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.viewmodel.seqfeatures.FeaturesDisplayed;
56 import java.awt.Color;
57 import java.io.IOException;
58 import java.io.Reader;
59 import java.util.ArrayList;
60 import java.util.Hashtable;
61 import java.util.Iterator;
62 import java.util.List;
63 import java.util.Vector;
65 import org.json.simple.JSONArray;
66 import org.json.simple.JSONObject;
67 import org.json.simple.parser.JSONParser;
69 public class JSONFile extends AlignFile implements ComplexAlignFile
71 private static String version = new BuildDetails().getVersion();
73 private String webstartUrl = "http://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 AlignExportSettingI exportSettings = getExportSettings();
127 // if no export settings were supplied use the following with all values
128 // defaulting to true
129 if (exportSettings == null)
131 exportSettings = new AlignExportSettingI()
134 public boolean isExportHiddenSequences()
140 public boolean isExportHiddenColumns()
146 public boolean isExportGroups()
152 public boolean isExportFeatures()
158 public boolean isExportAnnotations()
164 public boolean isCancelled()
172 for (SequenceI seq : sqs)
174 StringBuilder name = new StringBuilder();
175 name.append(seq.getName()).append("/").append(seq.getStart())
176 .append("-").append(seq.getEnd());
177 SequencePojo jsonSeqPojo = new SequencePojo();
178 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
179 jsonSeqPojo.setOrder(++count);
180 jsonSeqPojo.setEnd(seq.getEnd());
181 jsonSeqPojo.setStart(seq.getStart());
182 jsonSeqPojo.setName(name.toString());
183 jsonSeqPojo.setSeq(seq.getSequenceAsString());
184 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
186 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
187 jsonAlignmentPojo.getAppSettings().put("application", application);
188 jsonAlignmentPojo.getAppSettings().put("version", version);
189 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
190 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
191 String.valueOf(showSeqFeatures));
193 String[] hiddenSections = getHiddenSections();
194 if (hiddenSections != null)
196 if (hiddenSections[0] != null
197 && exportSettings.isExportHiddenColumns())
199 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
200 String.valueOf(hiddenSections[0]));
202 if (hiddenSections[1] != null
203 && exportSettings.isExportHiddenSequences())
205 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
206 String.valueOf(hiddenSections[1]));
210 if (exportSettings.isExportAnnotations())
213 .setAlignAnnotation(annotationToJsonPojo(annotations));
217 // These color schemes require annotation, disable them if annotations
219 if (globalColourScheme
220 .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
221 || globalColourScheme.equalsIgnoreCase(
222 JalviewColourScheme.TCoffee.toString()))
224 jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
228 if (exportSettings.isExportFeatures())
231 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
234 if (exportSettings.isExportGroups() && seqGroups != null
235 && seqGroups.size() > 0)
237 for (SequenceGroup seqGrp : seqGroups)
239 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
240 seqGrpPojo.setGroupName(seqGrp.getName());
241 seqGrpPojo.setColourScheme(ColourSchemeProperty
242 .getColourName(seqGrp.getColourScheme()));
243 seqGrpPojo.setColourText(seqGrp.getColourText());
244 seqGrpPojo.setDescription(seqGrp.getDescription());
245 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
246 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
247 seqGrpPojo.setEndRes(seqGrp.getEndRes());
248 seqGrpPojo.setStartRes(seqGrp.getStartRes());
249 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
250 for (SequenceI seq : seqGrp.getSequences())
252 seqGrpPojo.getSequenceRefs()
253 .add(String.valueOf(seq.hashCode()));
255 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
258 org.json.JSONObject generatedJSon = new org.json.JSONObject(
260 jsonOutput = generatedJSon.toString();
261 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
263 } catch (Exception e)
270 public String[] getHiddenSections()
