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.ColumnSelection;
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.schemes.JalviewColourScheme;
50 import jalview.schemes.ResidueColourScheme;
51 import jalview.util.ColorUtils;
52 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
54 import java.awt.Color;
55 import java.io.IOException;
56 import java.io.Reader;
57 import java.util.ArrayList;
58 import java.util.Hashtable;
59 import java.util.Iterator;
60 import java.util.List;
61 import java.util.Vector;
63 import org.json.simple.JSONArray;
64 import org.json.simple.JSONObject;
65 import org.json.simple.parser.JSONParser;
67 public class JSONFile extends AlignFile implements ComplexAlignFile
69 private static String version = new BuildDetails().getVersion();
71 private String webstartUrl = "http://www.jalview.org/services/launchApp";
73 private String application = "Jalview";
75 private String globalColourScheme;
77 private boolean showSeqFeatures;
79 private Hashtable<String, Sequence> seqMap;
81 private FeaturesDisplayedI displayedFeatures;
83 private FeatureRenderer fr;
85 private List<int[]> hiddenColumns;
87 private ColumnSelection columnSelection;
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
222 .equalsIgnoreCase(JalviewColourScheme.TCoffee
225 jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
229 if (exportSettings.isExportFeatures())
232 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
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(seqGrp.cs.getSchemeName());
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 List<int[]> hiddenCols = getViewport().getColumnSelection()
283 StringBuilder hiddenColsBuilder = new StringBuilder();
284 for (int[] range : hiddenCols)
286 hiddenColsBuilder.append(";").append(range[0]).append("-")
290 hiddenColsBuilder.deleteCharAt(0);
291 hiddenSections[0] = hiddenColsBuilder.toString();
294 // hidden rows/seqs business
295 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
296 .getHiddenSequences();
297 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
299 return hiddenSections;
302 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
303 StringBuilder hiddenSeqsBuilder = new StringBuilder();
304 for (SequenceI hiddenSeq : hiddenSeqs)
306 if (hiddenSeq != null)
308 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
311 if (hiddenSeqsBuilder.length() > 0)
313 hiddenSeqsBuilder.deleteCharAt(0);
315 hiddenSections[1] = hiddenSeqsBuilder.toString();
317 return hiddenSections;
320 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
321 SequenceI[] sqs, FeatureRenderer fr)
323 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
324 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
327 return sequenceFeaturesPojo;
330 for (SequenceI seq : sqs)
332 SequenceI dataSetSequence = seq.getDatasetSequence();
333 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
334 : seq.getDatasetSequence().getSequenceFeatures();
336 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
338 if (seqFeatures == null)
343 for (SequenceFeature sf : seqFeatures)
345 if (displayedFeatures != null
346 && displayedFeatures.isVisible(sf.getType()))
348 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
349 String.valueOf(seq.hashCode()));
351 String featureColour = (fr == null) ? null : jalview.util.Format
352 .getHexString(fr.findFeatureColour(Color.white, seq,
353 seq.findIndex(sf.getBegin())));
354 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
355 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
356 jsonFeature.setType(sf.getType());
357 jsonFeature.setDescription(sf.getDescription());
358 jsonFeature.setLinks(sf.links);
359 jsonFeature.setOtherDetails(sf.otherDetails);
360 jsonFeature.setScore(sf.getScore());
361 jsonFeature.setFillColor(featureColour);
362 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
363 sequenceFeaturesPojo.add(jsonFeature);
367 return sequenceFeaturesPojo;
370 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
371 Vector<AlignmentAnnotation> annotations)
373 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
374 if (annotations == null)
376 return jsonAnnotations;
378 for (AlignmentAnnotation annot : annotations)
380 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
381 alignAnnotPojo.setDescription(annot.description);
382 alignAnnotPojo.setLabel(annot.label);
383 if (!Double.isNaN(annot.score))
385 alignAnnotPojo.setScore(annot.score);
387 alignAnnotPojo.setCalcId(annot.getCalcId());
388 alignAnnotPojo.setGraphType(annot.graph);
390 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
391 annotSetting.setBelowAlignment(annot.belowAlignment);
392 annotSetting.setCentreColLabels(annot.centreColLabels);
393 annotSetting.setScaleColLabel(annot.scaleColLabel);
394 annotSetting.setShowAllColLabels(annot.showAllColLabels);
395 annotSetting.setVisible(annot.visible);
