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.AlignExportSettingsI;
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.AlignExportSettingsAdapter;
33 import jalview.datamodel.AlignmentAnnotation;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.Annotation;
36 import jalview.datamodel.HiddenColumns;
37 import jalview.datamodel.HiddenSequences;
38 import jalview.datamodel.Sequence;
39 import jalview.datamodel.SequenceFeature;
40 import jalview.datamodel.SequenceGroup;
41 import jalview.datamodel.SequenceI;
42 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
43 import jalview.json.binding.biojson.v1.AlignmentPojo;
44 import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
45 import jalview.json.binding.biojson.v1.AnnotationPojo;
46 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
47 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
48 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
49 import jalview.json.binding.biojson.v1.SequencePojo;
50 import jalview.renderer.seqfeatures.FeatureColourFinder;
51 import jalview.schemes.ColourSchemeProperty;
52 import jalview.schemes.JalviewColourScheme;
53 import jalview.schemes.ResidueColourScheme;
54 import jalview.util.ColorUtils;
55 import jalview.util.Format;
56 import jalview.util.JSONUtils;
57 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
59 import java.awt.Color;
60 import java.io.IOException;
61 import java.io.Reader;
62 import java.util.ArrayList;
63 import java.util.Hashtable;
64 import java.util.Iterator;
65 import java.util.List;
67 import java.util.Vector;
69 public class JSONFile extends AlignFile implements ComplexAlignFile
71 private static String version = new BuildDetails().getVersion();
73 private String webstartUrl = "https://www.jalview.org/services/launchApp";
75 private String application = "Jalview";
77 private String globalColourScheme;
79 private boolean showSeqFeatures;
81 private Hashtable<String, Sequence> seqMap;
83 private FeaturesDisplayedI displayedFeatures;
85 private FeatureRenderer fr;
87 private HiddenColumns hiddenColumns;
89 private List<String> hiddenSeqRefs;
91 private ArrayList<SequenceI> hiddenSequences;
93 private final static String TCOFFEE_SCORE = "TCoffeeScore";
100 public JSONFile(FileParse source) throws IOException
105 public JSONFile(String inFile, DataSourceType sourceType)
108 super(inFile, sourceType);
112 public void parse() throws IOException
119 public String print(SequenceI[] sqs, boolean jvsuffix)
121 String jsonOutput = null;
124 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
125 AlignExportSettingsI exportSettings = getExportSettings();
128 * if no export settings were supplied, provide an 'export all' setting
130 if (exportSettings == null)
132 exportSettings = new AlignExportSettingsAdapter(true);
136 for (SequenceI seq : sqs)
138 StringBuilder name = new StringBuilder();
139 name.append(seq.getName()).append("/").append(seq.getStart())
140 .append("-").append(seq.getEnd());
141 SequencePojo jsonSeqPojo = new SequencePojo();
142 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
143 jsonSeqPojo.setOrder(++count);
144 jsonSeqPojo.setEnd(seq.getEnd());
145 jsonSeqPojo.setStart(seq.getStart());
146 jsonSeqPojo.setName(name.toString());
147 jsonSeqPojo.setSeq(seq.getSequenceAsString());
148 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
150 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
151 jsonAlignmentPojo.getAppSettings().put("application", application);
152 jsonAlignmentPojo.getAppSettings().put("version", version);
153 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
154 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
155 String.valueOf(showSeqFeatures));
157 String[] hiddenSections = getHiddenSections();
158 if (hiddenSections != null)
160 if (hiddenSections[0] != null
161 && exportSettings.isExportHiddenColumns())
163 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
164 String.valueOf(hiddenSections[0]));
166 if (hiddenSections[1] != null
167 && exportSettings.isExportHiddenSequences())
169 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
170 String.valueOf(hiddenSections[1]));
174 if (exportSettings.isExportAnnotations())
177 .setAlignAnnotation(annotationToJsonPojo(annotations));
181 // These color schemes require annotation, disable them if annotations
183 if (globalColourScheme
184 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
185 || globalColourScheme.equalsIgnoreCase(
186 JalviewColourScheme.TCoffee.toString()))
