JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 60fd25c..9b0489e 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -32,6 +32,13 @@ import java.util.Vector;
 
 public class ResidueProperties
 {
+  // alphabet names used in Hidden Markov Model files
+  public static final String ALPHABET_RNA = "RNA";
+
+  public static final String ALPHABET_DNA = "DNA";
+
+  public static final String ALPHABET_AMINO = "amino";
+
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
 
@@ -2543,7 +2550,7 @@ public class ResidueProperties
     amino.put('I', 0.0593f);
     amino.put('P', 0.0472f);
     amino.put('V', 0.0686f);
-    backgroundFrequencies.put("amino", amino);
+    backgroundFrequencies.put(ALPHABET_AMINO, amino);
     // todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
     // are they?
   }
@@ -2557,7 +2564,7 @@ public class ResidueProperties
     dna.put('C', 0.25f);
     dna.put('T', 0.25f);
     dna.put('G', 0.25f);
-    backgroundFrequencies.put("DNA", dna);
+    backgroundFrequencies.put(ALPHABET_DNA, dna);
 
   }
 
@@ -2568,7 +2575,7 @@ public class ResidueProperties
     rna.put('C', 0.25f);
     rna.put('T', 0.25f);
     rna.put('G', 0.25f);
-    backgroundFrequencies.put("RNA", rna);
+    backgroundFrequencies.put(ALPHABET_RNA, rna);
 
   }