396 annotSetting.setHasIcon(annot.hasIcons);
397 alignAnnotPojo.setAnnotationSettings(annotSetting);
398 SequenceI refSeq = annot.sequenceRef;
401 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
403 for (Annotation annotation : annot.annotations)
405 AnnotationPojo annotationPojo = new AnnotationPojo();
406 if (annotation != null)
408 annotationPojo.setDescription(annotation.description);
409 annotationPojo.setValue(annotation.value);
411 .setSecondaryStructure(annotation.secondaryStructure);
412 String displayChar = annotation.displayCharacter == null ? null
413 : annotation.displayCharacter;
414 // System.out.println("--------------------->[" + displayChar + "]");
415 annotationPojo.setDisplayCharacter(displayChar);
416 if (annotation.colour != null)
418 annotationPojo.setColour(jalview.util.Format
419 .getHexString(annotation.colour));
421 alignAnnotPojo.getAnnotations().add(annotationPojo);
425 if (annot.getCalcId() != null
426 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
432 alignAnnotPojo.getAnnotations().add(annotationPojo);
436 jsonAnnotations.add(alignAnnotPojo);
438 return jsonAnnotations;
441 @SuppressWarnings("unchecked")
442 public JSONFile parse(Reader jsonAlignmentString)
446 JSONParser jsonParser = new JSONParser();
447 JSONObject alignmentJsonObj = (JSONObject) jsonParser
448 .parse(jsonAlignmentString);
449 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
450 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
451 .get("alignAnnotation");
452 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
454 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
456 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
459 if (jvSettingsJsonObj != null)
461 globalColourScheme = (String) jvSettingsJsonObj
462 .get("globalColorScheme");
463 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
464 "showSeqFeatures").toString());
465 setShowSeqFeatures(showFeatures);
466 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
467 parseHiddenCols(jvSettingsJsonObj);
470 hiddenSequences = new ArrayList<SequenceI>();
471 seqMap = new Hashtable<String, Sequence>();
472 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
475 JSONObject sequence = sequenceIter.next();
476 String sequcenceString = sequence.get("seq").toString();
477 String sequenceName = sequence.get("name").toString();
478 String seqUniqueId = sequence.get("id").toString();
479 int start = Integer.valueOf(sequence.get("start").toString());
480 int end = Integer.valueOf(sequence.get("end").toString());
481 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
483 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
485 hiddenSequences.add(seq);
488 seqMap.put(seqUniqueId, seq);
491 parseFeatures(jsonSeqArray);
493 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
496 JSONObject seqGrpObj = seqGrpIter.next();
497 String grpName = seqGrpObj.get("groupName").toString();
498 String colourScheme = seqGrpObj.get("colourScheme").toString();
499 String description = (seqGrpObj.get("description") == null) ? null
500 : seqGrpObj.get("description").toString();
501 boolean displayBoxes = Boolean.valueOf(seqGrpObj
502 .get("displayBoxes").toString());
503 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
505 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
507 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
508 "showNonconserved").toString());
509 int startRes = Integer
510 .valueOf(seqGrpObj.get("startRes").toString());
511 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
512 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
514 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
515 if (sequenceRefs.size() > 0)
517 Iterator<String> seqHashIter = sequenceRefs.iterator();
518 while (seqHashIter.hasNext())
520 String seqHash = seqHashIter.next();
521 Sequence sequence = seqMap.get(seqHash);
522 if (sequence != null)
524 grpSeqs.add(sequence);
528 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
529 displayBoxes, displayText, colourText, startRes, endRes);
530 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
532 seqGrp.setShowNonconserved(showNonconserved);
533 seqGrp.setDescription(description);
534 this.seqGroups.add(seqGrp);
538 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
541 JSONObject alAnnot = alAnnotIter.next();
542 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
543 Annotation[] annotations = new Annotation[annotJsonArray.size()];
545 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
548 JSONObject annot = annotIter.next();
551 annotations[count] = null;
555 float val = annot.get("value") == null ? null : Float
556 .valueOf(annot.get("value").toString());
557 String desc = annot.get("description") == null ? null : annot
558 .get("description").toString();
559 char ss = annot.get("secondaryStructure") == null
560 || annot.get("secondaryStructure").toString()
