From 32a155bca4be016568e45709831dac380c18803a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 28 Oct 2011 15:41:21 +0100
Subject: [PATCH] JAL-580 ensure WUSS annotation string is up to date, pair
 list regenerated if necessary and cope with parse errors

---
 src/jalview/datamodel/AlignmentAnnotation.java |  109 +++++++++++++++++++++---
 1 file changed, 95 insertions(+), 14 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 25bba51..3cf9244 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,6 +18,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -53,31 +54,42 @@ public class AlignmentAnnotation
    * RNA secondary structure contact positions
    */
   public SequenceFeature[] _rnasecstr = null;
-  
-  public String rnaStructure;
-
+  /**
+   * position of annotation resulting in invalid WUSS parsing or -1
+   */
+  private long invalidrnastruc=-1;
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
    * 
    * @param RNAannot
    */
-  private void _updateRnaSecStr(String RNAannot)
+  private void _updateRnaSecStr(CharSequence RNAannot)
   {
+    try {
     _rnasecstr = Rna.GetBasePairs(RNAannot);
+    invalidrnastruc=-1;
+    }
+    catch (WUSSParseException px)
+    {
+      invalidrnastruc=px.getProblemPos();
+    }
+    if (invalidrnastruc>-1)
+    {
+      return;
+    }
     Rna.HelixMap(_rnasecstr);
+    // setRNAStruc(RNAannot);
     
-    setRNAStruc(RNAannot);
-
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
       // show all the RNA secondary structure annotation symbols.
+      isrna=true;
       showAllColLabels = true;
       scaleColLabel = true;
     }
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
-  
   public java.util.Hashtable sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -148,6 +160,8 @@ public class AlignmentAnnotation
    */
   public boolean centreColLabels = false;
 
+  private boolean isrna;
+
   /*
    * (non-Javadoc)
    * 
@@ -205,7 +219,7 @@ public class AlignmentAnnotation
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
-    boolean isrna = false;
+    isrna = false;
     StringBuffer rnastring = new StringBuffer();
 
     char firstChar = 0;
@@ -301,19 +315,76 @@ public class AlignmentAnnotation
     {
       if (isrna)
       {
-        _updateRnaSecStr(rnastring.toString());
+        _updateRnaSecStr(new AnnotCharSequence());
       }
     }
 
     annotationId = this.hashCode() + "";
   }
-
-  public void setRNAStruc(String string) {
-	rnaStructure=string;	
-}
+  /**
+   * flyweight access to positions in the alignment annotation row for RNA processing
+   * @author jimp
+   *
+   */
+  private class AnnotCharSequence  implements CharSequence 
+  {
+    int offset=0;
+    int max=0;
+    
+    public AnnotCharSequence() {
+      this(0,annotations.length);
+    }
+    public AnnotCharSequence(int start, int end) {
+      offset=start;
+      max=end;
+    }
+    @Override
+    public CharSequence subSequence(int start, int end)
+    {
+      return new AnnotCharSequence(offset+start, offset+end);
+    }
+    
+    @Override
+    public int length()
+    {
+      return max-offset;
+    }
+    
+    @Override
+    public char charAt(int index)
+    {
+      String dc;
+      return ((index+offset<0) || (index+offset)>=max || annotations[index+offset]==null || (dc=annotations[index+offset].displayCharacter.trim()).length()<1)
+              ? '.' : dc.charAt(0);
+    }
+    public String toString()
+    {
+      char[] string=new char[max-offset];
+      int mx=annotations.length;
+        
+      for (int i=offset;i<mx;i++)
+      {
+        String dc;
+        string[i]=(annotations[i]==null || (dc=annotations[i].displayCharacter.trim()).length()<1 )? '.' : dc.charAt(0);
+      }
+      return new String(string);
+    }
+  };
   
+  private long _lastrnaannot=-1;
   public String getRNAStruc(){
-	  return rnaStructure;
+    if (isrna)
+    {
+      String rnastruc = new AnnotCharSequence().toString();
+      if (_lastrnaannot!=rnastruc.hashCode())
+      {
+        // ensure rna structure contacts are up to date
+        _lastrnaannot=rnastruc.hashCode();
+        _updateRnaSecStr(rnastruc);
+      }
+      return rnastruc;
+    }
+    return null;
   }
 
 /**
@@ -894,4 +965,14 @@ public class AlignmentAnnotation
     }
     return description;
   }
+
+  public boolean isValidStruc()
+  {
+    return invalidrnastruc==-1;
+  }
+  public long getInvalidStrucPos()
+  {
+    return invalidrnastruc;
+  }
+  
 }
-- 
1.7.10.2