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JAL-3285 delete duplicate variables in AlignmentViewport from merge
author
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 15:28:34 +0000
(16:28 +0100)
committer
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 15:28:34 +0000
(16:28 +0100)
src/jalview/viewmodel/AlignmentViewport.java
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diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
1a9684f
..
23c1d00
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-108,33
+108,11
@@
public abstract class AlignmentViewport
* alignment
*/
* alignment
*/
- private Map<SequenceI, SequenceCollectionI> 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 boolean ignoreBelowBackGroundFrequencyCalculation = false;
protected boolean infoLetterHeight = false;
- protected ResidueShaderI residueShading = new ResidueShader();
-
- protected AlignmentAnnotation consensus;
-
- protected AlignmentAnnotation complementConsensus;
-
protected AlignmentAnnotation occupancy;
protected AlignmentAnnotation occupancy;
-
- protected AlignmentAnnotation strucConsensus;
-
- protected AlignmentAnnotation conservation;
-
- protected AlignmentAnnotation quality;
/**
* results of alignment consensus analysis for visible portion of view
/**
* results of alignment consensus analysis for visible portion of view
@@
-146,19
+124,6
@@
public abstract class AlignmentViewport
*/
protected ProfilesI hmmProfiles;
*/
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);
public AlignmentViewport(AlignmentI al)
{
setAlignment(al);