X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=0ea479dd07671da35efe3dc112d86f8ad3754e0f;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=cf5a57a4e86a808182a842d87a75af60da874ae4;hpb=121674f0d3eed26524584cf4b50b36a67de8a556;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index cf5a57a..0ea479d 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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.
  * 
- * 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 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;
 
@@ -40,6 +39,10 @@ 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;
@@ -59,24 +62,49 @@ 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
    * 
    * @param align
-   *                AlignmentI
+   *          AlignmentI
    * @param s
-   *                SequenceI
+   *          SequenceI
    * @param tosort
-   *                sequences from align that are to be sorted.
+   *          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];
@@ -98,9 +126,9 @@ 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)
   {
@@ -130,9 +158,9 @@ 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)
   {
@@ -143,9 +171,9 @@ 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)
   {
@@ -174,7 +202,7 @@ public class AlignmentSorter
    * 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)
   {
@@ -204,12 +232,45 @@ public class AlignmentSorter
   }
 
   /**
+   * 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
+   *          sorts the given alignment object by group
    */
   public static void sortByGroup(AlignmentI align)
   {
@@ -281,7 +342,7 @@ public class AlignmentSorter
    * Converts Vector to array. java 1.18 does not have Vector.toArray()
    * 
    * @param tmp
-   *                Vector of SequenceI objects
+   *          Vector of SequenceI objects
    * 
    * @return array of Sequence[]
    */
@@ -301,16 +362,16 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param tmp
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param mask
-   *                DOCUMENT ME!
+   *          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++)
@@ -321,10 +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);
       }
     }
@@ -344,9 +405,9 @@ public class AlignmentSorter
    * 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)
   {
@@ -376,9 +437,9 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param align
-   *                alignment to order
+   *          alignment to order
    * @param tree
-   *                tree which has
+   *          tree which has
    * 
    * @return DOCUMENT ME!
    */
@@ -414,9 +475,9 @@ 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)
   {
@@ -447,9 +508,9 @@ public class AlignmentSorter
    * DOCUMENT ME!
    * 
    * @param align
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   private static void addStrays(AlignmentI align, Vector seqs)
   {
@@ -474,11 +535,11 @@ 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!
    */
@@ -544,17 +605,17 @@ 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;
@@ -566,7 +627,7 @@ 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];
@@ -598,7 +659,7 @@ public class AlignmentSorter
       {
         if (!hasScore[i])
         {
-          scores[i] = (max + i+1.0);
+          scores[i] = (max + i + 1.0);
         }
       }
     }
@@ -614,73 +675,94 @@ 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
+   * 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";
-  
+  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
+   * 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)
+  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);
+    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)
+
+  private static boolean containsIgnoreCase(final String lab,
+          final 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 (int q = 0; q < labs.length; q++)
     {
-      if (labs[q]!=null && lab.equalsIgnoreCase(labs[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)
+
+  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)
+    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(
+              "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
     }
-    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
+    for (int i = 0; featureLabels != null && i < featureLabels.length; i++)
     {
-      scoreLabel.append(featureLabels[i]==null ? "null" : featureLabels[i]);
+      scoreLabel.append(featureLabels[i] == null ? "null"
+              : featureLabels[i]);
     }
-    for (int i=0;groupLabels!=null && i<groupLabels.length; i++)
+    for (int i = 0; groupLabels != null && i < groupLabels.length; i++)
     {
-      scoreLabel.append(groupLabels[i]==null ? "null" : groupLabels[i]);
+      scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]);
     }
     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];
@@ -689,27 +771,29 @@ 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 && seqs[i].getDatasetSequence() != null)
       {
         sf = seqs[i].getDatasetSequence().getSequenceFeatures();
       }
-      if (sf==null)
+      if (sf == null)
       {
         sf = new SequenceFeature[0];
-      } else {
+      }
+      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 (
@@ -717,56 +801,62 @@ public class AlignmentSorter
         (sf[f].end < sstart || sf[f].begin > sstop)
                 ||
                 // or ignore based on selection criteria
-                (featureLabels != null && !AlignmentSorter.containsIgnoreCase(sf[f].type, featureLabels))
-                || (groupLabels != null 
-                        && (sf[f].getFeatureGroup() == null 
-                                || !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
+                (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 {
+        }
+        else
+        {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+          if (!ignoreScore && sf[f].getScore() != Float.NaN)
           {
-            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]));
         }
       }
       if (hasScore[i])
-      {      
+      {
         // compute average score
-        scores[i]/=seqScores[i];
+        scores[i] /= seqScores[i];
         // update the score bounds.
         if (hasScores == 1)
         {
@@ -785,51 +875,68 @@ 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])
+        return; // do nothing - no scores present to sort by.
+      }
+      // pad score matrix
+      if (hasScores < seqs.length)
+      {
+        for (int i = 0; i < seqs.length; 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]);
+          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);
+      jalview.util.QuickSort.sort(scores, seqs);
     }
-    else 
-      if (method==FEATURE_DENSITY)
+    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++)
       {
-        
-        // 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);
+        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]);
       }
-      else {
-        if (method==FEATURE_LABEL)
-        {
-          throw new Error("Not yet implemented.");
-        }
+      jalview.util.QuickSort.sort(scores, seqs);
+    }
+    else
+    {
+      if (method == FEATURE_LABEL)
+      {
+        throw new Error("Not yet implemented.");
       }
-    if (lastSortByFeatureScore ==null || scoreLabel.equals(lastSortByFeatureScore))
+    }
+    if (lastSortByFeatureScore == null
+            || !scoreLabel.toString().equals(lastSortByFeatureScore))
+    {
+      sortByFeatureScoreAscending = true;
+    }
+    else
+    {
+      sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+    }
+    if (sortByFeatureScoreAscending)
     {
       setOrder(alignment, seqs);
     }