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JAL-1551 formatting
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Jun 2022 11:52:49 +0000
(12:52 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Jun 2022 11:52:49 +0000
(12:52 +0100)
src/jalview/datamodel/Alignment.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
9825bff
..
ea04361
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-20,13
+20,6
@@
*/
package jalview.datamodel;
*/
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;
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 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
*/
/**
* 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)
{
@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()
{
@Override
public void setupJPredAlignment()
{
@@
-2034,8
+2035,7
@@
public class Alignment implements AlignmentI, AutoCloseable
Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
@Override
Map<Object, ContactMatrixI> 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)
{
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);
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());
if (cm.hasReferenceSeq())
{
aa.setSequenceRef(cm.getReferenceSeq());