From: janengelhardt <engelhardt87@googlemail.com>
Date: Mon, 23 May 2011 17:26:01 +0000 (+0200)
Subject: 'Update to Covariaton color scheme' merge; JAL-580
X-Git-Tag: Jalview_2_9~576^2~42
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=57d863cc978bfd638da0e21a37b425be6251ce13;p=jalview.git

'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
--- 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
--- 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);
     }
 
   }