272 String[] hiddenSections = new String[2];
273 if (getViewport() == null)
278 // hidden column business
279 if (getViewport().hasHiddenColumns())
281 hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
282 .regionsToString(";", "-");
285 // hidden rows/seqs business
286 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
287 .getHiddenSequences();
288 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
290 return hiddenSections;
293 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
294 StringBuilder hiddenSeqsBuilder = new StringBuilder();
295 for (SequenceI hiddenSeq : hiddenSeqs)
297 if (hiddenSeq != null)
299 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
302 if (hiddenSeqsBuilder.length() > 0)
304 hiddenSeqsBuilder.deleteCharAt(0);
306 hiddenSections[1] = hiddenSeqsBuilder.toString();
308 return hiddenSections;
311 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
312 SequenceI[] sqs, FeatureRenderer fr)
314 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
315 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
318 return sequenceFeaturesPojo;
321 FeatureColourFinder finder = new FeatureColourFinder(fr);
323 for (SequenceI seq : sqs)
325 SequenceI dataSetSequence = seq.getDatasetSequence();
326 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
327 : seq.getDatasetSequence().getSequenceFeatures();
329 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
331 if (seqFeatures == null)
336 for (SequenceFeature sf : seqFeatures)
338 if (displayedFeatures != null
339 && displayedFeatures.isVisible(sf.getType()))
341 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
342 String.valueOf(seq.hashCode()));
344 String featureColour = (fr == null) ? null
345 : jalview.util.Format.getHexString(
346 finder.findFeatureColour(Color.white, seq,
347 seq.findIndex(sf.getBegin())));
348 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
349 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
350 jsonFeature.setType(sf.getType());
351 jsonFeature.setDescription(sf.getDescription());
352 jsonFeature.setLinks(sf.links);
353 jsonFeature.setOtherDetails(sf.otherDetails);
354 jsonFeature.setScore(sf.getScore());
355 jsonFeature.setFillColor(featureColour);
356 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
357 sequenceFeaturesPojo.add(jsonFeature);
361 return sequenceFeaturesPojo;
364 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
365 Vector<AlignmentAnnotation> annotations)
367 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
368 if (annotations == null)
370 return jsonAnnotations;
372 for (AlignmentAnnotation annot : annotations)
374 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
375 alignAnnotPojo.setDescription(annot.description);
376 alignAnnotPojo.setLabel(annot.label);
377 if (!Double.isNaN(annot.score))
379 alignAnnotPojo.setScore(annot.score);
381 alignAnnotPojo.setCalcId(annot.getCalcId());
382 alignAnnotPojo.setGraphType(annot.graph);
384 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
385 annotSetting.setBelowAlignment(annot.belowAlignment);
386 annotSetting.setCentreColLabels(annot.centreColLabels);
387 annotSetting.setScaleColLabel(annot.scaleColLabel);
388 annotSetting.setShowAllColLabels(annot.showAllColLabels);
389 annotSetting.setVisible(annot.visible);
390 annotSetting.setHasIcon(annot.hasIcons);
391 alignAnnotPojo.setAnnotationSettings(annotSetting);
392 SequenceI refSeq = annot.sequenceRef;
395 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
397 for (Annotation annotation : annot.annotations)
399 AnnotationPojo annotationPojo = new AnnotationPojo();
400 if (annotation != null)
402 annotationPojo.setDescription(annotation.description);
403 annotationPojo.setValue(annotation.value);
405 .setSecondaryStructure(annotation.secondaryStructure);
406 String displayChar = annotation.displayCharacter == null ? null
407 : annotation.displayCharacter;
408 // System.out.println("--------------------->[" + displayChar + "]");
409 annotationPojo.setDisplayCharacter(displayChar);
410 if (annotation.colour != null)
412 annotationPojo.setColour(
413 jalview.util.Format.getHexString(annotation.colour));
