X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=693e7947f62fe281256ac8639894f43ff8e86a52;hb=2d3be0b3f26fa3e35480976cd5a90a5562d43dcf;hp=5ee4bcbfe112aaa0e82e22ba5296fd71111b810e;hpb=66d479709f80154ea834491afce7ac894128617e;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 5ee4bcb..693e794 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -27,7 +29,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.QuickSort;
 
@@ -66,7 +67,7 @@ public class AlignmentSorter
 
   static boolean sortOrderAscending = true;
 
-  static NJTree lastTree = null;
+  static TreeModel lastTree = null;
 
   static boolean sortTreeAscending = true;
 
@@ -87,46 +88,29 @@ public class AlignmentSorter
   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
    * @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)
+  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);
     }
 
@@ -447,7 +431,7 @@ public class AlignmentSorter
    * @return DOCUMENT ME!
    */
   private static List<SequenceI> getOrderByTree(AlignmentI align,
-          NJTree tree)
+          TreeModel tree)
   {
     int nSeq = align.getHeight();
 
@@ -487,7 +471,7 @@ public class AlignmentSorter
    * @param tree
    *          tree which has
    */
-  public static void sortByTree(AlignmentI align, NJTree tree)
+  public static void sortByTree(AlignmentI align, TreeModel tree)
   {
     List<SequenceI> tmp = getOrderByTree(align, tree);
 
@@ -719,10 +703,12 @@ public class AlignmentSorter
   public static void sortByFeature(String featureLabel, String groupLabel,
           int start, int stop, AlignmentI alignment, String method)
   {
-    sortByFeature(featureLabel == null ? null
+    sortByFeature(
+            featureLabel == null ? null
                     : Arrays.asList(new String[] { featureLabel }),
-            groupLabel == null ? null
-            : Arrays.asList(new String[]{ groupLabel }), start, stop, alignment, method);
+            groupLabel == null ? null : Arrays
+                    .asList(new String[] { groupLabel }), start, stop,
+            alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
@@ -747,8 +733,8 @@ public class AlignmentSorter
   }
 
   public static void sortByFeature(List<String> featureLabels,
-          List<String> groupLabels, int start, int stop, AlignmentI alignment,
-          String method)
+          List<String> groupLabels, int start, int stop,
+          AlignmentI alignment, String method)
   {
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)
@@ -825,17 +811,23 @@ public class AlignmentSorter
       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))))
+        SequenceFeature feature = sf[f];
+
+        /*
+         * double-check feature overlaps columns (JAL-2544)
+         * (could avoid this with a findPositions(fromCol, toCol) method)
+         * findIndex returns base 1 column values, startCol/endCol are base 0
+         */
+        boolean noOverlap = seqs[i].findIndex(feature.getBegin()) > stop + 1
+                || seqs[i].findIndex(feature.getEnd()) < start + 1;
+        boolean skipFeatureType = featureLabels != null
+                && !AlignmentSorter.containsIgnoreCase(feature.type,
+                        featureLabels);
+        boolean skipFeatureGroup = groupLabels != null
+                && (feature.getFeatureGroup() != null && !AlignmentSorter
+                        .containsIgnoreCase(feature.getFeatureGroup(),
+                                groupLabels));
+        if (noOverlap || skipFeatureType || skipFeatureGroup)
         {
           // forget about this feature
           sf[f] = null;
@@ -844,7 +836,7 @@ public class AlignmentSorter
         else
         {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
+          if (!ignoreScore && !Float.isNaN(feature.getScore()))
           {
             if (seqScores[i] == 0)
             {
@@ -852,7 +844,7 @@ public class AlignmentSorter
             }
             seqScores[i]++;
             hasScore[i] = true;
-            scores[i] += sf[f].getScore(); // take the first instance of this
+            scores[i] += feature.getScore(); // take the first instance of this
             // score.
           }
         }