Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 5f84ca0..0b62bb6 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -34,6 +34,13 @@ 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
 
@@ -50,6 +57,9 @@ 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];
@@ -2270,6 +2280,58 @@ 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);