415 alignAnnotPojo.getAnnotations().add(annotationPojo);
419 if (annot.getCalcId() != null
420 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
426 alignAnnotPojo.getAnnotations().add(annotationPojo);
430 jsonAnnotations.add(alignAnnotPojo);
432 return jsonAnnotations;
435 @SuppressWarnings("unchecked")
436 public JSONFile parse(Reader jsonAlignmentString)
440 JSONParser jsonParser = new JSONParser();
441 JSONObject alignmentJsonObj = (JSONObject) jsonParser
442 .parse(jsonAlignmentString);
443 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
444 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
445 .get("alignAnnotation");
446 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
448 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
450 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
453 if (jvSettingsJsonObj != null)
455 globalColourScheme = (String) jvSettingsJsonObj
456 .get("globalColorScheme");
457 Boolean showFeatures = Boolean.valueOf(
458 jvSettingsJsonObj.get("showSeqFeatures").toString());
459 setShowSeqFeatures(showFeatures);
460 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
461 parseHiddenCols(jvSettingsJsonObj);
464 hiddenSequences = new ArrayList<>();
465 seqMap = new Hashtable<>();
466 for (Iterator<JSONObject> sequenceIter = seqJsonArray
467 .iterator(); sequenceIter.hasNext();)
469 JSONObject sequence = sequenceIter.next();
470 String sequcenceString = sequence.get("seq").toString();
471 String sequenceName = sequence.get("name").toString();
472 String seqUniqueId = sequence.get("id").toString();
473 int start = Integer.valueOf(sequence.get("start").toString());
474 int end = Integer.valueOf(sequence.get("end").toString());
475 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
477 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
479 hiddenSequences.add(seq);
482 seqMap.put(seqUniqueId, seq);
485 parseFeatures(jsonSeqArray);
487 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
488 .iterator(); seqGrpIter.hasNext();)
490 JSONObject seqGrpObj = seqGrpIter.next();
491 String grpName = seqGrpObj.get("groupName").toString();
492 String colourScheme = seqGrpObj.get("colourScheme").toString();
493 String description = (seqGrpObj.get("description") == null) ? null
494 : seqGrpObj.get("description").toString();
495 boolean displayBoxes = Boolean
496 .valueOf(seqGrpObj.get("displayBoxes").toString());
497 boolean displayText = Boolean
498 .valueOf(seqGrpObj.get("displayText").toString());
499 boolean colourText = Boolean
500 .valueOf(seqGrpObj.get("colourText").toString());
501 boolean showNonconserved = Boolean
502 .valueOf(seqGrpObj.get("showNonconserved").toString());
503 int startRes = Integer
504 .valueOf(seqGrpObj.get("startRes").toString());
505 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
506 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
508 ArrayList<SequenceI> grpSeqs = new ArrayList<>();
509 if (sequenceRefs.size() > 0)
511 Iterator<String> seqHashIter = sequenceRefs.iterator();
512 while (seqHashIter.hasNext())
514 String seqHash = seqHashIter.next();
515 Sequence sequence = seqMap.get(seqHash);
516 if (sequence != null)
518 grpSeqs.add(sequence);
522 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
523 displayBoxes, displayText, colourText, startRes, endRes);
524 seqGrp.setColourScheme(ColourSchemeMapper
525 .getJalviewColourScheme(colourScheme, seqGrp));
526 seqGrp.setShowNonconserved(showNonconserved);
527 seqGrp.setDescription(description);
528 this.seqGroups.add(seqGrp);
532 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
533 .iterator(); alAnnotIter.hasNext();)
535 JSONObject alAnnot = alAnnotIter.next();
536 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
537 Annotation[] annotations = new Annotation[annotJsonArray.size()];
539 for (Iterator<JSONObject> annotIter = annotJsonArray
540 .iterator(); annotIter.hasNext();)
542 JSONObject annot = annotIter.next();
545 annotations[count] = null;
549 float val = annot.get("value") == null ? null
550 : Float.valueOf(annot.get("value").toString());
551 String desc = annot.get("description") == null ? null
