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
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ResidueShaderI residueShading;
+ protected ResidueShaderI residueShading = new ResidueShader();
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
public void setHiddenColumns(HiddenColumns hidden)
{
this.alignment.setHiddenColumns(hidden);
- // this.colSel = colsel;
}
@Override
protected boolean showOccupancy = true;
- private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+ private Map<SequenceI, Color> sequenceColours = new HashMap<>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ hiddenRepSequences = new Hashtable<>();
}
hiddenRepSequences.put(repSequence, sg);
@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;
public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly)
{
- ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
AlignmentAnnotation[] aa;
if ((aa = alignment.getAlignmentAnnotation()) != null)
{
// 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++)
selectionIsDefinedGroup = gps.contains(selectionGroup);
}
}
- return selectionGroup.getContext() == alignment
- || selectionIsDefinedGroup;
+ return selectionGroup.isDefined() || selectionIsDefinedGroup;
}
/**