import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
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 updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensus)
{
return;
}
public void setHiddenColumns(HiddenColumns hidden)
{
this.alignment.setHiddenColumns(hidden);
- // this.colSel = colsel;
}
@Override
protected boolean showConsensus = true;
- private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+ protected boolean showOccupancy = true;
+
+ 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)
{
{
initRNAStructure();
}
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- gapcounts = new AlignmentAnnotation("Occupancy",
- "Number of aligned positions",
- new Annotation[1], 0f, alignment.getHeight(),
- AlignmentAnnotation.BAR_GRAPH);
- initGapCounts(gapcounts);
+ initGapCounts();
initComplementConsensus();
}
if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
+ MessageManager
+ .getString("label.complement_consensus_descr"),
+ new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
initConsensus(complementConsensus);
return true;
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts(AlignmentAnnotation counts)
+ private void initGapCounts()
{
- counts.hasText = false;
- counts.autoCalculated = true;
- counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
- if (showConsensus)
+ if (showOccupancy)
{
- alignment.addAnnotation(counts);
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
}
}
if (conservation == null)
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps", new Annotation[1],
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()), new Annotation[1],
0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
if (quality == null)
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
+ MessageManager.getString("label.quality_descr"),
new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
{
if (alignment.hasRNAStructure() && strucConsensus == null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
// 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++)
viewStyle.setScaleProteinAsCdna(b);
}
+ @Override
+ public boolean isProteinFontAsCdna()
+ {
+ return viewStyle.isProteinFontAsCdna();
+ }
+
+ @Override
+ public void setProteinFontAsCdna(boolean b)
+ {
+ viewStyle.setProteinFontAsCdna(b);
+ }
+
/**
* @return true if view should scroll to show the highlighted region of a
* sequence
selectionIsDefinedGroup = gps.contains(selectionGroup);
}
}
- return selectionGroup.getContext() == alignment
- || selectionIsDefinedGroup;
+ return selectionGroup.isDefined() || selectionIsDefinedGroup;
}
/**