2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import jalview.api.AlignExportSettingI;
25 import jalview.api.AlignViewportI;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.api.ComplexAlignFile;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.FeatureSettingsModelI;
30 import jalview.api.FeaturesDisplayedI;
31 import jalview.bin.BuildDetails;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Annotation;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.HiddenSequences;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
42 import jalview.json.binding.biojson.v1.AlignmentPojo;
43 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
44 import jalview.json.binding.biojson.v1.AnnotationPojo;
45 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
46 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
47 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
48 import jalview.json.binding.biojson.v1.SequencePojo;
49 import jalview.renderer.seqfeatures.FeatureColourFinder;
50 import jalview.schemes.ColourSchemeProperty;
51 import jalview.schemes.JalviewColourScheme;
52 import jalview.schemes.ResidueColourScheme;
53 import jalview.util.ColorUtils;
54 import jalview.util.Format;
55 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
57 import java.awt.Color;
58 import java.io.IOException;
59 import java.io.Reader;
60 import java.util.ArrayList;
61 import java.util.Hashtable;
62 import java.util.Iterator;
63 import java.util.List;
64 import java.util.Vector;
66 import org.json.simple.JSONArray;
67 import org.json.simple.JSONObject;
68 import org.json.simple.parser.JSONParser;
70 public class JSONFile extends AlignFile implements ComplexAlignFile
72 private static String version = new BuildDetails().getVersion();
74 private String webstartUrl = "http://www.jalview.org/services/launchApp";
76 private String application = "Jalview";
78 private String globalColourScheme;
80 private boolean showSeqFeatures;
82 private Hashtable<String, Sequence> seqMap;
84 private FeaturesDisplayedI displayedFeatures;
86 private FeatureRenderer fr;
88 private HiddenColumns hiddenColumns;
90 private List<String> hiddenSeqRefs;
92 private ArrayList<SequenceI> hiddenSequences;
94 private final static String TCOFFEE_SCORE = "TCoffeeScore";
101 public JSONFile(FileParse source) throws IOException
106 public JSONFile(String inFile, DataSourceType sourceType)
109 super(inFile, sourceType);
113 public void parse() throws IOException
120 public String print(SequenceI[] sqs, boolean jvsuffix)
122 String jsonOutput = null;
125 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
126 AlignExportSettingI exportSettings = getExportSettings();
128 // if no export settings were supplied use the following with all values
129 // defaulting to true
130 if (exportSettings == null)
132 exportSettings = new AlignExportSettingI()
135 public boolean isExportHiddenSequences()
141 public boolean isExportHiddenColumns()
147 public boolean isExportGroups()
153 public boolean isExportFeatures()
159 public boolean isExportAnnotations()
165 public boolean isCancelled()
173 for (SequenceI seq : sqs)
175 StringBuilder name = new StringBuilder();
176 name.append(seq.getName()).append("/").append(seq.getStart())
177 .append("-").append(seq.getEnd());
178 SequencePojo jsonSeqPojo = new SequencePojo();
179 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
180 jsonSeqPojo.setOrder(++count);
181 jsonSeqPojo.setEnd(seq.getEnd());
182 jsonSeqPojo.setStart(seq.getStart());
183 jsonSeqPojo.setName(name.toString());
184 jsonSeqPojo.setSeq(seq.getSequenceAsString());
185 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
187 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
188 jsonAlignmentPojo.getAppSettings().put("application", application);
189 jsonAlignmentPojo.getAppSettings().put("version", version);
190 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
191 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
192 String.valueOf(showSeqFeatures));
194 String[] hiddenSections = getHiddenSections();
195 if (hiddenSections != null)
197 if (hiddenSections[0] != null
198 && exportSettings.isExportHiddenColumns())
200 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
201 String.valueOf(hiddenSections[0]));
203 if (hiddenSections[1] != null
204 && exportSettings.isExportHiddenSequences())
206 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
207 String.valueOf(hiddenSections[1]));
