JAL-2717 JAL-2668 fixes to HMMER colour scheme display names, enabled state, test...

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

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 581f481..eb68d09 100644 (file)
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -485,6 +485,14 @@ public class HiddenMarkovModel
     nodeLookup.put(column, node);
   }
 
+  /**
+   * Updates the mapping of nodes of the HMM to non-gapped positions of the
+   * sequence. Nodes 1, 2, 3... are mapped to the columns occupied by the first,
+   * second, third... residues of the sequence. The 'begin' node (node 0) of the
+   * HMM is not mapped.
+   * 
+   * @param sequence
+   */
   public void updateMapping(char[] sequence)
   {
     int nodeNo = 1;