X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=816346a9622e594d51b61db6f8159597b5a53f84;hb=4ff9ae2e29a4dc41fb5101a5e336809f097b88ae;hp=564dd64acbda10883a0b406af49b561469fbce7f;hpb=1b64bc7c6e51618b6a9acbbad423244d89eba203;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 564dd64..816346a 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; @@ -45,8 +46,11 @@ 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.UserColourScheme; +import jalview.schemes.JalviewColourScheme; +import jalview.schemes.ResidueColourScheme; +import jalview.util.ColorUtils; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import java.awt.Color; @@ -70,10 +74,6 @@ 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; @@ -84,9 +84,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private FeatureRenderer fr; - private List hiddenColumns; - - private ColumnSelection columnSelection; + private HiddenColumns hiddenColumns; private List hiddenSeqRefs; @@ -104,9 +102,10 @@ 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 +116,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } @Override - public String print() + public String print(SequenceI[] sqs, boolean jvsuffix) { String jsonOutput = null; try @@ -170,7 +169,7 @@ 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 +216,20 @@ 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 @@ -238,7 +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()); @@ -277,8 +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) { @@ -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())); @@ -482,7 +492,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile seqMap.put(seqUniqueId, seq); } - parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter @@ -521,10 +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); @@ -558,11 +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; } @@ -571,8 +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"); @@ -656,12 +666,12 @@ 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])); } } @@ -709,6 +719,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } + @Override public String getGlobalColourScheme() { return globalColourScheme; @@ -730,8 +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(); @@ -741,11 +757,14 @@ 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) { - annotations.add(annot); + if (annot != null && !annot.autoCalculated) + { + annotations.add(annot); + } } } globalColourScheme = ColourSchemeProperty.getColourName(viewport @@ -755,6 +774,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } + @Override public boolean isShowSeqFeatures() { return showSeqFeatures; @@ -770,21 +790,18 @@ 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()) @@ -864,4 +881,19 @@ 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(); + } }