211 if (exportSettings.isExportAnnotations())
214 .setAlignAnnotation(annotationToJsonPojo(annotations));
218 // These color schemes require annotation, disable them if annotations
220 if (globalColourScheme
221 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
222 || globalColourScheme
223 .equalsIgnoreCase(JalviewColourScheme.TCoffee
226 jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
230 if (exportSettings.isExportFeatures())
232 jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
235 if (exportSettings.isExportGroups() && seqGroups != null
236 && seqGroups.size() > 0)
238 for (SequenceGroup seqGrp : seqGroups)
240 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
241 seqGrpPojo.setGroupName(seqGrp.getName());
242 seqGrpPojo.setColourScheme(ColourSchemeProperty
243 .getColourName(seqGrp.getColourScheme()));
244 seqGrpPojo.setColourText(seqGrp.getColourText());
245 seqGrpPojo.setDescription(seqGrp.getDescription());
246 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
247 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
248 seqGrpPojo.setEndRes(seqGrp.getEndRes());
249 seqGrpPojo.setStartRes(seqGrp.getStartRes());
250 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
251 for (SequenceI seq : seqGrp.getSequences())
253 seqGrpPojo.getSequenceRefs()
254 .add(String.valueOf(seq.hashCode()));
256 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
259 org.json.JSONObject generatedJSon = new org.json.JSONObject(
261 jsonOutput = generatedJSon.toString();
262 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
264 } catch (Exception e)
271 public String[] getHiddenSections()
273 String[] hiddenSections = new String[2];
274 if (getViewport() == null)
279 // hidden column business
280 if (getViewport().hasHiddenColumns())
282 hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
283 .regionsToString(";", "-");
286 // hidden rows/seqs business
287 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
288 .getHiddenSequences();
289 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
291 return hiddenSections;
294 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
295 StringBuilder hiddenSeqsBuilder = new StringBuilder();
296 for (SequenceI hiddenSeq : hiddenSeqs)
298 if (hiddenSeq != null)
300 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
303 if (hiddenSeqsBuilder.length() > 0)
305 hiddenSeqsBuilder.deleteCharAt(0);
307 hiddenSections[1] = hiddenSeqsBuilder.toString();
309 return hiddenSections;
312 protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
315 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
316 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
319 return sequenceFeaturesPojo;
322 FeatureColourFinder finder = new FeatureColourFinder(fr);
324 String[] visibleFeatureTypes = displayedFeatures == null ? null
325 : displayedFeatures.getVisibleFeatures().toArray(
326 new String[displayedFeatures.getVisibleFeatureCount()]);
328 for (SequenceI seq : sqs)
331 * get all features currently visible (and any non-positional features)
333 List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
334 visibleFeatureTypes);
335 for (SequenceFeature sf : seqFeatures)
337 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
338 String.valueOf(seq.hashCode()));
340 String featureColour = (fr == null) ? null : Format
341 .getHexString(finder.findFeatureColour(Color.white, seq,
342 seq.findIndex(sf.getBegin())));
343 int xStart = sf.getBegin() == 0 ? 0
344 : seq.findIndex(sf.getBegin()) - 1;
345 int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
346 jsonFeature.setXstart(xStart);
347 jsonFeature.setXend(xEnd);
348 jsonFeature.setType(sf.getType());
349 jsonFeature.setDescription(sf.getDescription());
350 jsonFeature.setLinks(sf.links);
351 jsonFeature.setOtherDetails(sf.otherDetails);
352 jsonFeature.setScore(sf.getScore());
353 jsonFeature.setFillColor(featureColour);
354 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
355 sequenceFeaturesPojo.add(jsonFeature);
358 return sequenceFeaturesPojo;
361 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
362 Vector<AlignmentAnnotation> annotations)
364 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
365 if (annotations == null)
367 return jsonAnnotations;
369 for (AlignmentAnnotation annot : annotations)
371 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
372 alignAnnotPojo.setDescription(annot.description);
373 alignAnnotPojo.setLabel(annot.label);
