X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=36980f8d7616facc6103e358bc8d308b98136966;hb=f3392c352962c6827674ada5948500725e4eed1e;hp=8882f9702460d7fe6b06a8f086ca717e82e71e1c;hpb=ecdc53f0d45b7533878cef236fff851ea64ef9a9;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 8882f97..36980f8 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -21,46 +21,53 @@ package jalview.io; -import java.awt.Color; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.List; -import java.util.Vector; - -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; - -import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignExportSettingI; 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.HiddenSequences; 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; -public class JSONFile extends AlignFile -{ - private ColourSchemeI colourScheme; +import java.awt.Color; +import java.io.IOException; +import java.io.Reader; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Vector; - private String version = "2.9"; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; + +public class JSONFile extends AlignFile implements ComplexAlignFile +{ + private static String version = new BuildDetails().getVersion(); - private String webstartUrl = "www.jalview.org/services/launchApp"; + private String webstartUrl = "http://www.jalview.org/services/launchApp"; private String application = "Jalview"; @@ -68,7 +75,7 @@ public class JSONFile extends AlignFile public static final String FILE_DESC = "JSON"; - private String globalColorScheme; + private String globalColourScheme; private boolean showSeqFeatures; @@ -78,12 +85,16 @@ public class JSONFile extends AlignFile private FeatureRenderer fr; - private JSONExportSettings jsonExportSettings; - private List hiddenColumns; + private ColumnSelection columnSelection; + private List hiddenSeqRefs; + private ArrayList hiddenSequences; + + private final static String TCOFFEE_SCORE = "TCoffeeScore"; + public JSONFile() { super(); @@ -102,13 +113,7 @@ public class JSONFile extends AlignFile @Override public void parse() throws IOException { - StringBuilder jsonStringBuilder = new StringBuilder(); - String currentLine; - while ((currentLine = nextLine()) != null) - { - jsonStringBuilder.append(currentLine); - } - parse(jsonStringBuilder.toString()); + parse(getReader()); } @@ -118,24 +123,51 @@ public class JSONFile extends AlignFile String jsonOutput = null; try { - if (getJsonExportSettings() == null) - { - jsonExportSettings = new JSONExportSettings(); - jsonExportSettings.setExportAnnotations(true); - jsonExportSettings.setExportGroups(true); - jsonExportSettings.setExportJalviewSettings(true); - jsonExportSettings.setExportSequenceFeatures(true); - } - AlignmentPojo jsonAlignmentPojo = new AlignmentPojo(); - if (getViewport() != null) + AlignExportSettingI exportSettings = getExportSettings(); + + // if no export settings were supplied use the following with all values + // defaulting to true + if (exportSettings == null) { - globalColorScheme = ColourSchemeProperty - .getColourName(getViewport() - .getGlobalColourScheme()); - setDisplayedFeatures(getViewport().getFeaturesDisplayed()); - showSeqFeatures = getViewport().isShowSequenceFeatures(); - fr = getViewport().getFeatureRenderer(); + exportSettings = new AlignExportSettingI() + { + @Override + public boolean isExportHiddenSequences() + { + return true; + } + + @Override + public boolean isExportHiddenColumns() + { + return true; + } + + @Override + public boolean isExportGroups() + { + return true; + } + + @Override + public boolean isExportFeatures() + { + return true; + } + + @Override + public boolean isExportAnnotations() + { + return true; + } + + @Override + public boolean isCancelled() + { + return false; + } + }; } int count = 0; @@ -153,45 +185,53 @@ public class JSONFile extends AlignFile jsonSeqPojo.setSeq(seq.getSequenceAsString()); jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); } - - if (jsonExportSettings.isExportJalviewSettings()) + jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme); + jsonAlignmentPojo.getAppSettings().put("application", application); + jsonAlignmentPojo.getAppSettings().put("version", version); + jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl); + jsonAlignmentPojo.getAppSettings().put("showSeqFeatures", + String.valueOf(showSeqFeatures)); + + String[] hiddenSections = getHiddenSections(); + if (hiddenSections != null) { - jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme); - jsonAlignmentPojo.getAppSettings().put("application", application); - jsonAlignmentPojo.getAppSettings().put("version", version); - jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl); - jsonAlignmentPojo.getAppSettings().put("showSeqFeatures", - String.valueOf(showSeqFeatures)); - - String[] hiddenSections = exportHiddenSections(); - if (hiddenSections != null && getViewport().isIncludeHiddenRegion()) + if (hiddenSections[0] != null + && exportSettings.isExportHiddenColumns()) { - if (hiddenSections[0] != null) - { - jsonAlignmentPojo.getAppSettings().put("hiddenCols", - String.valueOf(hiddenSections[0])); - } - if (hiddenSections[1] != null) - { - jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", - String.valueOf(hiddenSections[1])); - } + jsonAlignmentPojo.getAppSettings().put("hiddenCols", + String.valueOf(hiddenSections[0])); + } + if (hiddenSections[1] != null + && exportSettings.isExportHiddenSequences()) + { + jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", + String.valueOf(hiddenSections[1])); } } - if (jsonExportSettings.isExportAnnotations()) + if (exportSettings.isExportAnnotations()) { 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 (jsonExportSettings.isExportSequenceFeatures()) + if (exportSettings.isExportFeatures()) { jsonAlignmentPojo .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr)); } - if (jsonExportSettings.isExportGroups() && seqGroups != null + if (exportSettings.isExportGroups() && seqGroups != null && seqGroups.size() > 0) { for (SequenceGroup seqGrp : seqGroups) @@ -209,7 +249,8 @@ public class JSONFile extends AlignFile 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); } @@ -226,7 +267,7 @@ public class JSONFile extends AlignFile return jsonOutput; } - public String[] exportHiddenSections() + public String[] getHiddenSections() { String[] hiddenSections = new String[2]; if (getViewport() == null) @@ -234,11 +275,9 @@ public class JSONFile extends AlignFile return null; } - System.out.println("--- Hidden Sections ---"); // hidden column business if (getViewport().hasHiddenColumns()) { - System.out.print("Hidden Cols : "); List hiddenCols = getViewport().getColumnSelection() .getHiddenColumns(); StringBuilder hiddenColsBuilder = new StringBuilder(); @@ -250,7 +289,6 @@ public class JSONFile extends AlignFile hiddenColsBuilder.deleteCharAt(0); hiddenSections[0] = hiddenColsBuilder.toString(); - System.out.println(hiddenSections[0]); } // hidden rows/seqs business @@ -262,8 +300,6 @@ public class JSONFile extends AlignFile } SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences; - System.out.print("Hidden Seqs : "); - // if(hiddenSeqs != null){ StringBuilder hiddenSeqsBuilder = new StringBuilder(); for (SequenceI hiddenSeq : hiddenSeqs) { @@ -273,21 +309,18 @@ public class JSONFile extends AlignFile } } if (hiddenSeqsBuilder.length() > 0) - { + { hiddenSeqsBuilder.deleteCharAt(0); - } + } hiddenSections[1] = hiddenSeqsBuilder.toString(); - System.out.println(hiddenSections[1]); - // } return hiddenSections; } - public static List sequenceFeatureToJsonPojo( + public List sequenceFeatureToJsonPojo( List seqs, FeatureRenderer fr) { - FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr - .getFeaturesDisplayed(); + displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); for (SequenceI seq : seqs) { @@ -309,9 +342,9 @@ public class JSONFile extends AlignFile { SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo( 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())); @@ -342,6 +375,26 @@ public class JSONFile extends AlignFile 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(); @@ -351,12 +404,28 @@ public class JSONFile extends AlignFile 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); @@ -365,7 +434,7 @@ public class JSONFile extends AlignFile } @SuppressWarnings("unchecked") - public JSONFile parse(String jsonAlignmentString) + public JSONFile parse(Reader jsonAlignmentString) { try { @@ -384,16 +453,16 @@ public class JSONFile extends AlignFile 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); } + hiddenSequences = new ArrayList(); seqMap = new Hashtable(); for (Iterator sequenceIter = seqJsonArray.iterator(); sequenceIter .hasNext();) @@ -408,11 +477,12 @@ public class JSONFile extends AlignFile end); if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId)) { - seq.setHidden(true); + hiddenSequences.add(seq); } seqs.add(seq); seqMap.put(seqUniqueId, seq); } + parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter @@ -434,12 +504,12 @@ public class JSONFile extends AlignFile 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(); @@ -450,9 +520,10 @@ public class JSONFile extends AlignFile } } } - ColourSchemeI scheme = getJalviewColorScheme(colourScheme); - SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme, + 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); @@ -480,12 +551,20 @@ public class JSONFile extends AlignFile .