From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 23 Jun 2013 18:03:53 +0000 (+0100)
Subject: JAL-1230 proxy method for synchronising internal AlignmentI state in response to... 
X-Git-Tag: Jalview_2_9~230^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6b2f5111b04caf7ee23fad5312187b1783c26b7d;p=jalview.git

JAL-1230 proxy method for synchronising internal AlignmentI state in response to changes in alignment annotation
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1553710..7b545c4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1479,5 +1479,13 @@ public class Alignment implements AlignmentI
 
     }
   }
-
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+   alignmentAnnotation.validateRangeAndDisplay();
+   if (isNucleotide() && alignmentAnnotation.isValidStruc())
+   {
+     hasRNAStructure = true;
+   }
+ }
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 06026ef..64dcabb 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -469,4 +469,10 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   public void moveSelectedSequencesByOne(SequenceGroup sg,
           Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+  /**
+   * validate annotation after an edit and update any alignment state flags accordingly
+   * @param alignmentAnnotation
+   */
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
 }