/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; 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.HiddenColumns; import jalview.datamodel.HiddenSequences; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; 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; 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; 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 = "http://www.jalview.org/services/launchApp"; private String application = "Jalview"; private String globalColourScheme; private boolean showSeqFeatures; private Hashtable seqMap; private FeaturesDisplayedI displayedFeatures; private FeatureRenderer fr; private HiddenColumns hiddenColumns; private List hiddenSeqRefs; private ArrayList hiddenSequences; private final static String TCOFFEE_SCORE = "TCoffeeScore"; public JSONFile() { super(); } public JSONFile(FileParse source) throws IOException { super(source); } public JSONFile(String inFile, DataSourceType sourceType) throws IOException { super(inFile, sourceType); } @Override public void parse() throws IOException { parse(getReader()); } @Override public String print(SequenceI[] sqs, boolean jvsuffix) { String jsonOutput = null; try { AlignmentPojo jsonAlignmentPojo = new AlignmentPojo(); AlignExportSettingI exportSettings = getExportSettings(); // if no export settings were supplied use the following with all values // defaulting to true if (exportSettings == null) { 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; for (SequenceI seq : sqs) { StringBuilder name = new StringBuilder(); name.append(seq.getName()).append("/").append(seq.getStart()) .append("-").append(seq.getEnd()); SequencePojo jsonSeqPojo = new SequencePojo(); jsonSeqPojo.setId(String.valueOf(seq.hashCode())); jsonSeqPojo.setOrder(++count); jsonSeqPojo.setEnd(seq.getEnd()); jsonSeqPojo.setStart(seq.getStart()); jsonSeqPojo.setName(name.toString()); jsonSeqPojo.setSeq(seq.getSequenceAsString()); jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); } 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) { if (hiddenSections[0] != null && exportSettings.isExportHiddenColumns()) { jsonAlignmentPojo.getAppSettings().put("hiddenCols", String.valueOf(hiddenSections[0])); } if (hiddenSections[1] != null && exportSettings.isExportHiddenSequences()) { jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", String.valueOf(hiddenSections[1])); } } if (exportSettings.isExportAnnotations()) { 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(sqs)); } if (exportSettings.isExportGroups() && seqGroups != null && seqGroups.size() > 0) { for (SequenceGroup seqGrp : seqGroups) { SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo(); seqGrpPojo.setGroupName(seqGrp.getName()); seqGrpPojo.setColourScheme(ColourSchemeProperty .getColourName(seqGrp.getColourScheme())); seqGrpPojo.setColourText(seqGrp.getColourText()); seqGrpPojo.setDescription(seqGrp.getDescription()); seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes()); seqGrpPojo.setDisplayText(seqGrp.getDisplayText()); seqGrpPojo.setEndRes(seqGrp.getEndRes()); seqGrpPojo.setStartRes(seqGrp.getStartRes()); seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved()); for (SequenceI seq : seqGrp.getSequences()) { seqGrpPojo.getSequenceRefs() .add(String.valueOf(seq.hashCode())); } jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo); } } org.json.JSONObject generatedJSon = new org.json.JSONObject( jsonAlignmentPojo); jsonOutput = generatedJSon.toString(); return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend", "xEnd"); } catch (Exception e) { e.printStackTrace(); } return jsonOutput; } public String[] getHiddenSections() { String[] hiddenSections = new String[2]; if (getViewport() == null) { return null; } // hidden column business if (getViewport().hasHiddenColumns()) { hiddenSections[0] = getViewport().getAlignment().getHiddenColumns() .regionsToString(";", "-"); } // hidden rows/seqs business HiddenSequences hiddenSeqsObj = getViewport().getAlignment() .getHiddenSequences(); if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null) { return hiddenSections; } SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences; StringBuilder hiddenSeqsBuilder = new StringBuilder(); for (SequenceI hiddenSeq : hiddenSeqs) { if (hiddenSeq != null) { hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode()); } } if (hiddenSeqsBuilder.length() > 0) { hiddenSeqsBuilder.deleteCharAt(0); } hiddenSections[1] = hiddenSeqsBuilder.toString(); return hiddenSections; } protected List