X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=14574d0e3263d1d1b9810e19e7b58fb93dc02ed3;hb=262f29f7b600e4c8d02461600b5184707192b9c1;hp=87255560200c77d24de557dce5fcf22ceaa8fec7;hpb=4513bd826c54623c14aa8946a51a2382f64e98f3;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 8725556..14574d0 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -26,12 +26,13 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ComplexAlignFile; import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; 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; @@ -39,12 +40,18 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo; import jalview.json.binding.biojson.v1.AlignmentPojo; +import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo; import jalview.json.binding.biojson.v1.AnnotationPojo; import jalview.json.binding.biojson.v1.ColourSchemeMapper; 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; @@ -68,10 +75,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private String application = "Jalview"; - public static final String FILE_EXT = "json"; - - public static final String FILE_DESC = "JSON"; - private String globalColourScheme; private boolean showSeqFeatures; @@ -82,14 +85,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private FeatureRenderer fr; - private List hiddenColumns; - - private ColumnSelection columnSelection; + private HiddenColumns hiddenColumns; private List hiddenSeqRefs; private ArrayList hiddenSequences; + private final static String TCOFFEE_SCORE = "TCoffeeScore"; + public JSONFile() { super(); @@ -100,9 +103,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile super(source); } - public JSONFile(String inFile, String type) throws IOException + public JSONFile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } @Override @@ -113,7 +117,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } @Override - public String print() + public String print(SequenceI[] sqs, boolean jvsuffix) { String jsonOutput = null; try @@ -166,7 +170,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } int count = 0; - for (SequenceI seq : seqs) + for (SequenceI seq : sqs) { StringBuilder name = new StringBuilder(); name.append(seq.getName()).append("/").append(seq.getStart()) @@ -209,11 +213,23 @@ public class JSONFile extends AlignFile implements ComplexAlignFile jsonAlignmentPojo .setAlignAnnotation(annotationToJsonPojo(annotations)); } + else + { + // These color schemes require annotation, disable them if annotations + // are not exported + if (globalColourScheme + .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString()) + || globalColourScheme + .equalsIgnoreCase(JalviewColourScheme.TCoffee + .toString())) + { + jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE); + } + } if (exportSettings.isExportFeatures()) { - jsonAlignmentPojo - .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr)); + jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs)); } if (exportSettings.isExportGroups() && seqGroups != null @@ -224,7 +240,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo(); seqGrpPojo.setGroupName(seqGrp.getName()); seqGrpPojo.setColourScheme(ColourSchemeProperty - .getColourName(seqGrp.cs)); + .getColourName(seqGrp.getColourScheme())); seqGrpPojo.setColourText(seqGrp.getColourText()); seqGrpPojo.setDescription(seqGrp.getDescription()); seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes()); @@ -263,8 +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) { @@ -302,46 +319,50 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return hiddenSections; } - public List sequenceFeatureToJsonPojo( - List seqs, FeatureRenderer fr) + protected List sequenceFeatureToJsonPojo( + SequenceI[] sqs) { displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); - for (SequenceI seq : seqs) + if (sqs == null) { - SequenceI dataSetSequence = seq.getDatasetSequence(); - SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null - : seq.getDatasetSequence().getSequenceFeatures(); + return sequenceFeaturesPojo; + } - seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures() - : seqFeatures; - if (seqFeatures == null) - { - continue; - } + FeatureColourFinder finder = new FeatureColourFinder(fr); + String[] visibleFeatureTypes = displayedFeatures == null ? null + : displayedFeatures.getVisibleFeatures().toArray( + new String[displayedFeatures.getVisibleFeatureCount()]); + + for (SequenceI seq : sqs) + { + /* + * 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(fr.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; @@ -360,6 +381,26 @@ public class JSONFile extends AlignFile implements ComplexAlignFile AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo(); alignAnnotPojo.setDescription(annot.description); alignAnnotPojo.setLabel(annot.label); + if (!Double.isNaN(annot.score)) + { + alignAnnotPojo.setScore(annot.score); + } + alignAnnotPojo.setCalcId(annot.getCalcId()); + alignAnnotPojo.setGraphType(annot.graph); + + AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo(); + annotSetting.setBelowAlignment(annot.belowAlignment); + annotSetting.setCentreColLabels(annot.centreColLabels); + annotSetting.setScaleColLabel(annot.scaleColLabel); + annotSetting.setShowAllColLabels(annot.showAllColLabels); + annotSetting.setVisible(annot.visible); + annotSetting.setHasIcon(annot.hasIcons); + alignAnnotPojo.setAnnotationSettings(annotSetting); + SequenceI refSeq = annot.sequenceRef; + if (refSeq != null) + { + alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode())); + } for (Annotation annotation : annot.annotations) { AnnotationPojo annotationPojo = new AnnotationPojo(); @@ -369,12 +410,28 @@ public class JSONFile extends AlignFile implements ComplexAlignFile annotationPojo.setValue(annotation.value); annotationPojo .setSecondaryStructure(annotation.secondaryStructure); - annotationPojo.setDisplayCharacter(annotation.displayCharacter); + String displayChar = annotation.displayCharacter == null ? null + : annotation.displayCharacter; + // System.out.println("--------------------->[" + displayChar + "]"); + annotationPojo.setDisplayCharacter(displayChar); + if (annotation.colour != null) + { + annotationPojo.setColour(jalview.util.Format + .getHexString(annotation.colour)); + } alignAnnotPojo.getAnnotations().add(annotationPojo); } else { - alignAnnotPojo.getAnnotations().add(annotationPojo); + if (annot.getCalcId() != null + && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE)) + { + // do nothing + } + else + { + alignAnnotPojo.getAnnotations().add(annotationPojo); + } } } jsonAnnotations.add(alignAnnotPojo); @@ -432,7 +489,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile seqMap.put(seqUniqueId, seq); } - parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter @@ -471,10 +527,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null, - displayBoxes, displayText, colourText, - startRes, endRes); - seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme, - seqGrp); + displayBoxes, displayText, colourText, startRes, endRes); + seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme( + colourScheme, seqGrp)); seqGrp.setShowNonconserved(showNonconserved); seqGrp.setDescription(description); this.seqGroups.add(seqGrp); @@ -510,6 +565,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile : annot.get("displayCharacter").toString(); annotations[count] = new Annotation(displayChar, desc, ss, val); + if (annot.get("colour") != null) + { + Color color = ColorUtils.parseColourString(annot.get( + "colour").toString()); + annotations[count].colour = color; + } } ++count; } @@ -517,7 +578,64 @@ public class JSONFile extends AlignFile implements ComplexAlignFile AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot .get("label").toString(), alAnnot.get("description") .toString(), annotations); + alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer + .valueOf(alAnnot.get("graphType").toString()); + + JSONObject diplaySettings = (JSONObject) alAnnot + .get("annotationSettings"); + if (diplaySettings != null) + { + + alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false + : Boolean.valueOf(diplaySettings.get("scaleColLabel") + .toString()); + alignAnnot.showAllColLabels = (diplaySettings + .get("showAllColLabels") == null) ? true : Boolean + .valueOf(diplaySettings.get("showAllColLabels") + .toString()); + alignAnnot.centreColLabels = (diplaySettings + .get("centreColLabels") == null) ? true + : Boolean.valueOf(diplaySettings.get("centreColLabels") + .toString()); + alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false + : Boolean.valueOf(diplaySettings.get("belowAlignment") + .toString()); + alignAnnot.visible = (diplaySettings.get("visible") == null) ? true + : Boolean.valueOf(diplaySettings.get("visible") + .toString()); + alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true + : Boolean.valueOf(diplaySettings.get("hasIcon") + .toString()); + + } + if (alAnnot.get("score") != null) + { + alignAnnot.score = Double + .valueOf(alAnnot.get("score").toString()); + } + + String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get( + "calcId").toString(); + alignAnnot.setCalcId(calcId); + String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot + .get("sequenceRef").toString() : null; + + Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null; + if (sequence != null) + { + alignAnnot.sequenceRef = sequence; + sequence.addAlignmentAnnotation(alignAnnot); + if (alignAnnot.label.equalsIgnoreCase("T-COFFEE")) + { + alignAnnot.createSequenceMapping(sequence, sequence.getStart(), + false); + sequence.addAlignmentAnnotation(alignAnnot); + alignAnnot.adjustForAlignment(); + } + } + alignAnnot.validateRangeAndDisplay(); this.annotations.add(alignAnnot); + } } catch (Exception e) { @@ -545,12 +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])); } } @@ -570,12 +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) { @@ -586,18 +715,14 @@ 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); } } } + @Override public String getGlobalColourScheme() { return globalColourScheme; @@ -619,8 +744,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.displayedFeatures = displayedFeatures; } + @Override public void configureForView(AlignmentViewPanel avpanel) { + if (avpanel == null) + { + return; + } super.configureForView(avpanel); AlignViewportI viewport = avpanel.getAlignViewport(); AlignmentI alignment = viewport.getAlignment(); @@ -630,15 +760,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile fr = avpanel.cloneFeatureRenderer(); // Add non auto calculated annotation to AlignFile - for (AlignmentAnnotation annot : annots) + if (annots != null) { - if (annot != null && !annot.autoCalculated) + for (AlignmentAnnotation annot : annots) { - if (!annot.visible) + if (annot != null && !annot.autoCalculated) { - continue; + annotations.add(annot); } - annotations.add(annot); } } globalColourScheme = ColourSchemeProperty.getColourName(viewport @@ -648,6 +777,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } + @Override public boolean isShowSeqFeatures() { return showSeqFeatures; @@ -663,21 +793,18 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return annotations; } - public List getHiddenColumns() + @Override + public HiddenColumns getHiddenColumns() { return hiddenColumns; } - public ColumnSelection getColumnSelection() + public void setHiddenColumns(HiddenColumns hidden) { - return columnSelection; - } - - public void setColumnSelection(ColumnSelection columnSelection) - { - this.columnSelection = columnSelection; + this.hiddenColumns = hidden; } + @Override public SequenceI[] getHiddenSequences() { if (hiddenSequences == null || hiddenSequences.isEmpty()) @@ -757,4 +884,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.exportJalviewSettings = exportJalviewSettings; } } + + /** + * Returns a descriptor for suitable feature display settings with + *
    + *
  • ResNums or insertions features visible
    • + *
  • insertions features coloured red
    • + *
  • ResNum features coloured by label
    • + *
  • Insertions displayed above (on top of) ResNums
    • + *
+ */ + @Override + public FeatureSettingsModelI getFeatureColourScheme() + { + return new PDBFeatureSettings(); + } }