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 private String globalColourScheme;
76 private boolean showSeqFeatures;
78 private Hashtable<String, Sequence> seqMap;
80 private FeaturesDisplayedI displayedFeatures;
82 private FeatureRenderer fr;
84 private List<int[]> hiddenColumns;
86 private ColumnSelection columnSelection;
88 private List<String> hiddenSeqRefs;
90 private ArrayList<SequenceI> hiddenSequences;
92 private final static String TCOFFEE_SCORE = "TCoffeeScore";
99 public JSONFile(FileParse source) throws IOException
104 public JSONFile(String inFile, DataSourceType sourceType)
107 super(inFile, sourceType);
111 public void parse() throws IOException
118 public String print(SequenceI[] sqs, boolean jvsuffix)
120 String jsonOutput = null;
123 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
124 AlignExportSettingI exportSettings = getExportSettings();
126 // if no export settings were supplied use the following with all values
127 // defaulting to true
128 if (exportSettings == null)
130 exportSettings = new AlignExportSettingI()
133 public boolean isExportHiddenSequences()
139 public boolean isExportHiddenColumns()
145 public boolean isExportGroups()
151 public boolean isExportFeatures()
157 public boolean isExportAnnotations()
163 public boolean isCancelled()
171 for (SequenceI seq : sqs)
173 StringBuilder name = new StringBuilder();
174 name.append(seq.getName()).append("/").append(seq.getStart())
175 .append("-").append(seq.getEnd());
176 SequencePojo jsonSeqPojo = new SequencePojo();
177 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
178 jsonSeqPojo.setOrder(++count);
179 jsonSeqPojo.setEnd(seq.getEnd());
180 jsonSeqPojo.setStart(seq.getStart());
181 jsonSeqPojo.setName(name.toString());
182 jsonSeqPojo.setSeq(seq.getSequenceAsString());
183 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
185 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
186 jsonAlignmentPojo.getAppSettings().put("application", application);
187 jsonAlignmentPojo.getAppSettings().put("version", version);
188 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
189 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
190 String.valueOf(showSeqFeatures));
192 String[] hiddenSections = getHiddenSections();
193 if (hiddenSections != null)
195 if (hiddenSections[0] != null
196 && exportSettings.isExportHiddenColumns())
198 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
199 String.valueOf(hiddenSections[0]));
201 if (hiddenSections[1] != null
202 && exportSettings.isExportHiddenSequences())
204 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
205 String.valueOf(hiddenSections[1]));
209 if (exportSettings.isExportAnnotations())
212 .setAlignAnnotation(annotationToJsonPojo(annotations));
216 // These color schemes require annotation, disable them if annotations
218 if (globalColourScheme.equalsIgnoreCase("RNA Helices")
219 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
221 jsonAlignmentPojo.setGlobalColorScheme("None");
225 if (exportSettings.isExportFeatures())
228 .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
231 if (exportSettings.isExportGroups() && seqGroups != null
232 && seqGroups.size() > 0)
234 for (SequenceGroup seqGrp : seqGroups)
236 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
237 seqGrpPojo.setGroupName(seqGrp.getName());
238 seqGrpPojo.setColourScheme(ColourSchemeProperty
239 .getColourName(seqGrp.cs));
240 seqGrpPojo.setColourText(seqGrp.getColourText());
241 seqGrpPojo.setDescription(seqGrp.getDescription());
242 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
243 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
244 seqGrpPojo.setEndRes(seqGrp.getEndRes());
245 seqGrpPojo.setStartRes(seqGrp.getStartRes());
246 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
247 for (SequenceI seq : seqGrp.getSequences())
249 seqGrpPojo.getSequenceRefs()
250 .add(String.valueOf(seq.hashCode()));
252 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
255 org.json.JSONObject generatedJSon = new org.json.JSONObject(
257 jsonOutput = generatedJSon.toString();
258 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
260 } catch (Exception e)
267 public String[] getHiddenSections()
269 String[] hiddenSections = new String[2];
270 if (getViewport() == null)
275 // hidden column business
276 if (getViewport().hasHiddenColumns())
278 List<int[]> hiddenCols = getViewport().getColumnSelection()
280 StringBuilder hiddenColsBuilder = new StringBuilder();
281 for (int[] range : hiddenCols)
283 hiddenColsBuilder.append(";").append(range[0]).append("-")
287 hiddenColsBuilder.deleteCharAt(0);
288 hiddenSections[0] = hiddenColsBuilder.toString();
291 // hidden rows/seqs business
292 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
293 .getHiddenSequences();
294 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
296 return hiddenSections;
299 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
300 StringBuilder hiddenSeqsBuilder = new StringBuilder();
301 for (SequenceI hiddenSeq : hiddenSeqs)
303 if (hiddenSeq != null)
305 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
308 if (hiddenSeqsBuilder.length() > 0)
