JAL-2629 hmmer searches include seqs past inclusion threshold in output

[jalview.git] / src / jalview / schemes / HmmerGlobalBackground.java

diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
index 31bcadf..a24b7ab 100644 (file)
--- a/src/jalview/schemes/HmmerGlobalBackground.java
+++ b/src/jalview/schemes/HmmerGlobalBackground.java
@@ -1,5 +1,6 @@
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 
@@ -58,4 +59,15 @@ public class HmmerGlobalBackground extends HmmerColourScheme
     return MAX_LOG_RATIO;
   }
 
+  /**
+   * Answers a new colour scheme instance based on the HMM of the first sequence
+   * in alignment that has an HMM
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI ac)
+  {
+    return newInstance(ac);
+  }
+
 }