552 : annot.get("description").toString();
553 char ss = annot.get("secondaryStructure") == null
554 || annot.get("secondaryStructure").toString()
555 .equalsIgnoreCase("u0000") ? ' '
556 : annot.get("secondaryStructure")
557 .toString().charAt(0);
558 String displayChar = annot.get("displayCharacter") == null ? ""
559 : annot.get("displayCharacter").toString();
561 annotations[count] = new Annotation(displayChar, desc, ss, val);
562 if (annot.get("colour") != null)
564 Color color = ColorUtils
565 .parseColourString(annot.get("colour").toString());
566 annotations[count].colour = color;
572 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
573 alAnnot.get("label").toString(),
574 alAnnot.get("description").toString(), annotations);
575 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
576 : Integer.valueOf(alAnnot.get("graphType").toString());
578 JSONObject diplaySettings = (JSONObject) alAnnot
579 .get("annotationSettings");
580 if (diplaySettings != null)
583 alignAnnot.scaleColLabel = (diplaySettings
584 .get("scaleColLabel") == null) ? false
585 : Boolean.valueOf(diplaySettings
586 .get("scaleColLabel").toString());
587 alignAnnot.showAllColLabels = (diplaySettings
588 .get("showAllColLabels") == null) ? true
589 : Boolean.valueOf(diplaySettings
590 .get("showAllColLabels").toString());
591 alignAnnot.centreColLabels = (diplaySettings
592 .get("centreColLabels") == null) ? true
593 : Boolean.valueOf(diplaySettings
594 .get("centreColLabels").toString());
595 alignAnnot.belowAlignment = (diplaySettings
596 .get("belowAlignment") == null) ? false
597 : Boolean.valueOf(diplaySettings
598 .get("belowAlignment").toString());
599 alignAnnot.visible = (diplaySettings.get("visible") == null)
602 diplaySettings.get("visible").toString());
603 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
606 diplaySettings.get("hasIcon").toString());
609 if (alAnnot.get("score") != null)
611 alignAnnot.score = Double
612 .valueOf(alAnnot.get("score").toString());
615 String calcId = (alAnnot.get("calcId") == null) ? ""
616 : alAnnot.get("calcId").toString();
617 alignAnnot.setCalcId(calcId);
618 String seqHash = (alAnnot.get("sequenceRef") != null)
619 ? alAnnot.get("sequenceRef").toString()
622 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
623 if (sequence != null)
625 alignAnnot.sequenceRef = sequence;
626 sequence.addAlignmentAnnotation(alignAnnot);
627 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
629 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
631 sequence.addAlignmentAnnotation(alignAnnot);
632 alignAnnot.adjustForAlignment();
635 alignAnnot.validateRangeAndDisplay();
636 this.annotations.add(alignAnnot);
639 } catch (Exception e)
646 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
648 hiddenSeqRefs = new ArrayList<>();
649 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
650 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
652 String[] seqRefs = hiddenSeqs.split(";");
653 for (String seqRef : seqRefs)
655 hiddenSeqRefs.add(seqRef);
660 public void parseHiddenCols(JSONObject jvSettingsJson)
662 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
663 if (hiddenCols != null && !hiddenCols.isEmpty())
665 hiddenColumns = new HiddenColumns();
666 String[] rangeStrings = hiddenCols.split(";");
667 for (String rangeString : rangeStrings)
669 String[] range = rangeString.split("-");
670 hiddenColumns.hideColumns(Integer.valueOf(range[0]),
671 Integer.valueOf(range[1]));
676 @SuppressWarnings("unchecked")
677 private void parseFeatures(JSONArray jsonSeqFeatures)
679 if (jsonSeqFeatures != null)
681 displayedFeatures = new FeaturesDisplayed();
682 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
683 .iterator(); seqFeatureItr.hasNext();)
685 JSONObject jsonFeature = seqFeatureItr.next();
686 Long begin = (Long) jsonFeature.get("xStart");
687 Long end = (Long) jsonFeature.get("xEnd");
688 String type = (String) jsonFeature.get("type");
689 String featureGrp = (String) jsonFeature.get("featureGroup");
690 String descripiton = (String) jsonFeature.get("description");
691 String seqRef = (String) jsonFeature.get("sequenceRef");