310 hiddenSeqsBuilder.deleteCharAt(0);
312 hiddenSections[1] = hiddenSeqsBuilder.toString();
314 return hiddenSections;
317 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
318 SequenceI[] sqs, FeatureRenderer fr)
320 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
321 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
324 return sequenceFeaturesPojo;
327 for (SequenceI seq : sqs)
329 SequenceI dataSetSequence = seq.getDatasetSequence();
330 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
331 : seq.getDatasetSequence().getSequenceFeatures();
333 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
335 if (seqFeatures == null)
340 for (SequenceFeature sf : seqFeatures)
342 if (displayedFeatures != null
343 && displayedFeatures.isVisible(sf.getType()))
345 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
346 String.valueOf(seq.hashCode()));
348 String featureColour = (fr == null) ? null : jalview.util.Format
349 .getHexString(fr.findFeatureColour(Color.white, seq,
350 seq.findIndex(sf.getBegin())));
351 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
352 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
353 jsonFeature.setType(sf.getType());
354 jsonFeature.setDescription(sf.getDescription());
355 jsonFeature.setLinks(sf.links);
356 jsonFeature.setOtherDetails(sf.otherDetails);
357 jsonFeature.setScore(sf.getScore());
358 jsonFeature.setFillColor(featureColour);
359 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
360 sequenceFeaturesPojo.add(jsonFeature);
364 return sequenceFeaturesPojo;
367 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
368 Vector<AlignmentAnnotation> annotations)
370 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
371 if (annotations == null)
373 return jsonAnnotations;
375 for (AlignmentAnnotation annot : annotations)
377 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
378 alignAnnotPojo.setDescription(annot.description);
379 alignAnnotPojo.setLabel(annot.label);
380 if (!Double.isNaN(annot.score))
382 alignAnnotPojo.setScore(annot.score);
384 alignAnnotPojo.setCalcId(annot.getCalcId());
385 alignAnnotPojo.setGraphType(annot.graph);
387 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
388 annotSetting.setBelowAlignment(annot.belowAlignment);
389 annotSetting.setCentreColLabels(annot.centreColLabels);
390 annotSetting.setScaleColLabel(annot.scaleColLabel);
391 annotSetting.setShowAllColLabels(annot.showAllColLabels);
392 annotSetting.setVisible(annot.visible);
393 annotSetting.setHasIcon(annot.hasIcons);
394 alignAnnotPojo.setAnnotationSettings(annotSetting);
395 SequenceI refSeq = annot.sequenceRef;
398 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
400 for (Annotation annotation : annot.annotations)
402 AnnotationPojo annotationPojo = new AnnotationPojo();
403 if (annotation != null)
405 annotationPojo.setDescription(annotation.description);
406 annotationPojo.setValue(annotation.value);
408 .setSecondaryStructure(annotation.secondaryStructure);
409 String displayChar = annotation.displayCharacter == null ? null
410 : annotation.displayCharacter;
411 // System.out.println("--------------------->[" + displayChar + "]");
412 annotationPojo.setDisplayCharacter(displayChar);
413 if (annotation.colour != null)
415 annotationPojo.setColour(jalview.util.Format
416 .getHexString(annotation.colour));
418 alignAnnotPojo.getAnnotations().add(annotationPojo);
422 if (annot.getCalcId() != null
423 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
429 alignAnnotPojo.getAnnotations().add(annotationPojo);
433 jsonAnnotations.add(alignAnnotPojo);
435 return jsonAnnotations;
438 @SuppressWarnings("unchecked")
439 public JSONFile parse(Reader jsonAlignmentString)
443 JSONParser jsonParser = new JSONParser();
444 JSONObject alignmentJsonObj = (JSONObject) jsonParser
445 .parse(jsonAlignmentString);
446 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
447 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
448 .get("alignAnnotation");
449 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
451 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
453 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
456 if (jvSettingsJsonObj != null)
458 globalColourScheme = (String) jvSettingsJsonObj
459 .get("globalColorScheme");
460 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
461 "showSeqFeatures").toString());
462 setShowSeqFeatures(showFeatures);
463 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
464 parseHiddenCols(jvSettingsJsonObj);
467 hiddenSequences = new ArrayList<SequenceI>();
468 seqMap = new Hashtable<String, Sequence>();
469 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
472 JSONObject sequence = sequenceIter.next();
473 String sequcenceString = sequence.get("seq").toString();
474 String sequenceName = sequence.get("name").toString();
475 String seqUniqueId = sequence.get("id").toString();
476 int start = Integer.valueOf(sequence.get("start").toString());
477 int end = Integer.valueOf(sequence.get("end").toString());
478 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
480 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
