X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FHMMProbabilityDistributionAnalyser.java;h=66ae5526e7c5cce7a2e49eefc6a8e00872f77f2b;hb=467426ae84382a85861a38d91e4f69f86c53e4c8;hp=c84b177a8dfb95166e105545d359e98197fc66f0;hpb=93b7c00c600a36f81c9a5f251366ed09ceae7597;p=jalview.git

diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index c84b177..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);
@@ -369,7 +373,7 @@ public class HMMProbabilityDistributionAnalyser
       {
         char symbol;
         int alignPos;
-        alignPos = hmm.getNodeAlignmentColumn(length);
+        alignPos = hmm.getNodeMapPosition(length);
 
         symbol = sequences.get(width).getCharAt(alignPos);
         if (ResidueProperties.backgroundFrequencies.get("amino")
@@ -403,7 +407,7 @@ public class HMMProbabilityDistributionAnalyser
       {
         char symbol;
         int alignPos;
-        alignPos = hmm.getNodeAlignmentColumn(length);
+        alignPos = hmm.getNodeMapPosition(length);
         
         symbol = sequences.get(width).getCharAt(alignPos);
         if (ResidueProperties.backgroundFrequencies.get("amino")