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.ColourSchemeProperty;
50 import jalview.schemes.UserColourScheme;
51 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
53 import java.awt.Color;
54 import java.io.IOException;
55 import java.io.Reader;
56 import java.util.ArrayList;
57 import java.util.Hashtable;
58 import java.util.Iterator;
59 import java.util.List;
60 import java.util.Vector;
62 import org.json.simple.JSONArray;
63 import org.json.simple.JSONObject;
64 import org.json.simple.parser.JSONParser;
66 public class JSONFile extends AlignFile implements ComplexAlignFile
68 private static String version = new BuildDetails().getVersion();
70 private String webstartUrl = "http://www.jalview.org/services/launchApp";
72 private String application = "Jalview";
74 public static final String FILE_EXT = "json";
76 public static final String FILE_DESC = "JSON";
78 private String globalColourScheme;
80 private boolean showSeqFeatures;
82 private Hashtable<String, Sequence> seqMap;
84 private FeaturesDisplayedI displayedFeatures;
86 private FeatureRenderer fr;
88 private List<int[]> hiddenColumns;
90 private ColumnSelection columnSelection;
92 private List<String> hiddenSeqRefs;
94 private ArrayList<SequenceI> hiddenSequences;
96 private final static String TCOFFEE_SCORE = "TCoffeeScore";
103 public JSONFile(FileParse source) throws IOException
108 public JSONFile(String inFile, String type) throws IOException
114 public void parse() throws IOException
121 public String print()
123 String jsonOutput = null;
126 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
127 AlignExportSettingI exportSettings = getExportSettings();
129 // if no export settings were supplied use the following with all values
130 // defaulting to true
131 if (exportSettings == null)
133 exportSettings = new AlignExportSettingI()
136 public boolean isExportHiddenSequences()
142 public boolean isExportHiddenColumns()
148 public boolean isExportGroups()
154 public boolean isExportFeatures()
160 public boolean isExportAnnotations()
166 public boolean isCancelled()
174 for (SequenceI seq : seqs)
176 StringBuilder name = new StringBuilder();
177 name.append(seq.getName()).append("/").append(seq.getStart())
178 .append("-").append(seq.getEnd());
179 SequencePojo jsonSeqPojo = new SequencePojo();
180 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
181 jsonSeqPojo.setOrder(++count);
182 jsonSeqPojo.setEnd(seq.getEnd());
183 jsonSeqPojo.setStart(seq.getStart());
184 jsonSeqPojo.setName(name.toString());
185 jsonSeqPojo.setSeq(seq.getSequenceAsString());
186 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
188 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
189 jsonAlignmentPojo.getAppSettings().put("application", application);
190 jsonAlignmentPojo.getAppSettings().put("version", version);
191 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
192 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
193 String.valueOf(showSeqFeatures));
195 String[] hiddenSections = getHiddenSections();
196 if (hiddenSections != null)
198 if (hiddenSections[0] != null
199 && exportSettings.isExportHiddenColumns())
201 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
202 String.valueOf(hiddenSections[0]));
204 if (hiddenSections[1] != null
205 && exportSettings.isExportHiddenSequences())
207 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
208 String.valueOf(hiddenSections[1]));
212 if (exportSettings.isExportAnnotations())
215 .setAlignAnnotation(annotationToJsonPojo(annotations));
219 // These color schemes require annotation, disable them if annotations
221 if (globalColourScheme.equalsIgnoreCase("RNA Helices")
222 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
224 jsonAlignmentPojo.setGlobalColorScheme("None");
228 if (exportSettings.isExportFeatures())
231 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, 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.cs));
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 List<SequenceI> seqs, FeatureRenderer fr)
323 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
324 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
325 for (SequenceI seq : seqs)
327 SequenceI dataSetSequence = seq.getDatasetSequence();
328 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