482 hiddenSequences.add(seq);
485 seqMap.put(seqUniqueId, seq);
488 parseFeatures(jsonSeqArray);
490 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
493 JSONObject seqGrpObj = seqGrpIter.next();
494 String grpName = seqGrpObj.get("groupName").toString();
495 String colourScheme = seqGrpObj.get("colourScheme").toString();
496 String description = (seqGrpObj.get("description") == null) ? null
497 : seqGrpObj.get("description").toString();
498 boolean displayBoxes = Boolean.valueOf(seqGrpObj
499 .get("displayBoxes").toString());
500 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
502 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
504 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
505 "showNonconserved").toString());
506 int startRes = Integer
507 .valueOf(seqGrpObj.get("startRes").toString());
508 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
509 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
511 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
512 if (sequenceRefs.size() > 0)
514 Iterator<String> seqHashIter = sequenceRefs.iterator();
515 while (seqHashIter.hasNext())
517 String seqHash = seqHashIter.next();
518 Sequence sequence = seqMap.get(seqHash);
519 if (sequence != null)
521 grpSeqs.add(sequence);
525 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
526 displayBoxes, displayText, colourText, startRes, endRes);
527 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
529 seqGrp.setShowNonconserved(showNonconserved);
530 seqGrp.setDescription(description);
531 this.seqGroups.add(seqGrp);
535 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
538 JSONObject alAnnot = alAnnotIter.next();
539 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
540 Annotation[] annotations = new Annotation[annotJsonArray.size()];
542 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
545 JSONObject annot = annotIter.next();
548 annotations[count] = null;
552 float val = annot.get("value") == null ? null : Float
553 .valueOf(annot.get("value").toString());
554 String desc = annot.get("description") == null ? null : annot
555 .get("description").toString();
556 char ss = annot.get("secondaryStructure") == null
557 || annot.get("secondaryStructure").toString()
558 .equalsIgnoreCase("u0000") ? ' ' : annot
559 .get("secondaryStructure").toString().charAt(0);
560 String displayChar = annot.get("displayCharacter") == null ? ""
561 : annot.get("displayCharacter").toString();
563 annotations[count] = new Annotation(displayChar, desc, ss, val);
564 if (annot.get("colour") != null)
566 Color color = UserColourScheme.getColourFromString(annot.get(
567 "colour").toString());
568 annotations[count].colour = color;
574 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
575 .get("label").toString(), alAnnot.get("description")
576 .toString(), annotations);
577 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
578 .valueOf(alAnnot.get("graphType").toString());
580 JSONObject diplaySettings = (JSONObject) alAnnot
581 .get("annotationSettings");
582 if (diplaySettings != null)
585 alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
586 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
588 alignAnnot.showAllColLabels = (diplaySettings
589 .get("showAllColLabels") == null) ? true : Boolean
590 .valueOf(diplaySettings.get("showAllColLabels")
592 alignAnnot.centreColLabels = (diplaySettings
593 .get("centreColLabels") == null) ? true
594 : Boolean.valueOf(diplaySettings.get("centreColLabels")
596 alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
597 : Boolean.valueOf(diplaySettings.get("belowAlignment")
599 alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
600 : Boolean.valueOf(diplaySettings.get("visible")
602 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
603 : Boolean.valueOf(diplaySettings.get("hasIcon")
607 if (alAnnot.get("score") != null)
609 alignAnnot.score = Double
610 .valueOf(alAnnot.get("score").toString());
613 String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
614 "calcId").toString();
615 alignAnnot.setCalcId(calcId);
616 String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
617 .get("sequenceRef").toString() : null;
619 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
620 if (sequence != null)
622 alignAnnot.sequenceRef = sequence;
623 sequence.addAlignmentAnnotation(alignAnnot);
624 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
626 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
628 sequence.addAlignmentAnnotation(alignAnnot);
629 alignAnnot.adjustForAlignment();
632 alignAnnot.validateRangeAndDisplay();
633 this.annotations.add(alignAnnot);
636 } catch (Exception e)
643 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
645 hiddenSeqRefs = new ArrayList<String>();
646 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
647 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
649 String[] seqRefs = hiddenSeqs.split(";");
650 for (String seqRef : seqRefs)
652 hiddenSeqRefs.add(seqRef);
657 public void parseHiddenCols(JSONObject jvSettingsJson)
659 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
660 if (hiddenCols != null && !hiddenCols.isEmpty())