561 .equalsIgnoreCase("u0000") ? ' ' : annot
562 .get("secondaryStructure").toString().charAt(0);
563 String displayChar = annot.get("displayCharacter") == null ? ""
564 : annot.get("displayCharacter").toString();
566 annotations[count] = new Annotation(displayChar, desc, ss, val);
567 if (annot.get("colour") != null)
569 Color color = ColorUtils.parseColourString(annot.get(
570 "colour").toString());
571 annotations[count].colour = color;
577 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
578 .get("label").toString(), alAnnot.get("description")
579 .toString(), annotations);
580 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
581 .valueOf(alAnnot.get("graphType").toString());
583 JSONObject diplaySettings = (JSONObject) alAnnot
584 .get("annotationSettings");
585 if (diplaySettings != null)
588 alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
589 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
591 alignAnnot.showAllColLabels = (diplaySettings
592 .get("showAllColLabels") == null) ? true : Boolean
593 .valueOf(diplaySettings.get("showAllColLabels")
595 alignAnnot.centreColLabels = (diplaySettings
596 .get("centreColLabels") == null) ? true
597 : Boolean.valueOf(diplaySettings.get("centreColLabels")
599 alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
600 : Boolean.valueOf(diplaySettings.get("belowAlignment")
602 alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
603 : Boolean.valueOf(diplaySettings.get("visible")
605 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
606 : Boolean.valueOf(diplaySettings.get("hasIcon")
610 if (alAnnot.get("score") != null)
612 alignAnnot.score = Double
613 .valueOf(alAnnot.get("score").toString());
616 String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
617 "calcId").toString();
618 alignAnnot.setCalcId(calcId);
619 String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
620 .get("sequenceRef").toString() : null;
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<String>();
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 columnSelection = new ColumnSelection();
666 String[] rangeStrings = hiddenCols.split(";");
667 for (String rangeString : rangeStrings)
669 String[] range = rangeString.split("-");
670 columnSelection.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.iterator(); seqFeatureItr
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 = viewport.getGlobalColourScheme().getSchemeName();
767 setDisplayedFeatures(viewport.getFeaturesDisplayed());
768 showSeqFeatures = viewport.isShowSequenceFeatures();
773 public boolean isShowSeqFeatures()
775 return showSeqFeatures;
778 public void setShowSeqFeatures(boolean showSeqFeatures)
780 this.showSeqFeatures = showSeqFeatures;
783 public Vector<AlignmentAnnotation> getAnnotations()
788 public List<int[]> getHiddenColumns()
790 return hiddenColumns;
794 public ColumnSelection getColumnSelection()
796 return columnSelection;
799 public void setColumnSelection(ColumnSelection columnSelection)
801 this.columnSelection = columnSelection;
805 public SequenceI[] getHiddenSequences()
807 if (hiddenSequences == null || hiddenSequences.isEmpty())
809 return new SequenceI[] {};
811 synchronized (hiddenSequences)
813 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
817 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
819 this.hiddenSequences = hiddenSequences;
822 public class JSONExportSettings
824 private boolean exportSequence;
826 private boolean exportSequenceFeatures;
828 private boolean exportAnnotations;
830 private boolean exportGroups;
832 private boolean exportJalviewSettings;
834 public boolean isExportSequence()
836 return exportSequence;
839 public void setExportSequence(boolean exportSequence)
841 this.exportSequence = exportSequence;
844 public boolean isExportSequenceFeatures()
846 return exportSequenceFeatures;
849 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
851 this.exportSequenceFeatures = exportSequenceFeatures;
854 public boolean isExportAnnotations()
856 return exportAnnotations;
859 public void setExportAnnotations(boolean exportAnnotations)
861 this.exportAnnotations = exportAnnotations;
864 public boolean isExportGroups()
869 public void setExportGroups(boolean exportGroups)
871 this.exportGroups = exportGroups;
874 public boolean isExportJalviewSettings()
876 return exportJalviewSettings;
879 public void setExportJalviewSettings(boolean exportJalviewSettings)
881 this.exportJalviewSettings = exportJalviewSettings;
886 * Returns a descriptor for suitable feature display settings with
888 * <li>ResNums or insertions features visible</li>
889 * <li>insertions features coloured red</li>
890 * <li>ResNum features coloured by label</li>
891 * <li>Insertions displayed above (on top of) ResNums</li>
895 public FeatureSettingsModelI getFeatureColourScheme()
897 return new PDBFeatureSettings();