From aabd13b02d9ad42455832e56e08ed7a5aaff0415 Mon Sep 17 00:00:00 2001 From: tva Date: Thu, 6 Jun 2019 10:20:33 +0100 Subject: [PATCH] JAL-3285 code changes to HMMER colour schemes not included in merge --- src/jalview/schemes/HmmerColourScheme.java | 6 +++--- src/jalview/schemes/HmmerGlobalBackground.java | 12 ++++++++++++ 2 files changed, 15 insertions(+), 3 deletions(-) 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 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); + } + } -- 1.7.10.2