X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=653c071579c754563068095bb0a0a2bf3e985c82;hb=608282e79f4dd02c92565235b7946265bdca847d;hp=b079a3c68ece5427ea872b54763e5598499e2319;hpb=3f3c6c3a2b99fee2e726d18302af1b3320331212;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index b079a3c..653c071 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -26,7 +26,9 @@ 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; @@ -36,15 +38,16 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.json.binding.v1.AlignmentAnnotationPojo; -import jalview.json.binding.v1.AlignmentPojo; -import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper; -import jalview.json.binding.v1.AnnotationPojo; -import jalview.json.binding.v1.SequenceFeaturesPojo; -import jalview.json.binding.v1.SequenceGrpPojo; -import jalview.json.binding.v1.SequencePojo; -import jalview.schemes.ColourSchemeI; +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.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import java.awt.Color; @@ -62,11 +65,9 @@ import org.json.simple.parser.JSONParser; public class JSONFile extends AlignFile implements ComplexAlignFile { - private ColourSchemeI colourScheme; + private static String version = new BuildDetails().getVersion(); - private String version = "2.9"; - - private String webstartUrl = "www.jalview.org/services/launchApp"; + private String webstartUrl = "http://www.jalview.org/services/launchApp"; private String application = "Jalview"; @@ -74,7 +75,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile public static final String FILE_DESC = "JSON"; - private String globalColorScheme; + private String globalColourScheme; private boolean showSeqFeatures; @@ -92,6 +93,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private ArrayList hiddenSequences; + private final static String TCOFFEE_SCORE = "TCoffeeScore"; public JSONFile() { @@ -114,6 +116,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile parse(getReader()); } + @Override public String print() { @@ -158,6 +161,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { return true; } + + @Override + public boolean isCancelled() + { + return false; + } }; } @@ -176,8 +185,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile jsonSeqPojo.setSeq(seq.getSequenceAsString()); jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); } - - jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme); + jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme); jsonAlignmentPojo.getAppSettings().put("application", application); jsonAlignmentPojo.getAppSettings().put("version", version); jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl); @@ -188,15 +196,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile if (hiddenSections != null) { if (hiddenSections[0] != null - && exportSettings - .isExportHiddenColumns()) + && exportSettings.isExportHiddenColumns()) { jsonAlignmentPojo.getAppSettings().put("hiddenCols", String.valueOf(hiddenSections[0])); } if (hiddenSections[1] != null - && exportSettings - .isExportHiddenSequences()) + && exportSettings.isExportHiddenSequences()) { jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", String.valueOf(hiddenSections[1])); @@ -208,6 +214,16 @@ 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("RNA Helices") + || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES")) + { + jsonAlignmentPojo.setGlobalColorScheme("None"); + } + } if (exportSettings.isExportFeatures()) { @@ -215,8 +231,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr)); } - if (exportSettings.isExportGroups() - && seqGroups != null + if (exportSettings.isExportGroups() && seqGroups != null && seqGroups.size() > 0) { for (SequenceGroup seqGrp : seqGroups) @@ -234,7 +249,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved()); for (SequenceI seq : seqGrp.getSequences()) { - seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode())); + seqGrpPojo.getSequenceRefs() + .add(String.valueOf(seq.hashCode())); } jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo); } @@ -304,8 +320,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile public List sequenceFeatureToJsonPojo( List seqs, FeatureRenderer fr) { - displayedFeatures = (fr == null) ? null : fr - .getFeaturesDisplayed(); + displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); for (SequenceI seq : seqs) { @@ -329,8 +344,7 @@ 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(fr.findFeatureColour(Color.white, seq, seq.findIndex(sf.getBegin()))); jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1); jsonFeature.setXend(seq.findIndex(sf.getEnd())); @@ -361,6 +375,26 @@ 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(); @@ -370,12 +404,28 @@ 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); @@ -403,11 +453,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile if (jvSettingsJsonObj != null) { - String jsColourScheme = (String) jvSettingsJsonObj + globalColourScheme = (String) jvSettingsJsonObj .get("globalColorScheme"); Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get( "showSeqFeatures").toString()); - setColourScheme(getJalviewColorScheme(jsColourScheme)); setShowSeqFeatures(showFeatures); parseHiddenSeqRefsAsList(jvSettingsJsonObj); parseHiddenCols(jvSettingsJsonObj); @@ -433,6 +482,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile seqs.add(seq); seqMap.put(seqUniqueId, seq); } + parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter @@ -454,12 +504,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile int startRes = Integer .valueOf(seqGrpObj.get("startRes").toString()); int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString()); - JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash"); + JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs"); ArrayList grpSeqs = new ArrayList(); - if (seqsHashArray.size() > 0) + if (sequenceRefs.size() > 0) { - Iterator seqHashIter = seqsHashArray.iterator(); + Iterator seqHashIter = sequenceRefs.iterator(); while (seqHashIter.hasNext()) { String seqHash = seqHashIter.next(); @@ -470,10 +520,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } } - ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme); - SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, - grpColourScheme, + SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null, displayBoxes, displayText, colourText, startRes, endRes); + seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme, + seqGrp); seqGrp.setShowNonconserved(showNonconserved); seqGrp.setDescription(description); this.seqGroups.add(seqGrp); @@ -501,12 +551,20 @@ public class JSONFile extends AlignFile implements ComplexAlignFile .valueOf(annot.get("value").toString()); String desc = annot.get("description") == null ? null : annot .get("description").toString(); - - char ss = annot.get("secondaryStructure") == null ? ' ' - : annot.get("secondaryStructure").toString().charAt(0); - String displayChar = annot.get("displayCharacter").toString(); + char ss = annot.get("secondaryStructure") == null + || annot.get("secondaryStructure").toString() + .equalsIgnoreCase("u0000") ? ' ' : annot + .get("secondaryStructure").toString().charAt(0); + String displayChar = annot.get("displayCharacter") == null ? "" + : annot.get("displayCharacter").toString(); annotations[count] = new Annotation(displayChar, desc, ss, val); + if (annot.get("colour") != null) + { + Color color = UserColourScheme.getColourFromString(annot.get( + "colour").toString()); + annotations[count].colour = color; + } } ++count; } @@ -514,9 +572,65 @@ 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) { e.printStackTrace(); @@ -528,9 +642,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { hiddenSeqRefs = new ArrayList(); String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs"); - if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){ + if (hiddenSeqs != null && !hiddenSeqs.isEmpty()) + { String[] seqRefs = hiddenSeqs.split(";"); - for(String seqRef : seqRefs){ + for (String seqRef : seqRefs) + { hiddenSeqRefs.add(seqRef); } } @@ -539,10 +655,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile public void parseHiddenCols(JSONObject jvSettingsJson) { String hiddenCols = (String) jvSettingsJson.get("hiddenCols"); - if(hiddenCols != null && !hiddenCols.isEmpty()){ + if (hiddenCols != null && !hiddenCols.isEmpty()) + { columnSelection = new ColumnSelection(); String[] rangeStrings = hiddenCols.split(";"); - for(String rangeString : rangeStrings){ + for (String rangeString : rangeStrings) + { String[] range = rangeString.split("-"); columnSelection.hideColumns(Integer.valueOf(range[0]), Integer.valueOf(range[1])); @@ -592,40 +710,15 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } - public static ColourSchemeI getJalviewColorScheme( - String bioJsColourSchemeName) - { - ColourSchemeI jalviewColor = null; - for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper - .values()) - { - if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)) - { - jalviewColor = cs.getJvColourScheme(); - break; - } - } - return jalviewColor; - } - - public String getGlobalColorScheme() - { - return globalColorScheme; - } - - public void setGlobalColorScheme(String globalColorScheme) - { - this.globalColorScheme = globalColorScheme; - } - - public ColourSchemeI getColourScheme() + @Override + public String getGlobalColourScheme() { - return colourScheme; + return globalColourScheme; } - public void setColourScheme(ColourSchemeI colourScheme) + public void setGlobalColorScheme(String globalColourScheme) { - this.colourScheme = colourScheme; + this.globalColourScheme = globalColourScheme; } @Override @@ -639,9 +732,13 @@ 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(); @@ -651,24 +748,24 @@ 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); } } - globalColorScheme = ColourSchemeProperty.getColourName(viewport + globalColourScheme = ColourSchemeProperty.getColourName(viewport .getGlobalColourScheme()); setDisplayedFeatures(viewport.getFeaturesDisplayed()); showSeqFeatures = viewport.isShowSequenceFeatures(); } + @Override public boolean isShowSeqFeatures() { return showSeqFeatures; @@ -689,6 +786,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return hiddenColumns; } + @Override public ColumnSelection getColumnSelection() { return columnSelection; @@ -699,12 +797,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.columnSelection = columnSelection; } + @Override public SequenceI[] getHiddenSequences() { if (hiddenSequences == null || hiddenSequences.isEmpty()) { - return new SequenceI[] - {}; + return new SequenceI[] {}; } synchronized (hiddenSequences) { @@ -779,4 +877,19 @@ 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(); + } }