align.getHeight();
 
-    Vector tmp = new Vector();
+    List<SequenceI> tmp = new ArrayList<SequenceI>();
 
     tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 
@@ -446,15 +443,19 @@ public class AlignmentSorter
       // 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)
+      if (tmp.size() != nSeq)
       {
         addStrays(align, tmp);
       }
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
-                + nSeq + " in getOrderByTree");
+        System.err
+                .println("WARNING: tmp.size()="
+                        + tmp.size()
+                        + " != nseq="
+                        + nSeq
+                        + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
 
@@ -465,13 +466,13 @@ public class AlignmentSorter
    * Sorts the alignment by a given tree
    * 
    * @param align
-   *                alignment to order
+   *          alignment to order
    * @param tree
-   *                tree which has
+   *          tree which has
    */
-  public static void sortByTree(AlignmentI align, NJTree tree)
+  public static void sortByTree(AlignmentI align, TreeModel tree)
   {
-    Vector tmp = getOrderByTree(align, tree);
+    List<SequenceI> tmp = getOrderByTree(align, tree);
 
     // tmp should properly permute align with tree.
     if (lastTree != tree)
@@ -498,23 +499,23 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param align
-   *                DOCUMENT ME!
-   * @param seqs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
+   * @param tmp
+   *          DOCUMENT ME!
    */
-  private static void addStrays(AlignmentI align, Vector seqs)
+  private static void addStrays(AlignmentI align, List<SequenceI> tmp)
   {
     int nSeq = align.getHeight();
 
     for (int i = 0; i < nSeq; i++)
     {
-      if (!seqs.contains(align.getSequenceAt(i)))
+      if (!tmp.contains(align.getSequenceAt(i)))
       {
-        seqs.addElement(align.getSequenceAt(i));
+        tmp.add(align.getSequenceAt(i));
       }
     }
 