188 jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
192 if (exportSettings.isExportFeatures())
194 jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
197 if (exportSettings.isExportGroups() && seqGroups != null
198 && seqGroups.size() > 0)
200 for (SequenceGroup seqGrp : seqGroups)
202 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
203 seqGrpPojo.setGroupName(seqGrp.getName());
204 seqGrpPojo.setColourScheme(ColourSchemeProperty
205 .getColourName(seqGrp.getColourScheme()));
206 seqGrpPojo.setColourText(seqGrp.getColourText());
207 seqGrpPojo.setDescription(seqGrp.getDescription());
208 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
209 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
210 seqGrpPojo.setEndRes(seqGrp.getEndRes());
211 seqGrpPojo.setStartRes(seqGrp.getStartRes());
212 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
213 for (SequenceI seq : seqGrp.getSequences())
215 seqGrpPojo.getSequenceRefs()
216 .add(String.valueOf(seq.hashCode()));
218 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
222 jsonOutput = JSONUtils.stringify(jsonAlignmentPojo);
223 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
225 } catch (Exception e)
232 public String[] getHiddenSections()
234 String[] hiddenSections = new String[2];
235 if (getViewport() == null)
240 // hidden column business
241 if (getViewport().hasHiddenColumns())
243 hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
244 .regionsToString(";", "-");
247 // hidden rows/seqs business
248 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
249 .getHiddenSequences();
250 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
252 return hiddenSections;
255 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
256 StringBuilder hiddenSeqsBuilder = new StringBuilder();
257 for (SequenceI hiddenSeq : hiddenSeqs)
259 if (hiddenSeq != null)
261 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
264 if (hiddenSeqsBuilder.length() > 0)
266 hiddenSeqsBuilder.deleteCharAt(0);
268 hiddenSections[1] = hiddenSeqsBuilder.toString();
270 return hiddenSections;
273 protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
276 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
277 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
280 return sequenceFeaturesPojo;
283 FeatureColourFinder finder = new FeatureColourFinder(fr);
285 String[] visibleFeatureTypes = displayedFeatures == null ? null
286 : displayedFeatures.getVisibleFeatures().toArray(
287 new String[displayedFeatures.getVisibleFeatureCount()]);
289 for (SequenceI seq : sqs)
292 * get all features currently visible (and any non-positional features)
294 List<SequenceFeature> seqFeatures = seq.getFeatures()
295 .getAllFeatures(visibleFeatureTypes);
296 for (SequenceFeature sf : seqFeatures)
298 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
299 String.valueOf(seq.hashCode()));
301 String featureColour = (fr == null) ? null
302 : Format.getHexString(finder.findFeatureColour(Color.white,
303 seq, seq.findIndex(sf.getBegin())));
304 int xStart = sf.getBegin() == 0 ? 0
305 : seq.findIndex(sf.getBegin()) - 1;
306 int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
307 jsonFeature.setXstart(xStart);
308 jsonFeature.setXend(xEnd);
309 jsonFeature.setType(sf.getType());
310 jsonFeature.setDescription(sf.getDescription());
311 jsonFeature.setLinks(sf.links);
312 jsonFeature.setOtherDetails(sf.otherDetails);
313 jsonFeature.setScore(sf.getScore());
314 jsonFeature.setFillColor(featureColour);
315 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
316 sequenceFeaturesPojo.add(jsonFeature);
319 return sequenceFeaturesPojo;
322 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
323 Vector<AlignmentAnnotation> annotations)
325 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
326 if (annotations == null)
328 return jsonAnnotations;
330 for (AlignmentAnnotation annot : annotations)
332 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
333 alignAnnotPojo.setDescription(annot.description);
334 alignAnnotPojo.setLabel(annot.label);
335 if (!Double.isNaN(annot.score))
337 alignAnnotPojo.setScore(annot.score);
339 alignAnnotPojo.setCalcId(annot.getCalcId());
340 alignAnnotPojo.setGraphType(annot.graph);
342 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
343 annotSetting.setBelowAlignment(annot.belowAlignment);
344 annotSetting.setCentreColLabels(annot.centreColLabels);
345 annotSetting.setScaleColLabel(annot.scaleColLabel);
