Merge branch 'develop' into menard

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 6212d4d..2f5f270 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,9 +20,12 @@ package jalview.datamodel;
 import jalview.analysis.Rna;
 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!
  * 
@@ -49,6 +52,8 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
+  
+  
 
   /**
    * RNA secondary structure contact positions
@@ -240,7 +245,37 @@ 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 == '1'
+                       || annotations[i].secondaryStructure == 'F'
+                       || annotations[i].secondaryStructure == 'G'
+                       || annotations[i].secondaryStructure == '2'
+                       || 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;
@@ -273,7 +308,36 @@ public class AlignmentAnnotation
                 firstChar != ' '
                 && firstChar != 'H'
                 && firstChar != 'E'
+                && firstChar != '('
+                && firstChar != '['
+                && firstChar != '>'
+                && firstChar != '{'
+                && firstChar != 'A'
+                && firstChar != 'B'
+                && firstChar != 'C'
+                && firstChar != 'D'
+                && firstChar != '1'
+                && firstChar != 'F'
+                && firstChar != 'G'
+                && firstChar != '2'
+                && 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)
         {
@@ -508,7 +572,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] != null)
         {
-          annotations[i].displayCharacter = "";
+          annotations[i].displayCharacter = "X";
         }
       }
     }
@@ -966,7 +1030,7 @@ 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);
@@ -1027,5 +1091,4 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
-
 }