Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 34a21e6..98f257f 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1057,8 +1057,18 @@ public class AlignSeq
           SequenceI[] originalSequences, String[] omitHidden, int start,
           int end, boolean ungapped)
   {
+    return (float[]) computeRedundancyMatrixWithRep(originalSequences,
+            omitHidden, start, end, ungapped)[0];
+  }
+
+  public static Object[] computeRedundancyMatrixWithRep(
+          SequenceI[] originalSequences, String[] omitHidden, int start,
+          int end, boolean ungapped)
+  {
+
     int height = originalSequences.length;
     float[] redundancy = new float[height];
+    SequenceI[] rep = new SequenceI[height];
     int[] lngth = new int[height];
     for (int i = 0; i < height; i++)
     {
@@ -1115,15 +1125,23 @@ public class AlignSeq
         // use real sequence length rather than string length
         if (lngth[j] < lngth[i])
         {
-          redundancy[j] = Math.max(pid, redundancy[j]);
+          if (pid > redundancy[j])
+          {
+            rep[j] = originalSequences[i];
+            redundancy[j] = pid;
+          }
         }
         else
         {
-          redundancy[i] = Math.max(pid, redundancy[i]);
+          if (pid > redundancy[i])
+          {
+            rep[i] = originalSequences[j];
+            redundancy[i] = pid;
+          }
         }
 
       }
     }
-    return redundancy;
+    return new Object[] { redundancy, rep };
   }
 }