-    if (nSeq != seqs.size())
+    if (nSeq != tmp.size())
     {
       System.err
               .println("ERROR: Size still not right even after addStrays");
@@ -525,16 +526,16 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param node
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param tmp
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqset
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  private static Vector _sortByTree(SequenceNode node, Vector tmp,
-          Vector seqset)
+  private static List<SequenceI> _sortByTree(SequenceNode node,
+          List<SequenceI> tmp, List<SequenceI> seqset)
   {
     if (node == null)
     {
@@ -550,9 +551,11 @@ public class AlignmentSorter
       {
         if (node.element() instanceof SequenceI)
         {
-          if (!tmp.contains(node.element()))
+          if (!tmp.contains(node.element())) // && (seqset==null ||
+                                             // seqset.size()==0 ||
+                                             // seqset.contains(tmp)))
           {
-            tmp.addElement((SequenceI) node.element());
+            tmp.add((SequenceI) node.element());
           }
         }
       }
@@ -595,17 +598,17 @@ public class AlignmentSorter
    * particular scoreLabel. Or reverse if same label was used previously
    * 
    * @param scoreLabel
-   *                exact label for sequence associated AlignmentAnnotation
-   *                scores to use for sorting.
+   *          exact label for sequence associated AlignmentAnnotation scores to
+   *          use for sorting.
    * @param alignment
-   *                sequences to be sorted
+   *          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
+    // presence
     int hasScores = 0; // number of scores present on set
     double[] scores = new double[seqs.length];
     double min = 0, max = 0;
@@ -617,7 +620,7 @@ public class AlignmentSorter
         hasScores++;
         hasScore[i] = true;
         scores[i] = scoreAnn[0].getScore(); // take the first instance of this
-                                            // score.
+        // score.
         if (hasScores == 1)
         {
           max = min = scores[i];
@@ -649,7 +652,7 @@ public class AlignmentSorter
       {
         if (!hasScore[i])
         {
-          scores[i] = (max + i+1.0);
+          scores[i] = (max + i + 1.0);
         }
       }
     }
@@ -665,73 +668,110 @@ public class AlignmentSorter
       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
+   * 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 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)
+  public static String FEATURE_SCORE = "average_score";
+
+  public static String FEATURE_LABEL = "text";
+
+  public static String FEATURE_DENSITY = "density";
+
+  private static boolean containsIgnoreCase(final String lab,
+          final List<String> labs)
   {
-    if (labs==null)
+    if (labs == null)
     {
       return true;
     }
-    if (lab==null)
+    if (lab == null)
     {
       return false;
     }
-    for (int q=0;q<labs.length;q++)
+    for (String label : labs)
     {
-      if (labs[q]!=null && lab.equalsIgnoreCase(labs[q]))
+      if (lab.equalsIgnoreCase(label))
       {
         return true;
       }
     }
     return false;
   }
-  public static void sortByFeature(String[] featureLabels, String[] groupLabels, int start, int stop, 
+
+  /**
+   * Sort sequences by feature score or density, optionally restricted by
+   * feature types, feature groups, or alignment start/end positions.
+   * <p>
+   * If the sort is repeated for the same combination of types and groups, sort
+   * order is reversed.
+   * 
+   * @param featureLabels
+   *          a list of feature types to include (or null for all)
+   * @param groupLabels
+   *          a list of feature groups to include (or null for all)
+   * @param start
+   *          start column position to include (base zero)
+   * @param stop
+   *          end column position to include (base zero)
+   * @param alignment
+   *          the alignment to be sorted
+   * @param method
+   *          either "average_score" or "density" ("text" not yet implemented)
+   */
+  public static void sortByFeature(List<String> featureLabels,
+          List<String> groupLabels, int start, int stop,
           AlignmentI alignment, String method)
   {
-    if (method!=FEATURE_SCORE && method!=FEATURE_LABEL && method!=FEATURE_DENSITY)
+    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.");
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_sortbyfeature"));
     }
-    boolean ignoreScore=method!=FEATURE_SCORE;
+
+    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(start + stop + method);
+    // This doesn't quite work yet - we'd like to have a canonical ordering that
+    // can be preserved from call to call
+    if (featureLabels != null)
     {
-      scoreLabel.append(featureLabels[i]==null ? "null" : featureLabels[i]);
+      for (String label : featureLabels)
+      {
+        scoreLabel.append(label);
+      }
     }
-    for (int i=0;groupLabels!=null && i<groupLabels.length; i++)
+    if (groupLabels != null)
     {
-      scoreLabel.append(groupLabels[i]==null ? "null" : groupLabels[i]);
+      for (String label : groupLabels)
+      {
+        scoreLabel.append(label);
+      }
     }
+
+    /*
+     * if resorting the same feature, toggle sort order
+     */
+    if (lastSortByFeatureScore == null
+            || !scoreLabel.toString().equals(lastSortByFeatureScore))
+    {
+      sortByFeatureScoreAscending = true;
+    }
+    else
+    {
+      sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+    }
+    lastSortByFeatureScore = scoreLabel.toString();
+
     SequenceI[] seqs = alignment.getSequencesArray();
-    
+
     boolean[] hasScore = new boolean[seqs.length]; // per sequence score
-                                                    // presence
+    // presence
     int hasScores = 0; // number of scores present on set
     double[] scores = new double[seqs.length];
     int[] seqScores = new int[seqs.length];
@@ -740,85 +780,87 @@ public class AlignmentSorter
     for (int i = 0; i < seqs.length; i++)
     {
       SequenceFeature[] sf = seqs[i].getSequenceFeatures();
-      if (sf==null && seqs[i].getDatasetSequence()!=null)
+      if (sf == null)
       {
-        sf = seqs[i].getDatasetSequence().getSequenceFeatures();
+        sf = new SequenceFeature[0];
       }
-      if (sf==null)
+      else
       {
-        sf = new SequenceFeature[0];
-      } else {
         SequenceFeature[] tmp = new SequenceFeature[sf.length];
-        for (int s=0; s<tmp.length;s++)
+        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++)
+      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))
+        (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))))
+                // 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 {
+        }
+        else
+        {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+          if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
           {
-            if (seqScores[i]==0)
+            if (seqScores[i] == 0)
             {
               hasScores++;
             }
             seqScores[i]++;
             hasScore[i] = true;
             scores[i] += sf[f].getScore(); // take the first instance of this
-                                            // score.
+            // score.
           }
         }
       }
       SequenceFeature[] fs;
       feats[i] = fs = new SequenceFeature[n];
-      if (n>0)
+      if (n > 0)
       {
-        n=0;
-        for (int f=0;f<sf.length;f++)
+        n = 0;
+        for (int f = 0; f < sf.length; f++)
         {
-          if (sf[f]!=null)
+          if (sf[f] != null)
           {
             ((SequenceFeature[]) feats[i])[n++] = sf[f];
           }
         }
-        if (method==FEATURE_LABEL)
+        if (method == FEATURE_LABEL)
         {
           // order the labels by alphabet
           String[] labs = new String[fs.length];
-          for (int l=0;l<labs.length; l++)
+          for (int l = 0; l < labs.length; l++)
           {
-            labs[l] = (fs[l].getDescription()!=null ? fs[l].getDescription() : fs[l].getType());
+            labs[l] = (fs[l].getDescription() != null ? fs[l]
+                    .getDescription() : fs[l].getType());
           }
-          jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+          QuickSort.sort(labs, ((Object[]) feats[i]));
         }
       }
       if (hasScore[i])
-      {      
+      {
         // compute average score
-        scores[i]/=seqScores[i];
+        scores[i] /= seqScores[i];
         // update the score bounds.
         if (hasScores == 1)
         {
@@ -837,59 +879,56 @@ public class AlignmentSorter
         }
       }
     }
-    
-    if (method==FEATURE_SCORE)
+
+    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]);
-        }
+        return; // do nothing - no scores present to sort by.
       }
-    }
-
-    jalview.util.QuickSort.sort(scores, seqs);
-    }
-    else 
-      if (method==FEATURE_DENSITY)
+      // pad score matrix
+      if (hasScores < seqs.length)
       {
-        
-        // 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)
+        for (int i = 0; i < seqs.length; i++)
         {
-          throw new Error("Not yet implemented.");
+          if (!hasScore[i])
+          {
+            scores[i] = (max + 1 + 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]);
+          }
         }
       }
-    if (lastSortByFeatureScore ==null || scoreLabel.equals(lastSortByFeatureScore))
+      QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending);
+    }
+    else if (method == FEATURE_DENSITY)
     {
-      setOrder(alignment, seqs);
+      for (int i = 0; i < seqs.length; i++)
+      {
+        int featureCount = feats[i] == null ? 0
+                : ((SequenceFeature[]) feats[i]).length;
+        scores[i] = featureCount;
+        // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+        // " Feats: "+featureCount+" Score : "+scores[i]);
+      }
+      QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending);
     }
     else
     {
-      setReverseOrder(alignment, seqs);
+      if (method == FEATURE_LABEL)
+      {
+        throw new Error(
+                MessageManager.getString("error.not_yet_implemented"));
+      }
     }
-    lastSortByFeatureScore = scoreLabel.toString();
+
+    setOrder(alignment, seqs);
   }
 
 }