374 if (!Double.isNaN(annot.score))
376 alignAnnotPojo.setScore(annot.score);
378 alignAnnotPojo.setCalcId(annot.getCalcId());
379 alignAnnotPojo.setGraphType(annot.graph);
381 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
382 annotSetting.setBelowAlignment(annot.belowAlignment);
383 annotSetting.setCentreColLabels(annot.centreColLabels);
384 annotSetting.setScaleColLabel(annot.scaleColLabel);
385 annotSetting.setShowAllColLabels(annot.showAllColLabels);
386 annotSetting.setVisible(annot.visible);
387 annotSetting.setHasIcon(annot.hasIcons);
388 alignAnnotPojo.setAnnotationSettings(annotSetting);
389 SequenceI refSeq = annot.sequenceRef;
392 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
394 for (Annotation annotation : annot.annotations)
396 AnnotationPojo annotationPojo = new AnnotationPojo();
397 if (annotation != null)
399 annotationPojo.setDescription(annotation.description);
400 annotationPojo.setValue(annotation.value);
402 .setSecondaryStructure(annotation.secondaryStructure);
403 String displayChar = annotation.displayCharacter == null ? null
404 : annotation.displayCharacter;
405 // System.out.println("--------------------->[" + displayChar + "]");
406 annotationPojo.setDisplayCharacter(displayChar);
407 if (annotation.colour != null)
409 annotationPojo.setColour(jalview.util.Format
410 .getHexString(annotation.colour));
412 alignAnnotPojo.getAnnotations().add(annotationPojo);
416 if (annot.getCalcId() != null
417 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
423 alignAnnotPojo.getAnnotations().add(annotationPojo);
427 jsonAnnotations.add(alignAnnotPojo);
429 return jsonAnnotations;
432 @SuppressWarnings("unchecked")
433 public JSONFile parse(Reader jsonAlignmentString)
437 JSONParser jsonParser = new JSONParser();
438 JSONObject alignmentJsonObj = (JSONObject) jsonParser
439 .parse(jsonAlignmentString);
440 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
441 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
442 .get("alignAnnotation");
443 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
445 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
447 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
450 if (jvSettingsJsonObj != null)
452 globalColourScheme = (String) jvSettingsJsonObj
453 .get("globalColorScheme");
454 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
455 "showSeqFeatures").toString());
456 setShowSeqFeatures(showFeatures);
457 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
458 parseHiddenCols(jvSettingsJsonObj);
461 hiddenSequences = new ArrayList<>();
462 seqMap = new Hashtable<>();
463 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
466 JSONObject sequence = sequenceIter.next();
467 String sequcenceString = sequence.get("seq").toString();
468 String sequenceName = sequence.get("name").toString();
469 String seqUniqueId = sequence.get("id").toString();
470 int start = Integer.valueOf(sequence.get("start").toString());
471 int end = Integer.valueOf(sequence.get("end").toString());
472 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
474 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
476 hiddenSequences.add(seq);
479 seqMap.put(seqUniqueId, seq);
482 parseFeatures(jsonSeqArray);
484 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
487 JSONObject seqGrpObj = seqGrpIter.next();
488 String grpName = seqGrpObj.get("groupName").toString();
489 String colourScheme = seqGrpObj.get("colourScheme").toString();
490 String description = (seqGrpObj.get("description") == null) ? null
491 : seqGrpObj.get("description").toString();
492 boolean displayBoxes = Boolean.valueOf(seqGrpObj
493 .get("displayBoxes").toString());
494 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
496 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
498 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
499 "showNonconserved").toString());
500 int startRes = Integer
501 .valueOf(seqGrpObj.get("startRes").toString());
502 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
503 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
505 ArrayList<SequenceI> grpSeqs = new ArrayList<>();
506 if (sequenceRefs.size() > 0)
508 Iterator<String> seqHashIter = sequenceRefs.iterator();
509 while (seqHashIter.hasNext())
511 String seqHash = seqHashIter.next();
512 Sequence sequence = seqMap.get(seqHash);
513 if (sequence != null)
515 grpSeqs.add(sequence);
519 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
