JAL-1674 update both status bars when mousing over linked sequences

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index aca75b7..4bb246a 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -20,12 +20,14 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.FeatureScoreModel;
 import jalview.analysis.scoremodels.PIDScoreModel;
 import jalview.api.analysis.ScoreModelI;
 
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -42,11 +44,11 @@ public class ResidueProperties
 
   public static final int[] purinepyrimidineIndex;
 
-  public static final Hashtable aa3Hash = new Hashtable();
+  public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
 
-  public static final Hashtable aa2Triplet = new Hashtable();
+  public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
 
-  public static final Hashtable nucleotideName = new Hashtable();
+  public static final Map<String, String> nucleotideName = new HashMap<String, String>();
 
   static
   {
@@ -675,6 +677,8 @@ public class ResidueProperties
 
   public static Vector STOP = new Vector();
 
+  public static String START = "ATG";
+
   static
   {
     codonHash.put("K", Lys);
@@ -1498,6 +1502,7 @@ 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()
@@ -1519,7 +1524,7 @@ public class ResidueProperties
     return hyd;
   }
 
-  public static Hashtable getAA3Hash()
+  public static Map<String, Integer> getAA3Hash()
   {
     return aa3Hash;
   }
@@ -1699,7 +1704,9 @@ 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 +1770,15 @@ 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 +1799,8 @@ 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 +1810,11 @@ 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)