Merge branch 'develop' into features/mchmmer

[jalview.git] / src / jalview / util / HMMProbabilityDistributionAnalyser.java

diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index c84b177..66ae552 100644 (file)
--- 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")