346 annotSetting.setShowAllColLabels(annot.showAllColLabels);
347 annotSetting.setVisible(annot.visible);
348 annotSetting.setHasIcon(annot.hasIcons);
349 alignAnnotPojo.setAnnotationSettings(annotSetting);
350 SequenceI refSeq = annot.sequenceRef;
353 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
355 for (Annotation annotation : annot.annotations)
357 AnnotationPojo annotationPojo = new AnnotationPojo();
358 if (annotation != null)
360 annotationPojo.setDescription(annotation.description);
361 annotationPojo.setValue(annotation.value);
363 .setSecondaryStructure(annotation.secondaryStructure);
364 String displayChar = annotation.displayCharacter == null ? null
365 : annotation.displayCharacter;
366 // jalview.bin.Console.outPrintln("--------------------->[" +
367 // displayChar + "]");
368 annotationPojo.setDisplayCharacter(displayChar);
369 if (annotation.colour != null)
371 annotationPojo.setColour(
372 jalview.util.Format.getHexString(annotation.colour));
374 alignAnnotPojo.getAnnotations().add(annotationPojo);
378 if (annot.getCalcId() != null
379 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
385 alignAnnotPojo.getAnnotations().add(annotationPojo);
389 jsonAnnotations.add(alignAnnotPojo);
391 return jsonAnnotations;
394 @SuppressWarnings("unchecked")
395 public JSONFile parse(Reader jsonAlignmentString)
399 Map<String, Object> alignmentJsonObj = (Map<String, Object>) JSONUtils
400 .parse(jsonAlignmentString);
401 List<Object> seqJsonArray = (List<Object>) alignmentJsonObj
403 List<Object> alAnnotJsonArray = (List<Object>) alignmentJsonObj
404 .get("alignAnnotation");
405 List<Object> jsonSeqArray = (List<Object>) alignmentJsonObj
407 List<Object> seqGrpJsonArray = (List<Object>) alignmentJsonObj
409 Map<String, Object> jvSettingsJsonObj = (Map<String, Object>) alignmentJsonObj
412 if (jvSettingsJsonObj != null)
414 globalColourScheme = (String) jvSettingsJsonObj
415 .get("globalColorScheme");
416 Boolean showFeatures = Boolean.valueOf(
417 jvSettingsJsonObj.get("showSeqFeatures").toString());
418 setShowSeqFeatures(showFeatures);
419 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
420 parseHiddenCols(jvSettingsJsonObj);
423 hiddenSequences = new ArrayList<>();
424 seqMap = new Hashtable<>();
425 for (Iterator<Object> sequenceIter = seqJsonArray
426 .iterator(); sequenceIter.hasNext();)
428 Map<String, Object> sequence = (Map<String, Object>) sequenceIter
430 String sequcenceString = sequence.get("seq").toString();
431 String sequenceName = sequence.get("name").toString();
432 String seqUniqueId = sequence.get("id").toString();
433 int start = Integer.valueOf(sequence.get("start").toString());
434 int end = Integer.valueOf(sequence.get("end").toString());
435 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
437 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
439 hiddenSequences.add(seq);
442 seqMap.put(seqUniqueId, seq);
445 parseFeatures(jsonSeqArray);
447 for (Iterator<Object> seqGrpIter = seqGrpJsonArray
448 .iterator(); seqGrpIter.hasNext();)
450 Map<String, Object> seqGrpObj = (Map<String, Object>) seqGrpIter
452 String grpName = seqGrpObj.get("groupName").toString();
453 String colourScheme = seqGrpObj.get("colourScheme").toString();
454 String description = (seqGrpObj.get("description") == null) ? null
455 : seqGrpObj.get("description").toString();
456 boolean displayBoxes = Boolean
457 .valueOf(seqGrpObj.get("displayBoxes").toString());
458 boolean displayText = Boolean
459 .valueOf(seqGrpObj.get("displayText").toString());
460 boolean colourText = Boolean
461 .valueOf(seqGrpObj.get("colourText").toString());
462 boolean showNonconserved = Boolean
463 .valueOf(seqGrpObj.get("showNonconserved").toString());
464 int startRes = Integer
465 .valueOf(seqGrpObj.get("startRes").toString());
466 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
467 List<Object> sequenceRefs = (List<Object>) seqGrpObj
468 .get("sequenceRefs");
470 ArrayList<SequenceI> grpSeqs = new ArrayList<>();
471 if (sequenceRefs.size() > 0)
473 Iterator<Object> seqHashIter = sequenceRefs.iterator();
474 while (seqHashIter.hasNext())
476 Sequence sequence = seqMap.get(seqHashIter.next());
477 if (sequence != null)
479 grpSeqs.add(sequence);
483 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
484 displayBoxes, displayText, colourText, startRes, endRes);
485 seqGrp.setColourScheme(ColourSchemeMapper
486 .getJalviewColourScheme(colourScheme, seqGrp));
487 seqGrp.setShowNonconserved(showNonconserved);
488 seqGrp.setDescription(description);
