From 6c7cac79652fa6c7050311f73f36b9a9d05e6a6b Mon Sep 17 00:00:00 2001 From: tva Date: Wed, 5 Jun 2019 16:28:34 +0100 Subject: [PATCH] JAL-3285 delete duplicate variables in AlignmentViewport from merge --- src/jalview/viewmodel/AlignmentViewport.java | 35 -------------------------- 1 file changed, 35 deletions(-) diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 1a9684f..23c1d00 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -108,33 +108,11 @@ public abstract class AlignmentViewport * alignment */ - private Map hiddenRepSequences; - - protected ColumnSelection colSel = new ColumnSelection(); - - public boolean autoCalculateConsensus = true; - - protected boolean autoCalculateStrucConsensus = true; - - protected boolean ignoreGapsInConsensusCalculation = false; - protected boolean ignoreBelowBackGroundFrequencyCalculation = false; protected boolean infoLetterHeight = false; - protected ResidueShaderI residueShading = new ResidueShader(); - - protected AlignmentAnnotation consensus; - - protected AlignmentAnnotation complementConsensus; - protected AlignmentAnnotation occupancy; - - protected AlignmentAnnotation strucConsensus; - - protected AlignmentAnnotation conservation; - - protected AlignmentAnnotation quality; /** * results of alignment consensus analysis for visible portion of view @@ -146,19 +124,6 @@ public abstract class AlignmentViewport */ protected ProfilesI hmmProfiles; - /** - * results of cDNA complement consensus visible portion of view - */ - protected Hashtable[] hcomplementConsensus; - - /** - * results of secondary structure base pair consensus for visible portion of - * view - */ - protected Hashtable[] hStrucConsensus; - - protected Conservation hconservation; - public AlignmentViewport(AlignmentI al) { setAlignment(al); -- 1.7.10.2