X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=1376b11a5e3f86174914907977c7d3b7c657a58d;hb=5ba9b9ce2c9b6e887430d4ac80efde577ca434d4;hp=82e8ae4c2993e2bb45c48ca78d43ce9b49cc495a;hpb=26ca64941c8b2c5d0d141b4212bfbc5a61e15b05;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 82e8ae4..1376b11 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,28 +1,34 @@
 /*
- * 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;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * DOCUMENT ME!
  * 
@@ -49,7 +55,10 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
+  
+  
 
+  public ArrayList<SimpleBP> bps=null;
   /**
    * RNA secondary structure contact positions
    */
@@ -68,13 +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)
     {
@@ -192,7 +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.
    * 
@@ -240,7 +255,37 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-        if (annotations[i].secondaryStructure == 'S')
+    	  //System.out.println(annotations[i].secondaryStructure);
+        if (annotations[i].secondaryStructure == '('
+        		|| annotations[i].secondaryStructure == '['
+        		|| annotations[i].secondaryStructure == '<'
+        		|| annotations[i].secondaryStructure == '{'
+        		|| annotations[i].secondaryStructure == 'A'
+        		|| annotations[i].secondaryStructure == 'B'
+        		|| annotations[i].secondaryStructure == 'C'
+        		|| annotations[i].secondaryStructure == 'D'
+        		|| annotations[i].secondaryStructure == 'E'
+        		|| annotations[i].secondaryStructure == 'F'
+        		|| annotations[i].secondaryStructure == 'G'
+        		|| annotations[i].secondaryStructure == 'H'
+        		|| annotations[i].secondaryStructure == 'I'
+        		|| annotations[i].secondaryStructure == 'J'
+        		|| annotations[i].secondaryStructure == 'K'
+        		|| annotations[i].secondaryStructure == 'L'
+        		|| annotations[i].secondaryStructure == 'M'
+        		|| annotations[i].secondaryStructure == 'N'
+        		|| annotations[i].secondaryStructure == 'O'
+        		|| annotations[i].secondaryStructure == 'P'
+        		|| annotations[i].secondaryStructure == 'Q'
+        		|| annotations[i].secondaryStructure == 'R'
+        		|| annotations[i].secondaryStructure == 'S'
+        		|| annotations[i].secondaryStructure == 'T'
+        		|| annotations[i].secondaryStructure == 'U'
+        		|| annotations[i].secondaryStructure == 'V'
+        		|| annotations[i].secondaryStructure == 'W'
+        		|| annotations[i].secondaryStructure == 'X'
+        		|| annotations[i].secondaryStructure == 'Y'
+        		|| annotations[i].secondaryStructure == 'Z')
         {
           hasIcons |= true;
           isrna |= true;
@@ -271,9 +316,38 @@ public class AlignmentAnnotation
                 // &&
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
-                && firstChar != 'H'
+                && firstChar != '$'
+                && firstChar != 'µ' // JBPNote should explicitly express as unicode number to avoid source code translation problems
+                && firstChar != '('
+                && firstChar != '['
+                && firstChar != '>'
+                && firstChar != '{'
+                && firstChar != 'A'
+                && firstChar != 'B'
+                && firstChar != 'C'
+                && firstChar != 'D'
                 && firstChar != 'E'
+                && firstChar != 'F'
+                && firstChar != 'G'
+                && firstChar != 'H'
+                && firstChar != 'I'
+                && firstChar != 'J'
+                && firstChar != 'K'
+                && firstChar != 'L'
+                && firstChar != 'M'
+                && firstChar != 'N'
+                && firstChar != 'O'
+                && firstChar != 'P'
+                && firstChar != 'Q'
+                && firstChar != 'R'
                 && firstChar != 'S'
+                && firstChar != 'T'
+                && firstChar != 'U'
+                && firstChar != 'V'
+                && firstChar != 'W'
+                && firstChar != 'X'
+                && firstChar != 'Y'
+                && firstChar != 'Z'
                 && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
@@ -452,7 +526,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-    _linecolour=null;
+    _linecolour = null;
     if (min == max)
     {
       min = 999999999;
@@ -508,7 +582,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] != null)
         {
-          annotations[i].displayCharacter = "";
+          annotations[i].displayCharacter = "X";
         }
       }
     }
@@ -557,10 +631,10 @@ public class AlignmentAnnotation
       this.annotations = new Annotation[ann.length];
       for (int i = 0; i < ann.length; i++)
       {
-        if (ann[i]!=null)
+        if (ann[i] != null)
         {
           annotations[i] = new Annotation(ann[i]);
-          if (_linecolour!=null)
+          if (_linecolour != null)
           {
             _linecolour = annotations[i].colour;
           }
@@ -973,7 +1047,7 @@ 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);
@@ -1034,5 +1108,4 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
-
 }