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; } @@ -493,9 +572,65 @@ public class JSONFile extends AlignFile 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(); @@ -507,9 +642,11 @@ public class JSONFile extends AlignFile { 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); } } @@ -517,14 +654,16 @@ public class JSONFile extends AlignFile public void parseHiddenCols(JSONObject jvSettingsJson) { - hiddenColumns = new ArrayList(); 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("-"); - hiddenColumns.add(new int[] - { Integer.valueOf(range[0]), Integer.valueOf(range[1]) }); + columnSelection.hideColumns(Integer.valueOf(range[0]), + Integer.valueOf(range[1])); } } } @@ -534,6 +673,7 @@ public class JSONFile extends AlignFile { if (jsonSeqFeatures != null) { + displayedFeatures = new FeaturesDisplayed(); for (Iterator seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr .hasNext();) { @@ -545,9 +685,6 @@ public class JSONFile extends AlignFile String descripiton = (String) jsonFeature.get("description"); String seqRef = (String) jsonFeature.get("sequenceRef"); Float score = Float.valueOf(jsonFeature.get("score").toString()); - // Hashtable otherDetails = (Hashtable) jsonFeature - // .get("otherDetails"); - // sequenceFeature.otherDetails = otherDetails; Sequence seq = seqMap.get(seqRef); SequenceFeature sequenceFeature = new SequenceFeature(); @@ -568,55 +705,23 @@ public class JSONFile extends AlignFile sequenceFeature.setBegin(seq.findPosition(begin.intValue())); sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1); seq.addSequenceFeature(sequenceFeature); + displayedFeatures.setVisible(type); } } } - 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 void applySettingsToAlignmentView(AlignViewControllerGuiI avc) - { - avc.setShowSeqFeatures(isShowSeqFeatures()); - avc.changeColour(getColourScheme()); - avc.setMenusForViewport(); - avc.hideColumns(hiddenColumns); - avc.syncHiddenSequences(); - } - - 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 public FeaturesDisplayedI getDisplayedFeatures() { return displayedFeatures; @@ -627,45 +732,33 @@ public class JSONFile extends AlignFile this.displayedFeatures = displayedFeatures; } - public JSONExportSettings getJsonExportSettings() - { - return jsonExportSettings; - } - - public void setJsonExportSettings(JSONExportSettings jsonExportSettings) + @Override + public void configureForView(AlignmentViewPanel avpanel) { - this.jsonExportSettings = jsonExportSettings; - } + super.configureForView(avpanel); + AlignViewportI viewport = avpanel.getAlignViewport(); + AlignmentI alignment = viewport.getAlignment(); + AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); - public static String getJSONData(AlignViewportI av) - { - JSONFile jsonFile = new JSONFile(); - jsonFile.setViewport(av); - jsonFile.seqGroups = av.getAlignment().getGroups(); - jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed()); + seqGroups = alignment.getGroups(); + fr = avpanel.cloneFeatureRenderer(); - for (SequenceI seq : av.getAlignment().getSequences()) - { - jsonFile.seqs.add(seq); - } - // Add non auto calculated annotation to AlignFile - for (AlignmentAnnotation annot : av.getAlignment() - .getAlignmentAnnotation()) + for (AlignmentAnnotation annot : annots) { if (annot != null && !annot.autoCalculated) { - if (annot.label.equals("PDB.CATempFactor")) - { - continue; - } - jsonFile.annotations.add(annot); + annotations.add(annot); } } - String jsonString = jsonFile.print(); - return jsonString; + globalColourScheme = ColourSchemeProperty.getColourName(viewport + .getGlobalColourScheme()); + setDisplayedFeatures(viewport.getFeaturesDisplayed()); + showSeqFeatures = viewport.isShowSequenceFeatures(); + } + @Override public boolean isShowSeqFeatures() { return showSeqFeatures; @@ -686,6 +779,35 @@ public class JSONFile extends AlignFile return hiddenColumns; } + @Override + public ColumnSelection getColumnSelection() + { + return columnSelection; + } + + public void setColumnSelection(ColumnSelection columnSelection) + { + this.columnSelection = columnSelection; + } + + @Override + public SequenceI[] getHiddenSequences() + { + if (hiddenSequences == null || hiddenSequences.isEmpty()) + { + return new SequenceI[] {}; + } + synchronized (hiddenSequences) + { + return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]); + } + } + + public void setHiddenSequences(ArrayList hiddenSequences) + { + this.hiddenSequences = hiddenSequences; + } + public class JSONExportSettings { private boolean exportSequence; @@ -748,4 +870,19 @@ public class JSONFile extends AlignFile 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(); + } }