From 4548727494c3bf521eeec90a07e3bc6c0bdfb64e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 10 Jun 2022 12:52:49 +0100 Subject: [PATCH] JAL-1551 formatting --- src/jalview/datamodel/Alignment.java | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 9825bff..ea04361 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -20,13 +20,6 @@ */ package jalview.datamodel; -import jalview.analysis.AlignmentUtils; -import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; -import jalview.io.FastaFile; -import jalview.util.Comparison; -import jalview.util.LinkedIdentityHashSet; -import jalview.util.MessageManager; - import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; @@ -41,6 +34,13 @@ import java.util.Map; import java.util.Set; import java.util.Vector; +import jalview.analysis.AlignmentUtils; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; +import jalview.io.FastaFile; +import jalview.util.Comparison; +import jalview.util.LinkedIdentityHashSet; +import jalview.util.MessageManager; + /** * Data structure to hold and manipulate a multiple sequence alignment */ @@ -1915,11 +1915,12 @@ public class Alignment implements AlignmentI, AutoCloseable @Override public boolean setHiddenColumns(HiddenColumns cols) { - boolean changed = cols == null ? hiddenCols != null - : !cols.equals(hiddenCols); - hiddenCols = cols; - return changed; + boolean changed = cols == null ? hiddenCols != null + : !cols.equals(hiddenCols); + hiddenCols = cols; + return changed; } + @Override public void setupJPredAlignment() { @@ -2034,8 +2035,7 @@ public class Alignment implements AlignmentI, AutoCloseable Map contactmaps = new HashMap<>(); @Override - public - ContactListI getContactListFor(AlignmentAnnotation _aa, int column) + public ContactListI getContactListFor(AlignmentAnnotation _aa, int column) { ContactMatrixI cm = contactmaps.get(_aa.annotationId); if (cm == null) @@ -2062,7 +2062,8 @@ public class Alignment implements AlignmentI, AutoCloseable aa.editable = false; // aa.autoCalculated = true; contactmaps.put(aa.annotationId, cm); - // TODO: contact matrices could be intra or inter - more than one refseq possible! + // TODO: contact matrices could be intra or inter - more than one refseq + // possible! if (cm.hasReferenceSeq()) { aa.setSequenceRef(cm.getReferenceSeq()); -- 1.7.10.2