X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=6c46a3e2dd225ec43a5e1917e59a8bc2876cbd0d;hb=b0f76adef2787dd14566525e66a4073278e75d67;hp=3fe73dc8ce1239828b4c8ccb1709af9c745197ff;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 3fe73dc..6c46a3e 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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);