329 : seq.getDatasetSequence().getSequenceFeatures();
331 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
333 if (seqFeatures == null)
338 for (SequenceFeature sf : seqFeatures)
340 if (displayedFeatures != null
341 && displayedFeatures.isVisible(sf.getType()))
343 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
344 String.valueOf(seq.hashCode()));
346 String featureColour = (fr == null) ? null : jalview.util.Format
347 .getHexString(fr.findFeatureColour(Color.white, seq,
348 seq.findIndex(sf.getBegin())));
349 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
350 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
351 jsonFeature.setType(sf.getType());
352 jsonFeature.setDescription(sf.getDescription());
353 jsonFeature.setLinks(sf.links);
354 jsonFeature.setOtherDetails(sf.otherDetails);
355 jsonFeature.setScore(sf.getScore());
356 jsonFeature.setFillColor(featureColour);
357 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
358 sequenceFeaturesPojo.add(jsonFeature);
362 return sequenceFeaturesPojo;
365 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
366 Vector<AlignmentAnnotation> annotations)
368 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
369 if (annotations == null)
371 return jsonAnnotations;
373 for (AlignmentAnnotation annot : annotations)
375 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
376 alignAnnotPojo.setDescription(annot.description);
377 alignAnnotPojo.setLabel(annot.label);
378 if (!Double.isNaN(annot.score))
380 alignAnnotPojo.setScore(annot.score);
382 alignAnnotPojo.setCalcId(annot.getCalcId());
383 alignAnnotPojo.setGraphType(annot.graph);
385 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
386 annotSetting.setBelowAlignment(annot.belowAlignment);
387 annotSetting.setCentreColLabels(annot.centreColLabels);
388 annotSetting.setScaleColLabel(annot.scaleColLabel);
389 annotSetting.setShowAllColLabels(annot.showAllColLabels);
390 annotSetting.setVisible(annot.visible);
391 annotSetting.setHasIcon(annot.hasIcons);
392 alignAnnotPojo.setAnnotationSettings(annotSetting);
393 SequenceI refSeq = annot.sequenceRef;
396 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
398 for (Annotation annotation : annot.annotations)
400 AnnotationPojo annotationPojo = new AnnotationPojo();
401 if (annotation != null)
403 annotationPojo.setDescription(annotation.description);
404 annotationPojo.setValue(annotation.value);
406 .setSecondaryStructure(annotation.secondaryStructure);
407 String displayChar = annotation.displayCharacter == null ? null
408 : annotation.displayCharacter;
409 // System.out.println("--------------------->[" + displayChar + "]");
410 annotationPojo.setDisplayCharacter(displayChar);
411 if (annotation.colour != null)
413 annotationPojo.setColour(jalview.util.Format
414 .getHexString(annotation.colour));
416 alignAnnotPojo.getAnnotations().add(annotationPojo);
420 if (annot.getCalcId() != null
421 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
427 alignAnnotPojo.getAnnotations().add(annotationPojo);
431 jsonAnnotations.add(alignAnnotPojo);
433 return jsonAnnotations;
436 @SuppressWarnings("unchecked")
437 public JSONFile parse(Reader jsonAlignmentString)
441 JSONParser jsonParser = new JSONParser();
442 JSONObject alignmentJsonObj = (JSONObject) jsonParser
443 .parse(jsonAlignmentString);
444 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
445 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
446 .get("alignAnnotation");
447 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
449 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
451 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
454 if (jvSettingsJsonObj != null)
456 globalColourScheme = (String) jvSettingsJsonObj
457 .get("globalColorScheme");
458 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
459 "showSeqFeatures").toString());
460 setShowSeqFeatures(showFeatures);
461 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
462 parseHiddenCols(jvSettingsJsonObj);
465 hiddenSequences = new ArrayList<SequenceI>();
466 seqMap = new Hashtable<String, Sequence>();
467 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
470 JSONObject sequence = sequenceIter.next();
471 String sequcenceString = sequence.get("seq").toString();
472 String sequenceName = sequence.get("name").toString();
