X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=053a65ed85720dfb536cd69d671cbef702efc5a0;hb=7f4b42c9b73c4e5e101aa2bb390af2d1df9a0f0a;hp=4e293dbe2a17366ff7534f9bbe228e45bdd757c4;hpb=384e43c561fbc2446923dd2ed227e2931a8ac406;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 4e293db..053a65e 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -26,6 +26,7 @@ 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; @@ -45,8 +46,10 @@ 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.schemes.ColourSchemeProperty; -import jalview.schemes.UserColourScheme; +import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.schemes.JalviewColourScheme; +import jalview.schemes.ResidueColourScheme; +import jalview.util.ColorUtils; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import java.awt.Color; @@ -70,10 +73,6 @@ 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; @@ -104,9 +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 @@ -117,7 +117,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } @Override - public String print() + public String print(SequenceI[] sqs, boolean jvsuffix) { String jsonOutput = null; try @@ -170,7 +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()) @@ -217,17 +217,20 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { // These color schemes require annotation, disable them if annotations // are not exported - if (globalColourScheme.equalsIgnoreCase("RNA Helices") - || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES")) + if (globalColourScheme + .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString()) + || globalColourScheme + .equalsIgnoreCase(JalviewColourScheme.TCoffee + .toString())) { - jsonAlignmentPojo.setGlobalColorScheme("None"); + jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE); } } if (exportSettings.isExportFeatures()) { jsonAlignmentPojo - .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr)); + .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr)); } if (exportSettings.isExportGroups() && seqGroups != null @@ -237,8 +240,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo(); seqGrpPojo.setGroupName(seqGrp.getName()); - seqGrpPojo.setColourScheme(ColourSchemeProperty - .getColourName(seqGrp.cs)); + seqGrpPojo.setColourScheme(seqGrp.getColourScheme() + .getSchemeName()); seqGrpPojo.setColourText(seqGrp.getColourText()); seqGrpPojo.setDescription(seqGrp.getDescription()); seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes()); @@ -317,11 +320,18 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } public List sequenceFeatureToJsonPojo( - List seqs, FeatureRenderer fr) + SequenceI[] sqs, FeatureRenderer fr) { displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); - for (SequenceI seq : seqs) + if (sqs == null) + { + return sequenceFeaturesPojo; + } + + FeatureColourFinder finder = new FeatureColourFinder(fr); + + for (SequenceI seq : sqs) { SequenceI dataSetSequence = seq.getDatasetSequence(); SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null @@ -343,7 +353,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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())); @@ -374,16 +384,20 @@ public class JSONFile extends AlignFile implements ComplexAlignFile AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo(); alignAnnotPojo.setDescription(annot.description); alignAnnotPojo.setLabel(annot.label); - alignAnnotPojo.setScore(annot.score); + 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.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) @@ -399,7 +413,10 @@ 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 @@ -475,7 +492,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile seqMap.put(seqUniqueId, seq); } - parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter @@ -514,10 +530,9 @@ 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); @@ -528,11 +543,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile .hasNext();) { JSONObject alAnnot = alAnnotIter.next(); - if (alAnnot == null) - { - continue; - } - JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations"); Annotation[] annotations = new Annotation[annotJsonArray.size()]; int count = 0; @@ -556,11 +566,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile .get("secondaryStructure").toString().charAt(0); String displayChar = annot.get("displayCharacter") == null ? "" : annot.get("displayCharacter").toString(); - Color color = annot.get("colour") == null ? Color.white - : UserColourScheme.getColourFromString(annot.get( - "colour").toString()); - annotations[count] = new Annotation(displayChar, desc, ss, val, - color); + + 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; } @@ -569,8 +582,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile .get("label").toString(), alAnnot.get("description") .toString(), annotations); alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer - .valueOf(alAnnot.get("graphType") - .toString()); + .valueOf(alAnnot.get("graphType").toString()); JSONObject diplaySettings = (JSONObject) alAnnot .get("annotationSettings"); @@ -594,6 +606,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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) @@ -621,7 +636,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile alignAnnot.adjustForAlignment(); } } + alignAnnot.validateRangeAndDisplay(); this.annotations.add(alignAnnot); + } } catch (Exception e) { @@ -702,6 +719,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } + @Override public String getGlobalColourScheme() { return globalColourScheme; @@ -723,8 +741,13 @@ 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(); @@ -734,20 +757,23 @@ 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) { - annotations.add(annot); + if (annot != null && !annot.autoCalculated) + { + annotations.add(annot); + } } } - globalColourScheme = ColourSchemeProperty.getColourName(viewport - .getGlobalColourScheme()); + globalColourScheme = viewport.getGlobalColourScheme().getSchemeName(); setDisplayedFeatures(viewport.getFeaturesDisplayed()); showSeqFeatures = viewport.isShowSequenceFeatures(); } + @Override public boolean isShowSeqFeatures() { return showSeqFeatures; @@ -768,6 +794,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return hiddenColumns; } + @Override public ColumnSelection getColumnSelection() { return columnSelection; @@ -778,6 +805,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.columnSelection = columnSelection; } + @Override public SequenceI[] getHiddenSequences() { if (hiddenSequences == null || hiddenSequences.isEmpty()) @@ -857,4 +885,19 @@ 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(); + } }