X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=25717d03bcfc77f8842648e3cbe2f6395e56eb4f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a3493f7d69363c7b7a274b84f3a44aaeb419e584;hpb=198a4921d78d176afc0cb709bdbcb4627afd1e8b;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index a3493f7..25717d0 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,20 +1,19 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
 
@@ -23,34 +22,88 @@ 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)
+/**
+ * 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
 {
+  /**
+   * todo: refactor searches to follow a basic pattern: (search property, last
+   * search state, current sort direction)
+   */
   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;
 
+  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
-   *
-   * @param align AlignmentI
-   * @param s SequenceI
-   * @param tosort sequences from align that are to be sorted.
+   * 
+   * @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)
+  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();
 
@@ -59,8 +112,8 @@ public class AlignmentSorter
 
     for (int i = 0; i < nSeq; i++)
     {
-      scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
-                                 s.getSequenceAsString());
+      scores[i] = Comparison.PID(align.getSequenceAt(i)
+              .getSequenceAsString(), s.getSequenceAsString());
       seqs[i] = align.getSequenceAt(i);
     }
 
@@ -71,9 +124,11 @@ public class AlignmentSorter
 
   /**
    * Reverse the order of the sort
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *          DOCUMENT ME!
+   * @param seqs
+   *          DOCUMENT ME!
    */
   private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -81,7 +136,7 @@ public class AlignmentSorter
 
     int len = 0;
 
-    if ( (nSeq % 2) == 0)
+    if ((nSeq % 2) == 0)
     {
       len = nSeq / 2;
     }
@@ -93,7 +148,7 @@ public class AlignmentSorter
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
     for (int i = 0; i < len; i++)
     {
-      //SequenceI tmp = seqs[i];
+      // SequenceI tmp = seqs[i];
       align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
       align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
     }
@@ -101,9 +156,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align Alignment object to be updated
-   * @param tmp sequences as a vector
+   * 
+   * @param align
+   *          Alignment object to be updated
+   * @param tmp
+   *          sequences as a vector
    */
   private static void setOrder(AlignmentI align, Vector tmp)
   {
@@ -112,9 +169,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs sequences as an array
+   * 
+   * @param align
+   *          DOCUMENT ME!
+   * @param seqs
+   *          sequences as an array
    */
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -131,7 +190,7 @@ public class AlignmentSorter
     }
 
     algn.removeAllElements();
-    //User may have hidden seqs, then clicked undo or redo
+    // User may have hidden seqs, then clicked undo or redo
     for (int i = 0; i < tmp.size(); i++)
     {
       algn.addElement(tmp.elementAt(i));
@@ -141,8 +200,9 @@ public class AlignmentSorter
 
   /**
    * Sorts by ID. Numbers are sorted before letters.
-   *
-   * @param align The alignment object to sort
+   * 
+   * @param align
+   *          The alignment object to sort
    */
   public static void sortByID(AlignmentI align)
   {
@@ -172,16 +232,50 @@ public class AlignmentSorter
   }
 
   /**
-   * 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
+   * 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
+    // MAINTAINS ORIGNAL SEQUENCE ORDER,
+    // ORDERS BY GROUP SIZE
     Vector groups = new Vector();
 
     if (groups.hashCode() != lastGroupHash)
@@ -194,8 +288,8 @@ public class AlignmentSorter
       sortGroupAscending = !sortGroupAscending;
     }
 
-    //SORTS GROUPS BY SIZE
-    //////////////////////
+    // SORTS GROUPS BY SIZE
+    // ////////////////////
     for (int i = 0; i < align.getGroups().size(); i++)
     {
       SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
@@ -218,8 +312,8 @@ public class AlignmentSorter
       }
     }
 
-    //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
-    ///////////////////////////////////////////////
+    // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+    // /////////////////////////////////////////////
     Vector seqs = new Vector();
 
     for (int i = 0; i < groups.size(); i++)
@@ -240,16 +334,16 @@ public class AlignmentSorter
     else
     {
       setReverseOrder(align,
-                      vectorSubsetToArray(seqs, align.getSequences()));
+              vectorSubsetToArray(seqs, align.getSequences()));
     }
   }
 
   /**
-   * Converts Vector to array.
-   * java 1.18 does not have Vector.toArray()
-   *
-   * @param tmp Vector of SequenceI objects
-   *
+   * 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)
@@ -266,16 +360,18 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tmp DOCUMENT ME!
-   * @param mask 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;
+    int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
     for (i = 0; i < mask.size(); i++)
@@ -286,10 +382,10 @@ public class AlignmentSorter
     for (i = 0; i < tmp.size(); i++)
     {
       Object sq = tmp.elementAt(i);
-
-      if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+      idx = mask.indexOf(sq);
+      if (idx > -1 && tmask[idx])
       {
-        tmask[mask.indexOf(sq)] = false;
+        tmask[idx] = false;
         seqs.addElement(sq);
       }
     }
@@ -307,9 +403,11 @@ public class AlignmentSorter
 
