X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=601339acc1f84b1af5117b2341465d4636f4944f;hb=01695c742a6ff14ef4928fc305e6d2a30035f9ac;hp=e39c0b781610b56f3e2be9fdaac1f516e76c3935;hpb=0e2054d29bc49351f000d478659dc3c4371b251c;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e39c0b7..601339a 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * 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.
+ * 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/>.
+ * 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;
@@ -55,10 +57,9 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
-  
-  
 
-  public ArrayList<SimpleBP> bps=null;
+  public ArrayList<SimpleBP> bps = null;
+
   /**
    * RNA secondary structure contact positions
    */
@@ -77,15 +78,15 @@ public class AlignmentAnnotation
    */
   private void _updateRnaSecStr(CharSequence RNAannot)
   {
-    try {
-    _rnasecstr = Rna.GetBasePairs(RNAannot);
-    bps = Rna.GetModeleBP(RNAannot);
-    invalidrnastruc=-1;
-    }
-    catch (WUSSParseException px)
+    try
+    {
+      _rnasecstr = Rna.GetBasePairs(RNAannot);
+      bps = Rna.GetModeleBP(RNAannot);
+      invalidrnastruc = -1;
+    } catch (WUSSParseException px)
     {
       // DEBUG System.out.println(px);
-      invalidrnastruc=px.getProblemPos();
+      invalidrnastruc = px.getProblemPos();
     }
     if (invalidrnastruc > -1)
     {
@@ -203,11 +204,13 @@ public class AlignmentAnnotation
       return NO_GRAPH;
     }
   }
-    // JBPNote: what does this do ?
+
+  // JBPNote: what does this do ?
   public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
   {
-	  bps = Rna.GetModeleBP(RNAannot);
+    bps = Rna.GetModeleBP(RNAannot);
   }
+
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -255,37 +258,38 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-    	  //System.out.println(annotations[i].secondaryStructure);
+        // System.out.println(annotations[i].secondaryStructure);
+        // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
         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')
+                || 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;
@@ -317,7 +321,7 @@ public class AlignmentAnnotation
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
                 && firstChar != '$'
-                && firstChar != 'µ' // JBPNote should explicitly express as unicode number to avoid source code translation problems
+                && firstChar != 0xCE
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -1047,7 +1051,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] == null)
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
-                  ' ', 0f,null);
+                  ' ', 0f, null);
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
           annotations[i].displayCharacter = String.valueOf(gapchar);
@@ -1108,4 +1112,9 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
+
+  public boolean isRNA()
+  {
+    return isrna;
+  }
 }