update spikes/mungo from JAL-3076 patch branch

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 9b0489e..a4e6480 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -32,13 +32,6 @@ 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
 
@@ -55,9 +48,6 @@ public class ResidueProperties
   // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
   public static final Map<String, String> modifications = new HashMap<>();
 
-  // residue background frequencies across different alphabets
-  public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
-
   static
   {
     aaIndex = new int[255];
@@ -2527,58 +2517,6 @@ public class ResidueProperties
 
   }
 
-  static
-  {
-    Map<Character, Float> amino = new HashMap<>();
-    amino.put('A', 0.0826f);
-    amino.put('Q', 0.0393f);
-    amino.put('L', 0.0965f);
-    amino.put('S', 0.0661f);
-    amino.put('R', 0.0553f);
-    amino.put('E', 0.0674f);
-    amino.put('K', 0.0582f);
-    amino.put('T', 0.0535f);
-    amino.put('N', 0.0406f);
-    amino.put('G', 0.0708f);
-    amino.put('M', 0.0241f);
-    amino.put('W', 0.0109f);
-    amino.put('D', 0.0546f);
-    amino.put('H', 0.0227f);
-    amino.put('F', 0.0386f);
-    amino.put('Y', 0.0292f);
-    amino.put('C', 0.0137f);
-    amino.put('I', 0.0593f);
-    amino.put('P', 0.0472f);
-    amino.put('V', 0.0686f);
-    backgroundFrequencies.put(ALPHABET_AMINO, amino);
-    // todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
-    // are they?
-  }
-
-  // TODO get correct frequencies
-
-  static
-  {
-    Map<Character, Float> dna = new HashMap<>();
-    dna.put('A', 0.25f);
-    dna.put('C', 0.25f);
-    dna.put('T', 0.25f);
-    dna.put('G', 0.25f);
-    backgroundFrequencies.put(ALPHABET_DNA, dna);
-
-  }
-
-  static
-  {
-    Map<Character, Float> rna = new HashMap<>();
-    rna.put('A', 0.25f);
-    rna.put('C', 0.25f);
-    rna.put('T', 0.25f);
-    rna.put('G', 0.25f);
-    backgroundFrequencies.put(ALPHABET_RNA, rna);
-
-  }
-
   public static String getCanonicalAminoAcid(String aA)
   {
     String canonical = modifications.get(aA);