520 displayBoxes, displayText, colourText, startRes, endRes);
521 seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
522 colourScheme, seqGrp));
523 seqGrp.setShowNonconserved(showNonconserved);
524 seqGrp.setDescription(description);
525 this.seqGroups.add(seqGrp);
529 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
532 JSONObject alAnnot = alAnnotIter.next();
533 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
534 Annotation[] annotations = new Annotation[annotJsonArray.size()];
536 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
539 JSONObject annot = annotIter.next();
542 annotations[count] = null;
546 float val = annot.get("value") == null ? null : Float
547 .valueOf(annot.get("value").toString());
548 String desc = annot.get("description") == null ? null : annot
549 .get("description").toString();
550 char ss = annot.get("secondaryStructure") == null
551 || annot.get("secondaryStructure").toString()
552 .equalsIgnoreCase("u0000") ? ' ' : annot
553 .get("secondaryStructure").toString().charAt(0);
554 String displayChar = annot.get("displayCharacter") == null ? ""
555 : annot.get("displayCharacter").toString();
557 annotations[count] = new Annotation(displayChar, desc, ss, val);
558 if (annot.get("colour") != null)
560 Color color = ColorUtils.parseColourString(annot.get(
561 "colour").toString());
562 annotations[count].colour = color;
568 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
569 .get("label").toString(), alAnnot.get("description")
570 .toString(), annotations);
571 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
572 .valueOf(alAnnot.get("graphType").toString());
574 JSONObject diplaySettings = (JSONObject) alAnnot
575 .get("annotationSettings");
576 if (diplaySettings != null)
579 alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
580 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
582 alignAnnot.showAllColLabels = (diplaySettings
583 .get("showAllColLabels") == null) ? true : Boolean
584 .valueOf(diplaySettings.get("showAllColLabels")
586 alignAnnot.centreColLabels = (diplaySettings
587 .get("centreColLabels") == null) ? true
588 : Boolean.valueOf(diplaySettings.get("centreColLabels")
590 alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
591 : Boolean.valueOf(diplaySettings.get("belowAlignment")
593 alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
594 : Boolean.valueOf(diplaySettings.get("visible")
596 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
597 : Boolean.valueOf(diplaySettings.get("hasIcon")
601 if (alAnnot.get("score") != null)
603 alignAnnot.score = Double
604 .valueOf(alAnnot.get("score").toString());
607 String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
608 "calcId").toString();
609 alignAnnot.setCalcId(calcId);
610 String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
611 .get("sequenceRef").toString() : null;
613 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
614 if (sequence != null)
616 alignAnnot.sequenceRef = sequence;
617 sequence.addAlignmentAnnotation(alignAnnot);
618 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
620 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
622 sequence.addAlignmentAnnotation(alignAnnot);
623 alignAnnot.adjustForAlignment();
626 alignAnnot.validateRangeAndDisplay();
627 this.annotations.add(alignAnnot);
630 } catch (Exception e)
637 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
639 hiddenSeqRefs = new ArrayList<>();
640 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
641 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
643 String[] seqRefs = hiddenSeqs.split(";");
644 for (String seqRef : seqRefs)
646 hiddenSeqRefs.add(seqRef);
651 public void parseHiddenCols(JSONObject jvSettingsJson)
653 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
654 if (hiddenCols != null && !hiddenCols.isEmpty())
656 hiddenColumns = new HiddenColumns();
657 String[] rangeStrings = hiddenCols.split(";");
658 for (String rangeString : rangeStrings)
660 String[] range = rangeString.split("-");
661 hiddenColumns.hideColumns(Integer.valueOf(range[0]),
662 Integer.valueOf(range[1]));
667 @SuppressWarnings("unchecked")
668 private void parseFeatures(JSONArray jsonSeqFeatures)
670 if (jsonSeqFeatures != null)
672 displayedFeatures = new FeaturesDisplayed();
673 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
676 JSONObject jsonFeature = seqFeatureItr.next();
677 Long begin = (Long) jsonFeature.get("xStart");