sequenceFeatureToJsonPojo( SequenceI[] sqs) { displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList<>(); if (sqs == null) { return sequenceFeaturesPojo; } 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) { 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; } public static List annotationToJsonPojo( Vector annotations) { List jsonAnnotations = new ArrayList<>(); if (annotations == null) { return jsonAnnotations; } for (AlignmentAnnotation annot : annotations) { 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(); if (annotation != null) { annotationPojo.setDescription(annotation.description); annotationPojo.setValue(annotation.value); annotationPojo .setSecondaryStructure(annotation.secondaryStructure); 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 { if (annot.getCalcId() != null && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE)) { // do nothing } else { alignAnnotPojo.getAnnotations().add(annotationPojo); } } } jsonAnnotations.add(alignAnnotPojo); } return jsonAnnotations; } @SuppressWarnings("unchecked") public JSONFile parse(Reader jsonAlignmentString) { try { JSONParser jsonParser = new JSONParser(); JSONObject alignmentJsonObj = (JSONObject) jsonParser .parse(jsonAlignmentString); JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs"); JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj .get("alignAnnotation"); JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj .get("seqFeatures"); JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj .get("seqGroups"); JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj .get("appSettings"); if (jvSettingsJsonObj != null) { globalColourScheme = (String) jvSettingsJsonObj .get("globalColorScheme"); Boolean showFeatures = Boolean.valueOf( jvSettingsJsonObj.get("showSeqFeatures").toString()); setShowSeqFeatures(showFeatures); parseHiddenSeqRefsAsList(jvSettingsJsonObj); parseHiddenCols(jvSettingsJsonObj); } hiddenSequences = new ArrayList<>(); seqMap = new Hashtable<>(); for (Iterator sequenceIter = seqJsonArray .iterator(); sequenceIter.hasNext();) { JSONObject sequence = sequenceIter.next(); String sequcenceString = sequence.get("seq").toString(); String sequenceName = sequence.get("name").toString(); String seqUniqueId = sequence.get("id").toString(); int start = Integer.valueOf(sequence.get("start").toString()); int end = Integer.valueOf(sequence.get("end").toString()); Sequence seq = new Sequence(sequenceName, sequcenceString, start, end); if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId)) { hiddenSequences.add(seq); } seqs.add(seq); seqMap.put(seqUniqueId, seq); } parseFeatures(jsonSeqArray); for (Iterator seqGrpIter = seqGrpJsonArray .iterator(); seqGrpIter.hasNext();) { JSONObject seqGrpObj = seqGrpIter.next(); String grpName = seqGrpObj.get("groupName").toString(); String colourScheme = seqGrpObj.get("colourScheme").toString(); String description = (seqGrpObj.get("description") == null) ? null : seqGrpObj.get("description").toString(); boolean displayBoxes = Boolean .valueOf(seqGrpObj.get("displayBoxes").toString()); boolean displayText = Boolean .valueOf(seqGrpObj.get("displayText").toString()); boolean colourText = Boolean .valueOf(seqGrpObj.get("colourText").toString()); boolean showNonconserved = Boolean .valueOf(seqGrpObj.get("showNonconserved").toString()); int startRes = Integer .valueOf(seqGrpObj.get("startRes").toString()); int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString()); JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs"); ArrayList grpSeqs = new ArrayList<>(); if (sequenceRefs.size() > 0) { Iterator seqHashIter = sequenceRefs.iterator(); while (seqHashIter.hasNext()) { String seqHash = seqHashIter.next(); Sequence sequence = seqMap.get(seqHash); if (sequence != null) { grpSeqs.add(sequence); } } } SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null, displayBoxes, displayText, colourText, startRes, endRes); seqGrp.setColourScheme(ColourSchemeMapper .getJalviewColourScheme(colourScheme, seqGrp)); seqGrp.setShowNonconserved(showNonconserved); seqGrp.setDescription(description); this.seqGroups.add(seqGrp); } for (Iterator alAnnotIter = alAnnotJsonArray .iterator(); alAnnotIter.hasNext();) { JSONObject alAnnot = alAnnotIter.next(); JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations"); Annotation[] annotations = new Annotation[annotJsonArray.size()]; int count = 0; for (Iterator annotIter = annotJsonArray .iterator(); annotIter.hasNext();) { JSONObject annot = annotIter.next(); if (annot == null) { annotations[count] = null; } else { float val = annot.get("value") == null ? null : Float.