(JAL-1071) hacked the square matrix that stores the interacting pairs to allow 36...

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 0c9f830..5f85916 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -406,7 +406,7 @@ public class StructureFrequency
   public static int[] extractProfile(Hashtable hconsensus,
           boolean ignoreGapsInConsensusCalculation)
   {
-    int[] rtnval = new int[52]; // 2*(5*5)+2
+    int[] rtnval = new int[74]; // 2*(5*5)+2
     int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
     int[][] pairs = (int[][]) hconsensus
             .get(StructureFrequency.PAIRPROFILE);

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index d063c5b..476d7f7 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -863,7 +863,7 @@ public class AnnotationRenderer
            * Therefore dc gets length 2, to have space for a basepair instead of
            * just a single nucleotide
            */
-          if (profl.length == 52)
+          if (profl.length == 74)
           {
             dc = new char[2];
           }