X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FHMMProbabilityDistributionAnalyser.java;h=66ae5526e7c5cce7a2e49eefc6a8e00872f77f2b;hb=09b8644607fb5b9debbfe39a7177922b0e66aa9a;hp=24b3bc3cbf288e41da1430b58c841b6fb79f2dd5;hpb=64c257f9df3d4e15e56d46ec580407b383a8c75e;p=jalview.git

diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index 24b3bc3..66ae552 100644
--- a/src/jalview/util/HMMProbabilityDistributionAnalyser.java
+++ b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
@@ -185,7 +185,8 @@ public class HMMProbabilityDistributionAnalyser
    *          The number of families to read before saving.
    * @throws IOException
    */
-  public void runToEnd(boolean keepRawData, boolean forClans)
+  public void runToEnd(int minCount, int maxCount, boolean keepRawData,
+          boolean forClans)
           throws IOException
   {
     keepRaw = keepRawData;
@@ -241,7 +242,10 @@ public class HMMProbabilityDistributionAnalyser
           readHMM(inputHMM);
 
         int count = countValidResidues();
-        processData(count);
+            if (count >= minCount && count < maxCount)
+            {
+              processData(count);
+            }
         filesRead++;
           System.out.println(filesRead);
       endReached = atEnd(inputSTO);
@@ -369,10 +373,10 @@ public class HMMProbabilityDistributionAnalyser
       {
         char symbol;
         int alignPos;
-        alignPos = hmm.getNodeAlignmentColumn(length);
+        alignPos = hmm.getNodeMapPosition(length);
 
         symbol = sequences.get(width).getCharAt(alignPos);
-        if (ResidueProperties.aminoBackgroundFrequencies
+        if (ResidueProperties.backgroundFrequencies.get("amino")
                 .containsKey(symbol))
         {
           count++;
@@ -403,17 +407,18 @@ public class HMMProbabilityDistributionAnalyser
       {
         char symbol;
         int alignPos;
-        alignPos = hmm.getNodeAlignmentColumn(length);
+        alignPos = hmm.getNodeMapPosition(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");