import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
private FeatureRenderer fr;
- private List<int[]> hiddenColumns;
-
- private ColumnSelection columnSelection;
+ private HiddenColumns hiddenColumns;
private List<String> hiddenSeqRefs;
{
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
seqGrpPojo.setGroupName(seqGrp.getName());
- seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
- .getSchemeName());
+ seqGrpPojo.setColourScheme(ColourSchemeProperty
+ .getColourName(seqGrp.getColourScheme()));
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
// hidden column business
if (getViewport().hasHiddenColumns())
{
- List<int[]> hiddenCols = getViewport().getColumnSelection()
- .getHiddenColumns();
StringBuilder hiddenColsBuilder = new StringBuilder();
- for (int[] range : hiddenCols)
+ for (int[] range : getViewport().getAlignment().getHiddenColumns())
{
hiddenColsBuilder.append(";").append(range[0]).append("-")
.append(range[1]);
SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
- List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
if (sqs == null)
{
return sequenceFeaturesPojo;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr.findFeatureColour(Color.white, seq,
+ .getHexString(finder.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
Vector<AlignmentAnnotation> annotations)
{
- List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+ List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
if (annotations == null)
{
return jsonAnnotations;
parseHiddenCols(jvSettingsJsonObj);
}
- hiddenSequences = new ArrayList<SequenceI>();
- seqMap = new Hashtable<String, Sequence>();
+ hiddenSequences = new ArrayList<>();
+ seqMap = new Hashtable<>();
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
{
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> grpSeqs = new ArrayList<>();
if (sequenceRefs.size() > 0)
{
Iterator<String> seqHashIter = sequenceRefs.iterator();
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
{
- hiddenSeqRefs = new ArrayList<String>();
+ hiddenSeqRefs = new ArrayList<>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
if (hiddenCols != null && !hiddenCols.isEmpty())
{
- columnSelection = new ColumnSelection();
+ hiddenColumns = new HiddenColumns();
String[] rangeStrings = hiddenCols.split(";");
for (String rangeString : rangeStrings)
{
String[] range = rangeString.split("-");
- columnSelection.hideColumns(Integer.valueOf(range[0]),
+ hiddenColumns.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
}
}
}
}
}
- globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
return annotations;
}
- public List<int[]> getHiddenColumns()
- {
- return hiddenColumns;
- }
-
@Override
- public ColumnSelection getColumnSelection()
+ public HiddenColumns getHiddenColumns()
{
- return columnSelection;
+ return hiddenColumns;
}
- public void setColumnSelection(ColumnSelection columnSelection)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.columnSelection = columnSelection;
+ this.hiddenColumns = hidden;
}
@Override