678 Long end = (Long) jsonFeature.get("xEnd");
679 String type = (String) jsonFeature.get("type");
680 String featureGrp = (String) jsonFeature.get("featureGroup");
681 String description = (String) jsonFeature.get("description");
682 String seqRef = (String) jsonFeature.get("sequenceRef");
683 Float score = Float.valueOf(jsonFeature.get("score").toString());
685 Sequence seq = seqMap.get(seqRef);
688 * begin/end of 0 is for a non-positional feature
690 int featureBegin = begin.intValue() == 0 ? 0 : seq
691 .findPosition(begin.intValue());
692 int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
695 SequenceFeature sequenceFeature = new SequenceFeature(type,
696 description, featureBegin, featureEnd, score, featureGrp);
698 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
699 if (linksJsonArray != null && linksJsonArray.size() > 0)
701 Iterator<String> linkList = linksJsonArray.iterator();
702 while (linkList.hasNext())
704 String link = linkList.next();
705 sequenceFeature.addLink(link);
709 seq.addSequenceFeature(sequenceFeature);
710 displayedFeatures.setVisible(type);
716 public String getGlobalColourScheme()
718 return globalColourScheme;
721 public void setGlobalColorScheme(String globalColourScheme)
723 this.globalColourScheme = globalColourScheme;
727 public FeaturesDisplayedI getDisplayedFeatures()
729 return displayedFeatures;
732 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
734 this.displayedFeatures = displayedFeatures;
738 public void configureForView(AlignmentViewPanel avpanel)
744 super.configureForView(avpanel);
745 AlignViewportI viewport = avpanel.getAlignViewport();
746 AlignmentI alignment = viewport.getAlignment();
747 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
749 seqGroups = alignment.getGroups();
750 fr = avpanel.cloneFeatureRenderer();
752 // Add non auto calculated annotation to AlignFile
755 for (AlignmentAnnotation annot : annots)
757 if (annot != null && !annot.autoCalculated)
759 annotations.add(annot);
763 globalColourScheme = ColourSchemeProperty.getColourName(viewport
764 .getGlobalColourScheme());
765 setDisplayedFeatures(viewport.getFeaturesDisplayed());
766 showSeqFeatures = viewport.isShowSequenceFeatures();
771 public boolean isShowSeqFeatures()
773 return showSeqFeatures;
776 public void setShowSeqFeatures(boolean showSeqFeatures)
778 this.showSeqFeatures = showSeqFeatures;
781 public Vector<AlignmentAnnotation> getAnnotations()
787 public HiddenColumns getHiddenColumns()
789 return hiddenColumns;
792 public void setHiddenColumns(HiddenColumns hidden)
794 this.hiddenColumns = hidden;
798 public SequenceI[] getHiddenSequences()
800 if (hiddenSequences == null || hiddenSequences.isEmpty())
802 return new SequenceI[] {};
804 synchronized (hiddenSequences)
806 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
810 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
812 this.hiddenSequences = hiddenSequences;
815 public class JSONExportSettings
817 private boolean exportSequence;
819 private boolean exportSequenceFeatures;
821 private boolean exportAnnotations;
823 private boolean exportGroups;
825 private boolean exportJalviewSettings;
827 public boolean isExportSequence()
829 return exportSequence;
832 public void setExportSequence(boolean exportSequence)
834 this.exportSequence = exportSequence;
837 public boolean isExportSequenceFeatures()
839 return exportSequenceFeatures;
842 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
844 this.exportSequenceFeatures = exportSequenceFeatures;
847 public boolean isExportAnnotations()
849 return exportAnnotations;
852 public void setExportAnnotations(boolean exportAnnotations)
854 this.exportAnnotations = exportAnnotations;
857 public boolean isExportGroups()
862 public void setExportGroups(boolean exportGroups)
864 this.exportGroups = exportGroups;
867 public boolean isExportJalviewSettings()
869 return exportJalviewSettings;
872 public void setExportJalviewSettings(boolean exportJalviewSettings)
874 this.exportJalviewSettings = exportJalviewSettings;
879 * Returns a descriptor for suitable feature display settings with
881 * <li>ResNums or insertions features visible</li>
882 * <li>insertions features coloured red</li>
883 * <li>ResNum features coloured by label</li>
884 * <li>Insertions displayed above (on top of) ResNums</li>
888 public FeatureSettingsModelI getFeatureColourScheme()
890 return new PDBFeatureSettings();