X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=1376b11a5e3f86174914907977c7d3b7c657a58d;hb=fca189f1ddefa155881dedeeb0f21c1cd0905e74;hp=2f5f2704b8842a15d824c2b00c1eb4a60a74172c;hpb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2f5f270..1376b11 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,23 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
 import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
@@ -55,6 +58,7 @@ public class AlignmentAnnotation
   
   
 
+  public ArrayList<SimpleBP> bps=null;
   /**
    * RNA secondary structure contact positions
    */
@@ -73,13 +77,15 @@ public class AlignmentAnnotation
    */
   private void _updateRnaSecStr(CharSequence RNAannot)
   {
-    try
-    {
-      _rnasecstr = Rna.GetBasePairs(RNAannot);
-      invalidrnastruc = -1;
-    } catch (WUSSParseException px)
+    try {
+    _rnasecstr = Rna.GetBasePairs(RNAannot);
+    bps = Rna.GetModeleBP(RNAannot);
+    invalidrnastruc=-1;
+    }
+    catch (WUSSParseException px)
     {
-      invalidrnastruc = px.getProblemPos();
+      // DEBUG System.out.println(px);
+      invalidrnastruc=px.getProblemPos();
     }
     if (invalidrnastruc > -1)
     {
@@ -197,7 +203,11 @@ public class AlignmentAnnotation
       return NO_GRAPH;
     }
   }
-
+    // JBPNote: what does this do ?
+  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+  {
+	  bps = Rna.GetModeleBP(RNAannot);
+  }
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -254,10 +264,10 @@ public class AlignmentAnnotation
         		|| annotations[i].secondaryStructure == 'B'
         		|| annotations[i].secondaryStructure == 'C'
         		|| annotations[i].secondaryStructure == 'D'
-        		|| annotations[i].secondaryStructure == '1'
+        		|| annotations[i].secondaryStructure == 'E'
         		|| annotations[i].secondaryStructure == 'F'
         		|| annotations[i].secondaryStructure == 'G'
-        		|| annotations[i].secondaryStructure == '2'
+        		|| annotations[i].secondaryStructure == 'H'
         		|| annotations[i].secondaryStructure == 'I'
         		|| annotations[i].secondaryStructure == 'J'
         		|| annotations[i].secondaryStructure == 'K'
@@ -306,8 +316,8 @@ public class AlignmentAnnotation
                 // &&
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
-                && firstChar != 'H'
-                && firstChar != 'E'
+                && firstChar != '$'
+                && firstChar != 'µ' // JBPNote should explicitly express as unicode number to avoid source code translation problems
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -316,10 +326,10 @@ public class AlignmentAnnotation
                 && firstChar != 'B'
                 && firstChar != 'C'
                 && firstChar != 'D'
-                && firstChar != '1'
+                && firstChar != 'E'
                 && firstChar != 'F'
                 && firstChar != 'G'
-                && firstChar != '2'
+                && firstChar != 'H'
                 && firstChar != 'I'
                 && firstChar != 'J'
                 && firstChar != 'K'
@@ -516,7 +526,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-    _linecolour=null;
+    _linecolour = null;
     if (min == max)
     {
       min = 999999999;
@@ -621,7 +631,14 @@ public class AlignmentAnnotation
       this.annotations = new Annotation[ann.length];
       for (int i = 0; i < ann.length; i++)
       {
-        annotations[i] = new Annotation(ann[i]);
+        if (ann[i] != null)
+        {
+          annotations[i] = new Annotation(ann[i]);
+          if (_linecolour != null)
+          {
+            _linecolour = annotations[i].colour;
+          }
+        }
       }
       ;
       if (annotation.sequenceRef != null)