692 Float score = Float.valueOf(jsonFeature.get("score").toString());
694 Sequence seq = seqMap.get(seqRef);
695 SequenceFeature sequenceFeature = new SequenceFeature();
696 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
697 if (linksJsonArray != null && linksJsonArray.size() > 0)
699 Iterator<String> linkList = linksJsonArray.iterator();
700 while (linkList.hasNext())
702 String link = linkList.next();
703 sequenceFeature.addLink(link);
706 sequenceFeature.setFeatureGroup(featureGrp);
707 sequenceFeature.setScore(score);
708 sequenceFeature.setDescription(descripiton);
709 sequenceFeature.setType(type);
710 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
711 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
712 seq.addSequenceFeature(sequenceFeature);
713 displayedFeatures.setVisible(type);
719 public String getGlobalColourScheme()
721 return globalColourScheme;
724 public void setGlobalColorScheme(String globalColourScheme)
726 this.globalColourScheme = globalColourScheme;
730 public FeaturesDisplayedI getDisplayedFeatures()
732 return displayedFeatures;
735 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
737 this.displayedFeatures = displayedFeatures;
741 public void configureForView(AlignmentViewPanel avpanel)
747 super.configureForView(avpanel);
748 AlignViewportI viewport = avpanel.getAlignViewport();
749 AlignmentI alignment = viewport.getAlignment();
750 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
752 seqGroups = alignment.getGroups();
753 fr = avpanel.cloneFeatureRenderer();
755 // Add non auto calculated annotation to AlignFile
758 for (AlignmentAnnotation annot : annots)
760 if (annot != null && !annot.autoCalculated)
762 annotations.add(annot);
766 globalColourScheme = ColourSchemeProperty
767 .getColourName(viewport.getGlobalColourScheme());
768 setDisplayedFeatures(viewport.getFeaturesDisplayed());
769 showSeqFeatures = viewport.isShowSequenceFeatures();
774 public boolean isShowSeqFeatures()
776 return showSeqFeatures;
779 public void setShowSeqFeatures(boolean showSeqFeatures)
781 this.showSeqFeatures = showSeqFeatures;
784 public Vector<AlignmentAnnotation> getAnnotations()
790 public HiddenColumns getHiddenColumns()
792 return hiddenColumns;
795 public void setHiddenColumns(HiddenColumns hidden)
797 this.hiddenColumns = hidden;
801 public SequenceI[] getHiddenSequences()
803 if (hiddenSequences == null || hiddenSequences.isEmpty())
805 return new SequenceI[] {};
807 synchronized (hiddenSequences)
809 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
813 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
815 this.hiddenSequences = hiddenSequences;
818 public class JSONExportSettings
820 private boolean exportSequence;
822 private boolean exportSequenceFeatures;
824 private boolean exportAnnotations;
826 private boolean exportGroups;
828 private boolean exportJalviewSettings;
830 public boolean isExportSequence()
832 return exportSequence;
835 public void setExportSequence(boolean exportSequence)
837 this.exportSequence = exportSequence;
840 public boolean isExportSequenceFeatures()
842 return exportSequenceFeatures;
845 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
847 this.exportSequenceFeatures = exportSequenceFeatures;
850 public boolean isExportAnnotations()
852 return exportAnnotations;
855 public void setExportAnnotations(boolean exportAnnotations)
857 this.exportAnnotations = exportAnnotations;
860 public boolean isExportGroups()
865 public void setExportGroups(boolean exportGroups)
867 this.exportGroups = exportGroups;
870 public boolean isExportJalviewSettings()
872 return exportJalviewSettings;
875 public void setExportJalviewSettings(boolean exportJalviewSettings)
877 this.exportJalviewSettings = exportJalviewSettings;
882 * Returns a descriptor for suitable feature display settings with
884 * <li>ResNums or insertions features visible</li>
885 * <li>insertions features coloured red</li>
886 * <li>ResNum features coloured by label</li>
887 * <li>Insertions displayed above (on top of) ResNums</li>
891 public FeatureSettingsModelI getFeatureColourScheme()
893 return new PDBFeatureSettings();