473 String seqUniqueId = sequence.get("id").toString();
474 int start = Integer.valueOf(sequence.get("start").toString());
475 int end = Integer.valueOf(sequence.get("end").toString());
476 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
478 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
480 hiddenSequences.add(seq);
483 seqMap.put(seqUniqueId, seq);
486 parseFeatures(jsonSeqArray);
488 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
491 JSONObject seqGrpObj = seqGrpIter.next();
492 String grpName = seqGrpObj.get("groupName").toString();
493 String colourScheme = seqGrpObj.get("colourScheme").toString();
494 String description = (seqGrpObj.get("description") == null) ? null
495 : seqGrpObj.get("description").toString();
496 boolean displayBoxes = Boolean.valueOf(seqGrpObj
497 .get("displayBoxes").toString());
498 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
500 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
502 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
503 "showNonconserved").toString());
504 int startRes = Integer
505 .valueOf(seqGrpObj.get("startRes").toString());
506 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
507 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
509 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
510 if (sequenceRefs.size() > 0)
512 Iterator<String> seqHashIter = sequenceRefs.iterator();
513 while (seqHashIter.hasNext())
515 String seqHash = seqHashIter.next();
516 Sequence sequence = seqMap.get(seqHash);
517 if (sequence != null)
519 grpSeqs.add(sequence);
523 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
524 displayBoxes, displayText, colourText, startRes, endRes);
525 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
527 seqGrp.setShowNonconserved(showNonconserved);
528 seqGrp.setDescription(description);
529 this.seqGroups.add(seqGrp);
533 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
536 JSONObject alAnnot = alAnnotIter.next();
537 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
538 Annotation[] annotations = new Annotation[annotJsonArray.size()];
540 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
543 JSONObject annot = annotIter.next();
546 annotations[count] = null;
550 float val = annot.get("value") == null ? null : Float
551 .valueOf(annot.get("value").toString());
552 String desc = annot.get("description") == null ? null : annot
553 .get("description").toString();
554 char ss = annot.get("secondaryStructure") == null
555 || annot.get("secondaryStructure").toString()
556 .equalsIgnoreCase("u0000") ? ' ' : annot
557 .get("secondaryStructure").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 = UserColourScheme.getColourFromString(annot.get(
565 "colour").toString());
566 annotations[count].colour = color;
572 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
573 .get("label").toString(), alAnnot.get("description")
574 .toString(), annotations);
575 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
576 .valueOf(alAnnot.get("graphType").toString());
578 JSONObject diplaySettings = (JSONObject) alAnnot
579 .get("annotationSettings");
580 if (diplaySettings != null)
583 alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
584 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
586 alignAnnot.showAllColLabels = (diplaySettings
587 .get("showAllColLabels") == null) ? true : Boolean
588 .valueOf(diplaySettings.get("showAllColLabels")
590 alignAnnot.centreColLabels = (diplaySettings
591 .get("centreColLabels") == null) ? true
592 : Boolean.valueOf(diplaySettings.get("centreColLabels")
594 alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
595 : Boolean.valueOf(diplaySettings.get("belowAlignment")
597 alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
598 : Boolean.valueOf(diplaySettings.get("visible")
600 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
601 : Boolean.valueOf(diplaySettings.get("hasIcon")
605 if (alAnnot.get("score") != null)
607 alignAnnot.score = Double
608 .valueOf(alAnnot.get("score").toString());
611 String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
612 "calcId").toString();
613 alignAnnot.setCalcId(calcId);
614 String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
615 .get("sequenceRef").toString() : null;
617 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