489 this.seqGroups.add(seqGrp);
493 for (Iterator<Object> alAnnotIter = alAnnotJsonArray
494 .iterator(); alAnnotIter.hasNext();)
496 Map<String, Object> alAnnot = (Map<String, Object>) alAnnotIter
498 List<Object> annotJsonArray = (List<Object>) alAnnot
500 Annotation[] annotations = new Annotation[annotJsonArray.size()];
502 for (Iterator<Object> annotIter = annotJsonArray
503 .iterator(); annotIter.hasNext();)
505 Map<String, Object> annot = (Map<String, Object>) annotIter
509 annotations[count] = null;
513 float val = annot.get("value") == null ? null
514 : Float.valueOf(annot.get("value").toString());
515 String desc = annot.get("description") == null ? null
516 : annot.get("description").toString();
517 char ss = annot.get("secondaryStructure") == null
518 || annot.get("secondaryStructure").toString()
519 .equalsIgnoreCase("u0000") ? ' '
520 : annot.get("secondaryStructure")
521 .toString().charAt(0);
522 String displayChar = annot.get("displayCharacter") == null ? ""
523 : annot.get("displayCharacter").toString();
525 annotations[count] = new Annotation(displayChar, desc, ss, val);
526 if (annot.get("colour") != null)
528 Color color = ColorUtils
529 .parseColourString(annot.get("colour").toString());
530 annotations[count].colour = color;
536 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
537 alAnnot.get("label").toString(),
538 alAnnot.get("description").toString(), annotations);
539 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
540 : Integer.valueOf(alAnnot.get("graphType").toString());
542 Map<String, Object> diplaySettings = (Map<String, Object>) alAnnot
543 .get("annotationSettings");
544 if (diplaySettings != null)
547 alignAnnot.scaleColLabel = (diplaySettings
548 .get("scaleColLabel") == null) ? false
549 : Boolean.valueOf(diplaySettings
550 .get("scaleColLabel").toString());
551 alignAnnot.showAllColLabels = (diplaySettings
552 .get("showAllColLabels") == null) ? true
553 : Boolean.valueOf(diplaySettings
554 .get("showAllColLabels").toString());
555 alignAnnot.centreColLabels = (diplaySettings
556 .get("centreColLabels") == null) ? true
557 : Boolean.valueOf(diplaySettings
558 .get("centreColLabels").toString());
559 alignAnnot.belowAlignment = (diplaySettings
560 .get("belowAlignment") == null) ? false
561 : Boolean.valueOf(diplaySettings
562 .get("belowAlignment").toString());
563 alignAnnot.visible = (diplaySettings.get("visible") == null)
566 diplaySettings.get("visible").toString());
567 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
570 diplaySettings.get("hasIcon").toString());
573 if (alAnnot.get("score") != null)
575 alignAnnot.score = Double
576 .valueOf(alAnnot.get("score").toString());
579 String calcId = (alAnnot.get("calcId") == null) ? ""
580 : alAnnot.get("calcId").toString();
581 alignAnnot.setCalcId(calcId);
582 String seqHash = (alAnnot.get("sequenceRef") != null)
583 ? alAnnot.get("sequenceRef").toString()
586 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
587 if (sequence != null)
589 alignAnnot.sequenceRef = sequence;
590 sequence.addAlignmentAnnotation(alignAnnot);
591 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
593 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
595 sequence.addAlignmentAnnotation(alignAnnot);
596 alignAnnot.adjustForAlignment();
599 alignAnnot.validateRangeAndDisplay();
600 this.annotations.add(alignAnnot);
603 } catch (Exception e)
610 public void parseHiddenSeqRefsAsList(Map<String, Object> jvSettingsJson)
612 hiddenSeqRefs = new ArrayList<>();
613 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
614 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
616 String[] seqRefs = hiddenSeqs.split(";");
617 for (int i = 0, n = seqRefs.length; i < n; i++)
619 hiddenSeqRefs.add(seqRefs[i]);
624 public void parseHiddenCols(Map<String, Object> jvSettingsJson)
626 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
627 if (hiddenCols != null && !hiddenCols.isEmpty())
629 hiddenColumns = new HiddenColumns();
630 String[] rangeStrings = hiddenCols.split(";");
631 for (int i = 0, n = rangeStrings.length; i < n; i++)
633 String[] range = rangeStrings[i].split("-");
634 hiddenColumns.hideColumns(Integer.valueOf(range[0]),
635 Integer.valueOf(range[1]));
640 @SuppressWarnings("unchecked")
641 private void parseFeatures(List<Object> jsonSeqFeatures)
643 if (jsonSeqFeatures != null)
645 displayedFeatures = new FeaturesDisplayed();
646 for (Object o : jsonSeqFeatures)
648 Map<String, Object> jsonFeature = (Map<String, Object>) o;
