JAL-2599 add ability to process RNA HMMer files

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

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index a7fc8b8..09092a6 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -51,19 +51,46 @@ public class HMMERColourScheme extends ResidueColourScheme
     }
     Double prob;
     prob = hmm.getMatchEmissionProbability(position, symbol);
-    double freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-    Double value = prob - freq;
-
+    double freq = 0;
+    if ("amino".equals(hmm.getAlphabetType()))
+    {
+      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);
+    }
+    else if ("RNA".equals(hmm.getAlphabetType()))
+    {
+      if (!ResidueProperties.rnaBackgroundFrequencies.containsKey(symbol))
+      {
+        return Color.white;
+      }
+      freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
+    }
+    if (prob == 0)
+    {
+      return Color.red;
+    }
+    Double value = Math.log(prob / freq);
     Color colour = null;
-    if (value >= 0)
+    if (value > 0)
     {
 
       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
-              Color.WHITE, 1f, Color.green);
+              Color.WHITE, 3f, Color.blue);
     }
     else if (value < 0)
     {
-      return Color.YELLOW;
+      return Color.ORANGE;
 
     }
     return colour;