add partial button fix to annotation and statistics output

[jalview.git] / src / jalview / datamodel / HiddenMarkovModel.java

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index bcfa1c9..4514a41 100644 (file)
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -16,6 +16,8 @@ import java.util.Scanner;
  */
 public class HiddenMarkovModel
 {
+
+
   // Stores file properties. Do not directly access this field as it contains
   // only string value - use the getter methods. For example, to find the length
   // of theHMM, use getModelLength()to return an int value
@@ -378,7 +380,7 @@ public class HiddenMarkovModel
   public Integer getNodeAlignmentColumn(int nodeIndex)
   {
     Integer value = nodes.get(nodeIndex).getAlignmentColumn();
-   return value;
+    return value - 1;
   }
   
   public char getConsensusResidue(int nodeIndex)