JAL-1841 bug fixes / code tidy for rna SS rendering / parsing

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 7990a5c..a5a38df 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -24,11 +24,11 @@ import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -79,7 +79,7 @@ public class AlignmentAnnotation
   /** Array of annotations placed in the current coordinate system */
   public Annotation[] annotations;
 
-  public ArrayList<SimpleBP> bps = null;
+  public List<SimpleBP> bps = null;
 
   /**
    * RNA secondary structure contact positions
@@ -102,8 +102,8 @@ public class AlignmentAnnotation
   {
     try
     {
-      _rnasecstr = Rna.GetBasePairs(RNAannot);
-      bps = Rna.GetModeleBP(RNAannot);
+      bps = Rna.getModeleBP(RNAannot);
+      _rnasecstr = Rna.getBasePairs(bps);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -272,7 +272,7 @@ public class AlignmentAnnotation
   // JBPNote: what does this do ?
   public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
   {
-    bps = Rna.GetModeleBP(RNAannot);
+    bps = Rna.getModeleBP(RNAannot);
   }
 
   /**
@@ -485,7 +485,7 @@ public class AlignmentAnnotation
       this(0, annotations.length);
     }
 
-    public AnnotCharSequence(int start, int end)
+    AnnotCharSequence(int start, int end)
     {
       offset = start;
       max = end;