649 Long begin = (Long) jsonFeature.get("xStart");
650 Long end = (Long) jsonFeature.get("xEnd");
651 String type = (String) jsonFeature.get("type");
652 String featureGrp = (String) jsonFeature.get("featureGroup");
653 String description = (String) jsonFeature.get("description");
654 String seqRef = (String) jsonFeature.get("sequenceRef");
655 Float score = Float.valueOf(jsonFeature.get("score").toString());
657 Sequence seq = seqMap.get(seqRef);
660 * begin/end of 0 is for a non-positional feature
662 int featureBegin = begin.intValue() == 0 ? 0
663 : seq.findPosition(begin.intValue());
664 int featureEnd = end.intValue() == 0 ? 0
665 : seq.findPosition(end.intValue()) - 1;
667 SequenceFeature sequenceFeature = new SequenceFeature(type,
668 description, featureBegin, featureEnd, score, featureGrp);
670 List<Object> linksJsonArray = (List<Object>) jsonFeature
672 if (linksJsonArray != null && linksJsonArray.size() > 0)
674 Iterator<Object> linkList = linksJsonArray.iterator();
675 while (linkList.hasNext())
677 sequenceFeature.addLink((String) linkList.next());
681 seq.addSequenceFeature(sequenceFeature);
682 displayedFeatures.setVisible(type);
688 public String getGlobalColourScheme()
690 return globalColourScheme;
693 public void setGlobalColorScheme(String globalColourScheme)
695 this.globalColourScheme = globalColourScheme;
699 public FeaturesDisplayedI getDisplayedFeatures()
701 return displayedFeatures;
704 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
706 this.displayedFeatures = displayedFeatures;
710 public void configureForView(AlignmentViewPanel avpanel)
716 super.configureForView(avpanel);
717 AlignViewportI viewport = avpanel.getAlignViewport();
718 AlignmentI alignment = viewport.getAlignment();
719 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
721 seqGroups = alignment.getGroups();
722 fr = avpanel.cloneFeatureRenderer();
724 // Add non auto calculated annotation to AlignFile
727 for (AlignmentAnnotation annot : annots)
729 if (annot != null && !annot.autoCalculated)
731 annotations.add(annot);
735 globalColourScheme = ColourSchemeProperty
736 .getColourName(viewport.getGlobalColourScheme());
737 setDisplayedFeatures(viewport.getFeaturesDisplayed());
738 showSeqFeatures = viewport.isShowSequenceFeatures();
743 public boolean isShowSeqFeatures()
745 return showSeqFeatures;
748 public void setShowSeqFeatures(boolean showSeqFeatures)
750 this.showSeqFeatures = showSeqFeatures;
753 public Vector<AlignmentAnnotation> getAnnotations()
759 public HiddenColumns getHiddenColumns()
761 return hiddenColumns;
764 public void setHiddenColumns(HiddenColumns hidden)
766 this.hiddenColumns = hidden;
770 public SequenceI[] getHiddenSequences()
772 if (hiddenSequences == null || hiddenSequences.isEmpty())
774 return new SequenceI[] {};
776 synchronized (hiddenSequences)
778 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
782 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
784 this.hiddenSequences = hiddenSequences;
787 public class JSONExportSettings
789 private boolean exportSequence;
791 private boolean exportSequenceFeatures;
793 private boolean exportAnnotations;
795 private boolean exportGroups;
797 private boolean exportJalviewSettings;
799 public boolean isExportSequence()
801 return exportSequence;
804 public void setExportSequence(boolean exportSequence)
806 this.exportSequence = exportSequence;
809 public boolean isExportSequenceFeatures()
811 return exportSequenceFeatures;
814 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
816 this.exportSequenceFeatures = exportSequenceFeatures;
819 public boolean isExportAnnotations()
821 return exportAnnotations;
824 public void setExportAnnotations(boolean exportAnnotations)
826 this.exportAnnotations = exportAnnotations;
829 public boolean isExportGroups()
834 public void setExportGroups(boolean exportGroups)
836 this.exportGroups = exportGroups;
839 public boolean isExportJalviewSettings()
841 return exportJalviewSettings;
844 public void setExportJalviewSettings(boolean exportJalviewSettings)
846 this.exportJalviewSettings = exportJalviewSettings;
851 * Returns a descriptor for suitable feature display settings with
853 * <li>ResNums or insertions features visible</li>
854 * <li>insertions features coloured red</li>
855 * <li>ResNum features coloured by label</li>
856 * <li>Insertions displayed above (on top of) ResNums</li>
860 public FeatureSettingsModelI getFeatureColourScheme()
862 return new PDBFeatureSettings();