618 if (sequence != null)
620 alignAnnot.sequenceRef = sequence;
621 sequence.addAlignmentAnnotation(alignAnnot);
622 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
624 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
626 sequence.addAlignmentAnnotation(alignAnnot);
627 alignAnnot.adjustForAlignment();
630 alignAnnot.validateRangeAndDisplay();
631 this.annotations.add(alignAnnot);
634 } catch (Exception e)
641 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
643 hiddenSeqRefs = new ArrayList<String>();
644 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
645 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
647 String[] seqRefs = hiddenSeqs.split(";");
648 for (String seqRef : seqRefs)
650 hiddenSeqRefs.add(seqRef);
655 public void parseHiddenCols(JSONObject jvSettingsJson)
657 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
658 if (hiddenCols != null && !hiddenCols.isEmpty())
660 columnSelection = new ColumnSelection();
661 String[] rangeStrings = hiddenCols.split(";");
662 for (String rangeString : rangeStrings)
664 String[] range = rangeString.split("-");
665 columnSelection.hideColumns(Integer.valueOf(range[0]),
666 Integer.valueOf(range[1]));
671 @SuppressWarnings("unchecked")
672 private void parseFeatures(JSONArray jsonSeqFeatures)
674 if (jsonSeqFeatures != null)
676 displayedFeatures = new FeaturesDisplayed();
677 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
680 JSONObject jsonFeature = seqFeatureItr.next();
681 Long begin = (Long) jsonFeature.get("xStart");
682 Long end = (Long) jsonFeature.get("xEnd");
683 String type = (String) jsonFeature.get("type");
684 String featureGrp = (String) jsonFeature.get("featureGroup");
685 String descripiton = (String) jsonFeature.get("description");
686 String seqRef = (String) jsonFeature.get("sequenceRef");
687 Float score = Float.valueOf(jsonFeature.get("score").toString());
689 Sequence seq = seqMap.get(seqRef);
690 SequenceFeature sequenceFeature = new SequenceFeature();
691 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
692 if (linksJsonArray != null && linksJsonArray.size() > 0)
694 Iterator<String> linkList = linksJsonArray.iterator();
695 while (linkList.hasNext())
697 String link = linkList.next();
698 sequenceFeature.addLink(link);
701 sequenceFeature.setFeatureGroup(featureGrp);
702 sequenceFeature.setScore(score);
703 sequenceFeature.setDescription(descripiton);
704 sequenceFeature.setType(type);
705 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
706 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
707 seq.addSequenceFeature(sequenceFeature);
708 displayedFeatures.setVisible(type);
714 public String getGlobalColourScheme()
716 return globalColourScheme;
719 public void setGlobalColorScheme(String globalColourScheme)
721 this.globalColourScheme = globalColourScheme;
725 public FeaturesDisplayedI getDisplayedFeatures()
727 return displayedFeatures;
730 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
732 this.displayedFeatures = displayedFeatures;
736 public void configureForView(AlignmentViewPanel avpanel)
742 super.configureForView(avpanel);
743 AlignViewportI viewport = avpanel.getAlignViewport();
744 AlignmentI alignment = viewport.getAlignment();
745 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
747 seqGroups = alignment.getGroups();
748 fr = avpanel.cloneFeatureRenderer();
750 // Add non auto calculated annotation to AlignFile
753 for (AlignmentAnnotation annot : annots)
755 if (annot != null && !annot.autoCalculated)
757 annotations.add(annot);
761 globalColourScheme = ColourSchemeProperty.getColourName(viewport
762 .getGlobalColourScheme());
763 setDisplayedFeatures(viewport.getFeaturesDisplayed());
764 showSeqFeatures = viewport.isShowSequenceFeatures();
769 public boolean isShowSeqFeatures()
771 return showSeqFeatures;
774 public void setShowSeqFeatures(boolean showSeqFeatures)
776 this.showSeqFeatures = showSeqFeatures;
779 public Vector<AlignmentAnnotation> getAnnotations()
784 public List<int[]> getHiddenColumns()
786 return hiddenColumns;
790 public ColumnSelection getColumnSelection()
792 return columnSelection;
795 public void setColumnSelection(ColumnSelection columnSelection)
797 this.columnSelection = columnSelection;
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();