JAL-1473 refactor score matrices and tree score calculations to interface/api and...

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 62e46be..98be0c8 100755 (executable)
--- 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,17 +14,20 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
+
 import java.util.*;
 import java.util.List;
-
 import java.awt.*;
 
 public class ResidueProperties
 {
-  public static Hashtable scoreMatrices = new Hashtable();
+  public static Hashtable<String,ScoreModelI> scoreMatrices = new Hashtable();
 
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
@@ -813,13 +816,13 @@ public class ResidueProperties
     codonHash2.put("AAC", "N");
     codonHash2.put("AAT", "N");
 
-    codonHash2.put("CAA", "E");
-    codonHash2.put("CAG", "E");
+    codonHash2.put("CAA", "Q");
+    codonHash2.put("CAG", "Q");
     codonHash2.put("CAC", "H");
     codonHash2.put("CAT", "H");
 
-    codonHash2.put("GAA", "Q");
-    codonHash2.put("GAG", "Q");
+    codonHash2.put("GAA", "E");
+    codonHash2.put("GAG", "E");
     codonHash2.put("GAC", "D");
     codonHash2.put("GAT", "D");
 
@@ -827,9 +830,9 @@ public class ResidueProperties
     codonHash2.put("TAT", "Y");
 
     codonHash2.put("ACA", "T");
-    codonHash2.put("AAG", "T");
     codonHash2.put("ACC", "T");
     codonHash2.put("ACT", "T");
+    codonHash2.put("ACG", "T");
 
     codonHash2.put("CCA", "P");
     codonHash2.put("CCG", "P");
@@ -1415,6 +1418,10 @@ public class ResidueProperties
     propHash.put("proline", proline);
     propHash.put("polar", polar);
   }
+  static
+  {
+    scoreMatrices.put("PID", new PIDScoreModel());
+  }
 
   private ResidueProperties()
   {
@@ -1539,12 +1546,22 @@ public class ResidueProperties
   public static ScoreMatrix getScoreMatrix(String pwtype)
   {
     Object val = scoreMatrices.get(pwtype);
-    if (val != null)
+    if (val != null && val instanceof ScoreMatrix)
     {
       return (ScoreMatrix) val;
     }
     return null;
   }
+  /**
+   * get a ScoreModel based on its string name
+   * 
+   * @param pwtype
+   * @return scoremodel of type pwtype or null
+   */
+  public static ScoreModelI getScoreModel(String pwtype)
+  {
+    return scoreMatrices.get(pwtype);
+  }
 
   public static int getPAM250(char c, char d)
   {