JAL-2599 fix background frequency storage and correct colour scheme

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 5ea892b..046c589 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -853,18 +853,8 @@ public class AAFrequency
     for (char symbol : hmm.getSymbols())
     {
       float freq = 0f;
-      if ("amino".equals(hmm.getAlphabetType()))
-      {
-        freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-      }
-      if ("DNA".equals(hmm.getAlphabetType()))
-      {
-        freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
-      }
-      if ("RNA".equals(hmm.getAlphabetType()))
-      {
-        freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
-      }
+      freq = ResidueProperties.backgroundFrequencies
+              .get(hmm.getAlphabetType()).get(symbol);
       Double hmmProb = hmm.getMatchEmissionProbability(column, symbol);
       float prob = hmmProb.floatValue();
       informationContent += prob * (Math.log(prob / freq) / Math.log(2));
@@ -952,30 +942,12 @@ public class AAFrequency
     value = hmm.getMatchEmissionProbability(column, symbol);
     double freq;
 
-    if (AMINO.equals(alph) && removeBelowBackground)
+    freq = ResidueProperties.backgroundFrequencies.get(alph).get(symbol);
+    if (value < freq && removeBelowBackground)
     {
-      freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-      if (value < freq)
-      {
-        value = 0d;
-      }
-    }
-    else if (DNA.equals(alph) && removeBelowBackground)
-    {
-      freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
-      if (value < freq)
-      {
-        value = 0d;
-      }
-    }
-    else if (RNA.equals(alph) && removeBelowBackground)
-    {
-      freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
-      if (value < freq)
-      {
-        value = 0d;
-      }
+      return 0;
     }
+
     value = value * 10000;
     return Math.round(value.floatValue());
   }

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 113afd1..e5b242d 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -56,41 +56,26 @@ public class HMMERColourScheme extends ResidueColourScheme
     Double prob;
     prob = hmm.getMatchEmissionProbability(position, symbol);
     double freq = 0;
-    if ("amino".equals(hmm.getAlphabetType()))
+    String alpha = hmm.getAlphabetType();
+    if (!ResidueProperties.backgroundFrequencies.get(alpha).containsKey(symbol))
     {
-      if (!ResidueProperties.aminoBackgroundFrequencies.containsKey(symbol))
-      {
-        return Color.white;
-      }
-      freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-    }
-    else if ("DNA".equals(hmm.getAlphabetType()))
-    {
-      if (!ResidueProperties.dnaBackgroundFrequencies.containsKey(symbol))
-      {
-        return Color.white;
-      }
-      freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
+      return Color.white;
     }
-    else if ("RNA".equals(hmm.getAlphabetType()))
+    else
     {
-      if (!ResidueProperties.rnaBackgroundFrequencies.containsKey(symbol))
-      {
-        return Color.white;
-      }
-      freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
+      freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
     }
     if (prob == 0)
     {
       return new Color(230, 0, 0);
     }
-    Double value = Math.log(prob / freq);
+    Double value = Math.log(prob / freq) / Math.log(2);
     Color colour = null;
     if (value > 0)
     {
 
       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
-              Color.WHITE, 4.52f, Color.blue);
+              Color.WHITE, 6.52f, Color.blue);
     }
     else if (value < 0)
     {

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 8451e8a..a8b20d4 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -48,14 +48,8 @@ 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<>();
 
-  // amino acid background Frequencies
-  public static final Map<Character, Float> aminoBackgroundFrequencies = new HashMap<>();
-
-  // dna background Frequencies
-  public static final Map<Character, Float> dnaBackgroundFrequencies = new HashMap<>();
-
-  // rna background Frequencies
-  public static final Map<Character, Float> rnaBackgroundFrequencies = new HashMap<>();
+  // residue background frequencies across different alphabets
+  public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
 
   static
   {
@@ -2520,26 +2514,28 @@ public class ResidueProperties
 
   static
   {
-    aminoBackgroundFrequencies.put('A', 0.0826f);
-    aminoBackgroundFrequencies.put('Q', 0.0393f);
-    aminoBackgroundFrequencies.put('L', 0.0965f);
-    aminoBackgroundFrequencies.put('S', 0.0661f);
-    aminoBackgroundFrequencies.put('R', 0.0553f);
-    aminoBackgroundFrequencies.put('E', 0.0674f);
-    aminoBackgroundFrequencies.put('K', 0.0582f);
-    aminoBackgroundFrequencies.put('T', 0.0535f);
-    aminoBackgroundFrequencies.put('N', 0.0406f);
-    aminoBackgroundFrequencies.put('G', 0.0708f);
-    aminoBackgroundFrequencies.put('M', 0.0241f);
-    aminoBackgroundFrequencies.put('W', 0.0109f);
-    aminoBackgroundFrequencies.put('D', 0.0546f);
-    aminoBackgroundFrequencies.put('H', 0.0227f);
-    aminoBackgroundFrequencies.put('F', 0.0386f);
-    aminoBackgroundFrequencies.put('Y', 0.0292f);
-    aminoBackgroundFrequencies.put('C', 0.0137f);
-    aminoBackgroundFrequencies.put('I', 0.0593f);
-    aminoBackgroundFrequencies.put('P', 0.0472f);
-    aminoBackgroundFrequencies.put('V', 0.0686f);
+    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("amino", amino);
 
   }
 
@@ -2547,19 +2543,23 @@ public class ResidueProperties
 
   static
   {
-    dnaBackgroundFrequencies.put('A', 0.25f);
-    dnaBackgroundFrequencies.put('C', 0.25f);
-    dnaBackgroundFrequencies.put('T', 0.25f);
-    dnaBackgroundFrequencies.put('G', 0.25f);
+    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("DNA", dna);
 
   }
 
   static
   {
-    rnaBackgroundFrequencies.put('A', 0.25f);
-    rnaBackgroundFrequencies.put('C', 0.25f);
-    rnaBackgroundFrequencies.put('T', 0.25f);
-    rnaBackgroundFrequencies.put('G', 0.25f);
+    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("RNA", rna);
 
   }
 

diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index 24b3bc3..c84b177 100644 (file)
--- a/src/jalview/util/HMMProbabilityDistributionAnalyser.java
+++ b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
@@ -372,7 +372,7 @@ public class HMMProbabilityDistributionAnalyser
         alignPos = hmm.getNodeAlignmentColumn(length);
 
         symbol = sequences.get(width).getCharAt(alignPos);
-        if (ResidueProperties.aminoBackgroundFrequencies
+        if (ResidueProperties.backgroundFrequencies.get("amino")
                 .containsKey(symbol))
         {
           count++;
@@ -406,14 +406,15 @@ public class HMMProbabilityDistributionAnalyser
         alignPos = hmm.getNodeAlignmentColumn(length);
         
         symbol = sequences.get(width).getCharAt(alignPos);
-        if (ResidueProperties.aminoBackgroundFrequencies
+        if (ResidueProperties.backgroundFrequencies.get("amino")
                 .containsKey(symbol))
         {
           Double prob;
           Float bfreq;
           Double llr;
           prob = hmm.getMatchEmissionProbability(alignPos, symbol);
-          bfreq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
+          bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+                  .get(symbol);
           if (prob == 0 || bfreq == 0)
           {
             System.out.println("error");