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;
+import jalview.util.Format;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
if (exportSettings.isExportFeatures())
{
- jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+ jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
}
if (exportSettings.isExportGroups() && seqGroups != null
{
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().getAlignment()
- .getHiddenColumns()
- .getListOfCols();
- StringBuilder hiddenColsBuilder = new StringBuilder();
- for (int[] range : hiddenCols)
- {
- hiddenColsBuilder.append(";").append(range[0]).append("-")
- .append(range[1]);
- }
-
- hiddenColsBuilder.deleteCharAt(0);
- hiddenSections[0] = hiddenColsBuilder.toString();
+ hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
+ .regionsToString(";", "-");
}
// hidden rows/seqs business
return hiddenSections;
}
- public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- SequenceI[] sqs, FeatureRenderer fr)
+ protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ SequenceI[] sqs)
{
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);
+ String[] visibleFeatureTypes = displayedFeatures == null ? null
+ : displayedFeatures.getVisibleFeatures().toArray(
+ new String[displayedFeatures.getVisibleFeatureCount()]);
+
for (SequenceI seq : sqs)
{
- SequenceI dataSetSequence = seq.getDatasetSequence();
- SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
- : seq.getDatasetSequence().getSequenceFeatures();
-
- seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
- : seqFeatures;
- if (seqFeatures == null)
- {
- continue;
- }
-
+ /*
+ * get all features currently visible (and any non-positional features)
+ */
+ List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
+ visibleFeatureTypes);
for (SequenceFeature sf : seqFeatures)
{
- if (displayedFeatures != null
- && displayedFeatures.isVisible(sf.getType()))
- {
- SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
- String.valueOf(seq.hashCode()));
-
- String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(finder.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
- jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
- jsonFeature.setXend(seq.findIndex(sf.getEnd()));
- jsonFeature.setType(sf.getType());
- jsonFeature.setDescription(sf.getDescription());
- jsonFeature.setLinks(sf.links);
- jsonFeature.setOtherDetails(sf.otherDetails);
- jsonFeature.setScore(sf.getScore());
- jsonFeature.setFillColor(featureColour);
- jsonFeature.setFeatureGroup(sf.getFeatureGroup());
- sequenceFeaturesPojo.add(jsonFeature);
- }
+ SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+ String.valueOf(seq.hashCode()));
+
+ String featureColour = (fr == null) ? null : Format
+ .getHexString(finder.findFeatureColour(Color.white, seq,
+ seq.findIndex(sf.getBegin())));
+ int xStart = sf.getBegin() == 0 ? 0
+ : seq.findIndex(sf.getBegin()) - 1;
+ int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
+ jsonFeature.setXstart(xStart);
+ jsonFeature.setXend(xEnd);
+ jsonFeature.setType(sf.getType());
+ jsonFeature.setDescription(sf.getDescription());
+ jsonFeature.setLinks(sf.links);
+ jsonFeature.setOtherDetails(sf.otherDetails);
+ jsonFeature.setScore(sf.getScore());
+ jsonFeature.setFillColor(featureColour);
+ jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+ sequenceFeaturesPojo.add(jsonFeature);
}
}
return sequenceFeaturesPojo;
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())
{
Long end = (Long) jsonFeature.get("xEnd");
String type = (String) jsonFeature.get("type");
String featureGrp = (String) jsonFeature.get("featureGroup");
- String descripiton = (String) jsonFeature.get("description");
+ String description = (String) jsonFeature.get("description");
String seqRef = (String) jsonFeature.get("sequenceRef");
Float score = Float.valueOf(jsonFeature.get("score").toString());
Sequence seq = seqMap.get(seqRef);
- SequenceFeature sequenceFeature = new SequenceFeature();
+
+ /*
+ * begin/end of 0 is for a non-positional feature
+ */
+ int featureBegin = begin.intValue() == 0 ? 0 : seq
+ .findPosition(begin.intValue());
+ int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
+ .intValue()) - 1;
+
+ SequenceFeature sequenceFeature = new SequenceFeature(type,
+ description, featureBegin, featureEnd, score, featureGrp);
+
JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
if (linksJsonArray != null && linksJsonArray.size() > 0)
{
sequenceFeature.addLink(link);
}
}
- sequenceFeature.setFeatureGroup(featureGrp);
- sequenceFeature.setScore(score);
- sequenceFeature.setDescription(descripiton);
- sequenceFeature.setType(type);
- sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
- sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
+
seq.addSequenceFeature(sequenceFeature);
displayedFeatures.setVisible(type);
}
}
}
}
- globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
git://source.jalview.org / jalview.git / blobdiff