X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=14574d0e3263d1d1b9810e19e7b58fb93dc02ed3;hb=262f29f7b600e4c8d02461600b5184707192b9c1;hp=053a65ed85720dfb536cd69d671cbef702efc5a0;hpb=2888e7307e1f7c8239234941498cb86e8c65ab36;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 053a65e..14574d0 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -32,7 +32,7 @@ import jalview.bin.BuildDetails; 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; @@ -47,9 +47,11 @@ 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; +import jalview.util.Format; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import java.awt.Color; @@ -83,9 +85,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private FeatureRenderer fr; - private List hiddenColumns; - - private ColumnSelection columnSelection; + private HiddenColumns hiddenColumns; private List hiddenSeqRefs; @@ -229,8 +229,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile if (exportSettings.isExportFeatures()) { - jsonAlignmentPojo - .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr)); + jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs)); } if (exportSettings.isExportGroups() && seqGroups != null @@ -240,8 +239,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { 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()); @@ -280,8 +279,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile // hidden column business if (getViewport().hasHiddenColumns()) { - List hiddenCols = getViewport().getColumnSelection() - .getHiddenColumns(); + List hiddenCols = getViewport().getAlignment() + .getHiddenColumns() + .getHiddenRegions(); StringBuilder hiddenColsBuilder = new StringBuilder(); for (int[] range : hiddenCols) { @@ -319,8 +319,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return hiddenSections; } - public List sequenceFeatureToJsonPojo( - SequenceI[] sqs, FeatureRenderer fr) + protected List sequenceFeatureToJsonPojo( + SequenceI[] sqs) { displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); @@ -331,41 +331,38 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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 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; @@ -666,12 +663,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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])); } } @@ -691,12 +688,23 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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) { @@ -707,12 +715,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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); } @@ -767,7 +770,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } } - globalColourScheme = viewport.getGlobalColourScheme().getSchemeName(); + globalColourScheme = ColourSchemeProperty.getColourName(viewport + .getGlobalColourScheme()); setDisplayedFeatures(viewport.getFeaturesDisplayed()); showSeqFeatures = viewport.isShowSequenceFeatures(); @@ -789,20 +793,15 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return annotations; } - public List 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