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() .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 = ColorUtils .parseColourString(annot.get("colour").toString()); annotations[count].colour = color; } } ++count; } 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(); } return this; } public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson) { hiddenSeqRefs = new ArrayList<>(); String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs"); if (hiddenSeqs != null && !hiddenSeqs.isEmpty()) { String[] seqRefs = hiddenSeqs.split(";"); for (String seqRef : seqRefs) { hiddenSeqRefs.add(seqRef); } } } public void parseHiddenCols(JSONObject jvSettingsJson) { String hiddenCols = (String) jvSettingsJson.get("hiddenCols"); if (hiddenCols != null && !hiddenCols.isEmpty()) { hiddenColumns = new HiddenColumns(); String[] rangeStrings = hiddenCols.split(";"); for (String rangeString : rangeStrings) { String[] range = rangeString.split("-"); hiddenColumns.hideColumns(Integer.valueOf(range[0]), Integer.valueOf(range[1])); } } } @SuppressWarnings("unchecked") private void parseFeatures(JSONArray jsonSeqFeatures) { if (jsonSeqFeatures != null) { displayedFeatures = new FeaturesDisplayed(); for (Iterator seqFeatureItr = jsonSeqFeatures .iterator(); seqFeatureItr.hasNext();) { JSONObject jsonFeature = seqFeatureItr.next(); Long begin = (Long) jsonFeature.get("xStart"); Long end = (Long) jsonFeature.get("xEnd"); String type = (String) jsonFeature.get("type"); String featureGrp = (String) jsonFeature.get("featureGroup"); 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); /* * 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) { Iterator linkList = linksJsonArray.iterator(); while (linkList.hasNext()) { String link = linkList.next(); sequenceFeature.addLink(link); } } seq.addSequenceFeature(sequenceFeature); displayedFeatures.setVisible(type); } } } @Override public String getGlobalColourScheme() { return globalColourScheme; } public void setGlobalColorScheme(String globalColourScheme) { this.globalColourScheme = globalColourScheme; } @Override public FeaturesDisplayedI getDisplayedFeatures() { return displayedFeatures; } public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures) { this.displayedFeatures = displayedFeatures; } @Override public void configureForView(AlignmentViewPanel avpanel) { if (avpanel == null) { return; } super.configureForView(avpanel); AlignViewportI viewport = avpanel.getAlignViewport(); AlignmentI alignment = viewport.getAlignment(); AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); seqGroups = alignment.getGroups(); fr = avpanel.cloneFeatureRenderer(); // Add non auto calculated annotation to AlignFile if (annots != null) { for (AlignmentAnnotation annot : annots) { if (annot != null && !annot.autoCalculated) { annotations.add(annot); } } } globalColourScheme = ColourSchemeProperty .getColourName(viewport.getGlobalColourScheme()); setDisplayedFeatures(viewport.getFeaturesDisplayed()); showSeqFeatures = viewport.isShowSequenceFeatures(); } @Override public boolean isShowSeqFeatures() { return showSeqFeatures; } public void setShowSeqFeatures(boolean showSeqFeatures) { this.showSeqFeatures = showSeqFeatures; } public Vector getAnnotations() { return annotations; } @Override public HiddenColumns getHiddenColumns() { return hiddenColumns; } public void setHiddenColumns(HiddenColumns hidden) { this.hiddenColumns = hidden; } @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; private boolean exportSequenceFeatures; private boolean exportAnnotations; private boolean exportGroups; private boolean exportJalviewSettings; public boolean isExportSequence() { return exportSequence; } public void setExportSequence(boolean exportSequence) { this.exportSequence = exportSequence; } public boolean isExportSequenceFeatures() { return exportSequenceFeatures; } public void setExportSequenceFeatures(boolean exportSequenceFeatures) { this.exportSequenceFeatures = exportSequenceFeatures; } public boolean isExportAnnotations() { return exportAnnotations; } public void setExportAnnotations(boolean exportAnnotations) { this.exportAnnotations = exportAnnotations; } public boolean isExportGroups() { return exportGroups; } public void setExportGroups(boolean exportGroups) { this.exportGroups = exportGroups; } public boolean isExportJalviewSettings() { return exportJalviewSettings; } public void setExportJalviewSettings(boolean exportJalviewSettings) { 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(); } }