662 columnSelection = new ColumnSelection();
663 String[] rangeStrings = hiddenCols.split(";");
664 for (String rangeString : rangeStrings)
666 String[] range = rangeString.split("-");
667 columnSelection.hideColumns(Integer.valueOf(range[0]),
668 Integer.valueOf(range[1]));
673 @SuppressWarnings("unchecked")
674 private void parseFeatures(JSONArray jsonSeqFeatures)
676 if (jsonSeqFeatures != null)
678 displayedFeatures = new FeaturesDisplayed();
679 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
682 JSONObject jsonFeature = seqFeatureItr.next();
683 Long begin = (Long) jsonFeature.get("xStart");
684 Long end = (Long) jsonFeature.get("xEnd");
685 String type = (String) jsonFeature.get("type");
686 String featureGrp = (String) jsonFeature.get("featureGroup");
687 String descripiton = (String) jsonFeature.get("description");
688 String seqRef = (String) jsonFeature.get("sequenceRef");
689 Float score = Float.valueOf(jsonFeature.get("score").toString());
691 Sequence seq = seqMap.get(seqRef);
692 SequenceFeature sequenceFeature = new SequenceFeature();
693 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
694 if (linksJsonArray != null && linksJsonArray.size() > 0)
696 Iterator<String> linkList = linksJsonArray.iterator();
697 while (linkList.hasNext())
699 String link = linkList.next();
700 sequenceFeature.addLink(link);
703 sequenceFeature.setFeatureGroup(featureGrp);
704 sequenceFeature.setScore(score);
705 sequenceFeature.setDescription(descripiton);
706 sequenceFeature.setType(type);
707 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
708 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
709 seq.addSequenceFeature(sequenceFeature);
710 displayedFeatures.setVisible(type);
716 public String getGlobalColourScheme()
718 return globalColourScheme;
721 public void setGlobalColorScheme(String globalColourScheme)
723 this.globalColourScheme = globalColourScheme;
727 public FeaturesDisplayedI getDisplayedFeatures()
729 return displayedFeatures;
732 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
734 this.displayedFeatures = displayedFeatures;
738 public void configureForView(AlignmentViewPanel avpanel)
744 super.configureForView(avpanel);
745 AlignViewportI viewport = avpanel.getAlignViewport();
746 AlignmentI alignment = viewport.getAlignment();
747 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
749 seqGroups = alignment.getGroups();
750 fr = avpanel.cloneFeatureRenderer();
752 // Add non auto calculated annotation to AlignFile
755 for (AlignmentAnnotation annot : annots)
757 if (annot != null && !annot.autoCalculated)
759 annotations.add(annot);
763 globalColourScheme = ColourSchemeProperty.getColourName(viewport
764 .getGlobalColourScheme());
765 setDisplayedFeatures(viewport.getFeaturesDisplayed());
766 showSeqFeatures = viewport.isShowSequenceFeatures();
771 public boolean isShowSeqFeatures()
773 return showSeqFeatures;
776 public void setShowSeqFeatures(boolean showSeqFeatures)
778 this.showSeqFeatures = showSeqFeatures;
781 public Vector<AlignmentAnnotation> getAnnotations()
786 public List<int[]> getHiddenColumns()
788 return hiddenColumns;
792 public ColumnSelection getColumnSelection()
794 return columnSelection;
797 public void setColumnSelection(ColumnSelection columnSelection)
799 this.columnSelection = columnSelection;
803 public SequenceI[] getHiddenSequences()
805 if (hiddenSequences == null || hiddenSequences.isEmpty())
807 return new SequenceI[] {};
809 synchronized (hiddenSequences)
811 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
815 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
817 this.hiddenSequences = hiddenSequences;
820 public class JSONExportSettings
822 private boolean exportSequence;
824 private boolean exportSequenceFeatures;
826 private boolean exportAnnotations;
828 private boolean exportGroups;
830 private boolean exportJalviewSettings;
832 public boolean isExportSequence()
834 return exportSequence;
837 public void setExportSequence(boolean exportSequence)
839 this.exportSequence = exportSequence;
842 public boolean isExportSequenceFeatures()
844 return exportSequenceFeatures;
847 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
849 this.exportSequenceFeatures = exportSequenceFeatures;
852 public boolean isExportAnnotations()
854 return exportAnnotations;
857 public void setExportAnnotations(boolean exportAnnotations)
859 this.exportAnnotations = exportAnnotations;
862 public boolean isExportGroups()
867 public void setExportGroups(boolean exportGroups)
869 this.exportGroups = exportGroups;
872 public boolean isExportJalviewSettings()
874 return exportJalviewSettings;
877 public void setExportJalviewSettings(boolean exportJalviewSettings)
879 this.exportJalviewSettings = exportJalviewSettings;
884 * Returns a descriptor for suitable feature display settings with
886 * <li>ResNums or insertions features visible</li>
887 * <li>insertions features coloured red</li>
888 * <li>ResNum features coloured by label</li>
889 * <li>Insertions displayed above (on top of) ResNums</li>
893 public FeatureSettingsModelI getFeatureColourScheme()
895 return new PDBFeatureSettings();