JAL-2416 scoreMatrices removed from ResidueProperties

[jalview.git] / src / jalview / analysis / scoremodels / ScoreModels.java

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 377fdef..07840fc 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -14,8 +14,17 @@ import java.util.Map;
  */
 public class ScoreModels
 {
-  private static ScoreModels instance = new ScoreModels();
+  /*
+   * constants for built-in score model names
+   * NB! these have to match names in loaded score matrix files
+   */
+  public static final String BLOSUM62 = "BLOSUM62";
+
+  public static final String PAM250 = "PAM250";
 
+  public static final String DNA = "DNA";
+
+  private static ScoreModels instance = new ScoreModels();
   private Map<String, ScoreModelI> models;
 
   public static ScoreModels getInstance()
@@ -99,4 +108,17 @@ public class ScoreModels
     }
     models.put(sm.getName(), sm);
   }
+
+  /**
+   * Returns the default peptide or nucleotide score model, currently BLOSUM62
+   * or DNA
+   * 
+   * @param forPeptide
+   * @return
+   */
+  public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+  {
+    return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
+            : forName("DNA"));
+  }
 }