JAL-2629 tidy tests, refactor hmmer node mapping slightly

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6a5e4d0..e798525 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1783,7 +1783,8 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
+        String id = ann.getCalcId();
+        if (id != null && id.equals(calcId)
                 && ann.label != null && ann.label.equals(label))
         {
           result.add(ann);
@@ -1896,18 +1897,11 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void updateHMMMapping()
   {
-    int node = 1;
-    int column = 0;
-    hmm.emptyNodeLookup();
-    for (char residue : sequence)
+    if (hmm == null)
     {
-      if (!Comparison.isGap(residue))
-      {
-        hmm.setAlignmentColumn(node, column);
-        node++;
-      }
-      column++;
+      return;
     }
+    hmm.updateMapping(sequence);
   }
 
   /**
@@ -1921,7 +1915,7 @@ public class Sequence extends ASequence implements SequenceI
     if (this.isHMMConsensusSequence)
     {
       int node = 1;
-      hmm.emptyNodeLookup();
+      hmm.clearNodeLookup();
       for (int i = 0; i < getLength(); i++)
       {
         if (rf.annotations[i].displayCharacter.equals("x")