   /**
    * Sorts by a given AlignmentOrder object
-   *
-   * @param align Alignment to order
-   * @param order specified order for alignment
+   * 
+   * @param align
+   *          Alignment to order
+   * @param order
+   *          specified order for alignment
    */
   public static void sortBy(AlignmentI align, AlignmentOrder order)
   {
@@ -331,17 +429,18 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align alignment to order
-   * @param tree tree which has
-   *
+   * 
+   * @param align
+   *          alignment to order
+   * @param tree
+   *          tree which has
+   * 
    * @return DOCUMENT ME!
    */
   private static Vector getOrderByTree(AlignmentI align, NJTree tree)
@@ -356,16 +455,16 @@ 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)
+      // sequences)
+      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");
       }
     }
 
@@ -374,9 +473,11 @@ public class AlignmentSorter
 
   /**
    * Sorts the alignment by a given tree
-   *
-   * @param align alignment to order
-   * @param tree tree which has
+   * 
+   * @param align
+   *          alignment to order
+   * @param tree
+   *          tree which has
    */
   public static void sortByTree(AlignmentI align, NJTree tree)
   {
@@ -399,16 +500,17 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *          DOCUMENT ME!
+   * @param seqs
+   *          DOCUMENT ME!
    */
   private static void addStrays(AlignmentI align, Vector seqs)
   {
@@ -424,22 +526,25 @@ public class AlignmentSorter
 
     if (nSeq != seqs.size())
     {
-      System.err.println(
-          "ERROR: Size still not right even after addStrays");
+      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!
-   *
+   * 
+   * @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)
+          Vector seqset)
   {
     if (node == null)
     {
@@ -449,15 +554,15 @@ public class AlignmentSorter
     SequenceNode left = (SequenceNode) node.left();
     SequenceNode right = (SequenceNode) node.right();
 
-    if ( (left == null) && (right == null))
+    if ((left == null) && (right == null))
     {
       if (!node.isPlaceholder() && (node.element() != null))
       {
         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.addElement((SequenceI) node.element());
           }
         }
       }
@@ -474,7 +579,8 @@ public class AlignmentSorter
   }
 
   // Ordering Objects
-  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+  // appropriate order
   //
 
   /**
@@ -487,42 +593,52 @@ public class AlignmentSorter
 
     for (int i = 0; i < alignment.length; i++)
     {
-      ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+      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
+   * 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)
+  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
+    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;
+    double min = 0, max = 0;
     for (int i = 0; i < seqs.length; i++)
     {
       AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
-      if (scoreAnn!=null)
+      if (scoreAnn != null)
       {
         hasScores++;
         hasScore[i] = true;
-        scores[i] = scoreAnn[0].getScore(); // take the first instance of this score.
-        if (hasScores==1)
+        scores[i] = scoreAnn[0].getScore(); // take the first instance of this
+        // score.
+        if (hasScores == 1)
         {
           max = min = scores[i];
-        } else
+        }
+        else
         {
-          if (max<scores[i])
+          if (max < scores[i])
           {
             max = scores[i];
           }
-          if (min>scores[i])
+          if (min > scores[i])
           {
             min = scores[i];
           }
@@ -533,28 +649,301 @@ public class AlignmentSorter
         hasScore[i] = false;
       }
     }
-    if (hasScores==0)
+    if (hasScores == 0)
     {
       return; // do nothing - no scores present to sort by.
     }
-    if (hasScores<seqs.length)
+    if (hasScores < seqs.length)
     {
-      for (int i=0; i<seqs.length;i++)
+      for (int i = 0; i < seqs.length; i++)
       {
         if (!hasScore[i])
         {
-          scores[i] = (max+i);
+          scores[i] = (max + i + 1.0);
         }
       }
     }
-    
+
     jalview.util.QuickSort.sort(scores, seqs);
-    if (lastSortByScore!=scoreLabel)
+    if (lastSortByScore != scoreLabel)
     {
       lastSortByScore = scoreLabel;
       setOrder(alignment, seqs);
-    } else {
+    }
+    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 quite 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 + 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]);
+          }
+        }
+      }
+
+      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.toString().equals(lastSortByFeatureScore))
+    {
+      sortByFeatureScoreAscending = true;
+    }
+    else
+    {
+      sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+    }
+    if (sortByFeatureScoreAscending)
+    {
+      setOrder(alignment, seqs);
+    }
+    else
+    {
+      setReverseOrder(alignment, seqs);
+    }
+    lastSortByFeatureScore = scoreLabel.toString();
+  }
+
 }