JAL-2629 some tidying of Hmmer commands (wip)

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 10ae253..04f34dd 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -353,7 +353,7 @@ public class AAFrequency
    */
   public static float completeInformation(AlignmentAnnotation information,
           ProfilesI profiles, int startCol, int endCol, long nseq,
-          Float currentMax)
+          float currentMax)
   {
     // long now = System.currentTimeMillis();
     if (information == null || information.annotations == null
@@ -366,48 +366,40 @@ public class AAFrequency
       return 0;
     }
 
-    Float max = 0f;
+    float max = 0f;
+    SequenceI hmmSeq = information.sequenceRef;
+    HiddenMarkovModel hmm = hmmSeq.getHMM();
 
-    for (int i = startCol; i < endCol; i++)
+    for (int column = startCol; column < endCol; column++)
     {
-      ProfileI profile = profiles.get(i);
+      ProfileI profile = profiles.get(column);
       if (profile == null)
       {
         /*
          * happens if sequences calculated over were 
          * shorter than alignment width
          */
-        information.annotations[i] = null;
-        return 0;
+        information.annotations[column] = null;
+        return 0f;
       }
       
-      SequenceI hmmSeq = information.sequenceRef;
-      
-      HiddenMarkovModel hmm = hmmSeq.getHMM();
-      
-      float value = hmm.getInformationContent(i);
-
-      if (value > max)
+      float value = hmm.getInformationContent(column);
+      if (!Float.isNaN(value))
       {
-        max = value;
+        max = Math.max(max, value);
       }
 
-      String description = value + " bits";
-      information.annotations[i] = new Annotation(
+      String description = Float.isNaN(value) ? null
+              : String.format("%.4f bits", value);
+      information.annotations[column] = new Annotation(
               Character.toString(Character
-                      .toUpperCase(hmm.getConsensusAtAlignColumn(i))),
+                      .toUpperCase(hmm.getConsensusAtAlignColumn(column))),
               description, ' ', value);
     }
-    if (max > currentMax)
-    {
-      information.graphMax = max;
-      return max;
-    }
-    else
-    {
-      information.graphMax = currentMax;
-      return currentMax;
-    }
+
+    max = Math.max(max, currentMax);
+    information.graphMax = max;
+    return max;
   }
 
   /**