X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=989d62ad2cb4f5d70fce59505828399fa866451e;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=4c6e2a56a24ba992a70ba1c81d82bd69ebc50302;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 4c6e2a5..989d62a 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -57,10 +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
    */
@@ -79,15 +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)
     {
@@ -205,11 +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.
    * 
@@ -257,37 +258,37 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-    	  //System.out.println(annotations[i].secondaryStructure);
+        // 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')
+                || 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;
@@ -319,7 +320,9 @@ public class AlignmentAnnotation
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
                 && firstChar != '$'
-                && firstChar != '�' // JBPNote should explicitly express as unicode number to avoid source code translation problems
+                && firstChar != '�' // JBPNote should explicitly express as
+                                    // unicode number to avoid source code
+                                    // translation problems
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -1049,7 +1052,7 @@ 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);