'Update to Covariaton color scheme' merge; JAL-580

Change-Id: Iaf439847f280e8be7336437a8447f3a439098b09

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index c4268e2..9037008 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -339,7 +339,7 @@ public class AlignmentAnnotation
    * checks graphMin and graphMax, secondary structure symbols, sets graphType
    * appropriately, sets null labels to the empty string if appropriate.
    */
-  private void validateRangeAndDisplay()
+  public void validateRangeAndDisplay()
   {
 
     if (annotations == null)

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 1e1b777..abc7a16 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -127,7 +127,17 @@ public abstract class AlignFile extends FileParse
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+      // detect if annotations.elementAt(i) rna secondary structure
+      // if so then do:
+      /*
+       * SequenceFeature[] pairArray =
+       * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+       * Rna.HelixMap(pairArray);
+       */
+      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+              .elementAt(i);
+      an.validateRangeAndDisplay();
+      al.addAnnotation(an);
     }
 
   }