JAL-2668 add tests for HMMER commands, annotation and io

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 54fa3b0..0da30ba 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -51,12 +51,16 @@ public class Sequence extends ASequence implements SequenceI
 
   private char[] sequence;
 
+  int previousPosition;
+
   String description;
 
   int start;
 
   int end;
 
+  boolean hasInfo;
+
   HiddenMarkovModel hmm;
 
   boolean isHMMConsensusSequence = false;
@@ -1529,6 +1533,43 @@ public class Sequence extends ASequence implements SequenceI
     this.isHMMConsensusSequence = isHMMConsensusSequence;
   }
 
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    return hasInfo;
+    /*
+    if (annotation == null)
+    {
+      return false;
+    }
+    
+    for (AlignmentAnnotation annot : annotation)
+    {
+      if (annot.label.contains("_HMM"))
+      {
+        return true;
+      }
+    }
+    return false;
+    */
+  }
+
+  @Override
+  public void setHasInfo(boolean status)
+  {
+    hasInfo = true;
+  }
+
+  @Override
+  public int getPreviousPosition()
+  {
+    return previousPosition;
+  }
 
+  @Override
+  public void setPreviousPosition(int previousPosition)
+  {
+    this.previousPosition = previousPosition;
+  }
 
 }