From: tva <tva@10.205.251.175>
Date: Thu, 6 Jun 2019 09:20:33 +0000 (+0100)
Subject: JAL-3285 code changes to HMMER colour schemes not included in merge
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=aabd13b02d9ad42455832e56e08ed7a5aaff0415

JAL-3285 code changes to HMMER colour schemes not included in merge
---

diff --git a/src/jalview/schemes/HmmerColourScheme.java b/src/jalview/schemes/HmmerColourScheme.java
index 0f81ec1..05c9b66 100644
--- a/src/jalview/schemes/HmmerColourScheme.java
+++ b/src/jalview/schemes/HmmerColourScheme.java
@@ -1,8 +1,8 @@
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.HiddenMarkovModel;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
@@ -145,8 +145,8 @@ public abstract class HmmerColourScheme extends ResidueColourScheme
    * in ac that has an HMM
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI ac,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI ac)
   {
     return newInstance(ac);
   }
diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
index 31bcadf..a24b7ab 100644
--- 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);
+  }
+
 }