git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2034 Added isDefined flag to SequenceGroup
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
cdf0758
..
60cee46
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-92,9
+92,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
FeaturesDisplayedI featuresDisplayed = null;
FeaturesDisplayedI featuresDisplayed = null;
- protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+ protected Deque<CommandI> historyList = new ArrayDeque<>();
- protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+ protected Deque<CommandI> redoList = new ArrayDeque<>();
/**
* alignment displayed in the viewport. Please use get/setter
/**
* alignment displayed in the viewport. Please use get/setter
@@
-1113,7
+1113,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void setHiddenColumns(HiddenColumns hidden)
{
this.alignment.setHiddenColumns(hidden);
public void setHiddenColumns(HiddenColumns hidden)
{
this.alignment.setHiddenColumns(hidden);
- // this.colSel = colsel;
}
@Override
}
@Override
@@
-1298,7
+1297,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected boolean showOccupancy = true;
protected boolean showOccupancy = true;
- private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+ private Map<SequenceI, Color> sequenceColours = new HashMap<>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
protected SequenceAnnotationOrder sortAnnotationsBy = null;
@@
-1528,7
+1527,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
if (hiddenRepSequences == null)
{
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ hiddenRepSequences = new Hashtable<>();
}
hiddenRepSequences.put(repSequence, sg);
}
hiddenRepSequences.put(repSequence, sg);
@@
-1736,7
+1735,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
- ArrayList<int[]> regions = new ArrayList<int[]>();
+ ArrayList<int[]> regions = new ArrayList<>();
int start = min;
int end = max;
int start = min;
int end = max;
@@
-1779,7
+1778,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly)
{
public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly)
{
- ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
AlignmentAnnotation[] aa;
if ((aa = alignment.getAlignmentAnnotation()) != null)
{
AlignmentAnnotation[] aa;
if ((aa = alignment.getAlignmentAnnotation()) != null)
{
@@
-2133,7
+2132,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
// intersect alignment annotation with alignment groups
AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
// intersect alignment annotation with alignment groups
AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
- List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> oldrfs = new ArrayList<>();
if (aan != null)
{
for (int an = 0; an < aan.length; an++)
if (aan != null)
{
for (int an = 0; an < aan.length; an++)
@@
-2846,8
+2845,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
selectionIsDefinedGroup = gps.contains(selectionGroup);
}
}
selectionIsDefinedGroup = gps.contains(selectionGroup);
}
}
- return selectionGroup.getContext() == alignment
- || selectionIsDefinedGroup;
+ return selectionGroup.isDefined() || selectionIsDefinedGroup;
}
/**
}
/**