v2

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f5d34a6..1196d05 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,9 +20,12 @@ package jalview.datamodel;
 import jalview.analysis.Rna;
 import jalview.analysis.WUSSParseException;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * DOCUMENT ME!
  * 
@@ -49,6 +52,8 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
+  
+  
 
   /**
    * RNA secondary structure contact positions
@@ -237,7 +242,8 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-        if (annotations[i].secondaryStructure == 'S')
+        if (annotations[i].secondaryStructure == 'S'
+                       || annotations[i].secondaryStructure == 'C')
         {
           hasIcons |= true;
           isrna |= true;
@@ -945,7 +951,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] == null)
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
-                  ' ', 0f);
+                  ' ', 0f,null);
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
           annotations[i].displayCharacter = String.valueOf(gapchar);
@@ -998,4 +1004,6 @@ public class AlignmentAnnotation
     this.calcId = calcId;
   }
   
+ 
+  
 }