JAL-2616 add documentation for probability analyser

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cce4e67..44d96ca 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4702,6 +4702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             Integer alpha = 0;
             final int AMINO = 0;
             final int DNA = 1;
+            final int RNA = 2;
             if ("amino".equals(hmm.getAlphabetType()))
             {
               alpha = AMINO;
@@ -4710,6 +4711,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               alpha = DNA;
             }
+            else if ("RNA".equals(hmm.getAlphabetType()))
+            {
+              alpha = RNA;
+            }
             
 
             int size = 0;
@@ -4723,16 +4728,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getCharAt(hmm.getNodeAlignmentColumn(l));
                 character = Character.toUpperCase(character);
 
-                boolean containedN;
+                boolean containedD;
+                boolean containedR;
                 boolean containedA;
 
-                containedN = ResidueProperties.nucleotideBackgroundFrequencies
+                containedD = ResidueProperties.dnaBackgroundFrequencies
                         .containsKey(character);
                 containedA = ResidueProperties.aminoBackgroundFrequencies
                         .containsKey(character);
+                containedR = ResidueProperties.rnaBackgroundFrequencies
+                        .containsKey(character);
 
                 if (!Comparison.isGap(character)
-                        && ((alpha == DNA && containedN)
+                        && ((alpha == DNA && containedD)
                                 || (alpha == AMINO && containedA)))
                 {
                   size++;
@@ -4752,11 +4760,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 character = Character.toUpperCase(character);
                 boolean containedN;
                 boolean containedA;
+                boolean containedR;
 
-                containedN = ResidueProperties.nucleotideBackgroundFrequencies
+                containedN = ResidueProperties.dnaBackgroundFrequencies
                         .containsKey(character);
                 containedA = ResidueProperties.aminoBackgroundFrequencies
                         .containsKey(character);
+                containedR = ResidueProperties.rnaBackgroundFrequencies
+                        .containsKey(character);
 
                 if (!Comparison.isGap(character)
                         && ((alpha == DNA && containedN)
@@ -4777,7 +4788,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                   if (alpha == DNA)
                   {
-                    freq = ResidueProperties.nucleotideBackgroundFrequencies
+                    freq = ResidueProperties.dnaBackgroundFrequencies
+                            .get(character);
+                  }
+                  if (alpha == RNA)
+                  {
+                    freq = ResidueProperties.rnaBackgroundFrequencies
                             .get(character);
                   }
                     Double doubleValue = Math.log(prob / freq);