X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=593e83db10bbd1eefe0a75b1fbd4c8012aeb4811;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=aca75b742694e8ae6fc665cdf29e049e0ed174a3;hpb=f6483e3414133aeadc65a9fb24f1b81cbbf3f39f;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index aca75b7..593e83d 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.FeatureScoreModel;
 import jalview.analysis.scoremodels.PIDScoreModel;
 import jalview.api.analysis.ScoreModelI;
 
@@ -1498,6 +1499,7 @@ public class ResidueProperties
     // scoreMatrices.put("Conservation EnhPos", new
     // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
     scoreMatrices.put("PID", new PIDScoreModel());
+    scoreMatrices.put("Displayed Features", new FeatureScoreModel());
   }
 
   private ResidueProperties()
@@ -1699,7 +1701,9 @@ public class ResidueProperties
    * Used by getRNASecStrucState
    * 
    */
-  public static Hashtable toRNAssState;
+  public static Hashtable<String, String> toRNAssState;
+
+  public static boolean RNAcloseParen[] = new boolean[255];
   static
   {
     toRNAssState = new Hashtable<String, String>();
@@ -1763,7 +1767,15 @@ public class ResidueProperties
     toRNAssState.put("y", "Y");
     toRNAssState.put("Z", "Z");
     toRNAssState.put("z", "Z");
-
+    for (int p = 0; p < RNAcloseParen.length; p++)
+    {
+      RNAcloseParen[p] = false;
+    }
+    for (String k : toRNAssState.keySet())
+    {
+      RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+              .charAt(0);
+    }
   }
 
   /**
@@ -1784,7 +1796,8 @@ public class ResidueProperties
       String ssc = ssstring.substring(i, i + 1);
       if (toRNAssState.containsKey(ssc))
       {
-        ss.append((String) toRNAssState.get(ssc));
+        // valid ss character - so return it
+        ss.append(ssc); // (String) toRNAssState.get(ssc));
       }
       else
       {
@@ -1794,6 +1807,11 @@ public class ResidueProperties
     return ss.toString();
   }
 
+  public static boolean isCloseParenRNA(char dc)
+  {
+    return RNAcloseParen[dc];
+  }
+
   // main method generates perl representation of residue property hash
   // / cut here
   public static void main(String[] args)