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.Colour;
50 import jalview.schemes.ColourSchemeProperty;
51 import jalview.schemes.UserColourScheme;
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 public static final String FILE_EXT = "json";
77 public static final String FILE_DESC = "JSON";
79 private String globalColourScheme;
81 private boolean showSeqFeatures;
83 private Hashtable<String, Sequence> seqMap;
85 private FeaturesDisplayedI displayedFeatures;
87 private FeatureRenderer fr;
89 private List<int[]> hiddenColumns;
91 private ColumnSelection columnSelection;
93 private List<String> hiddenSeqRefs;
95 private ArrayList<SequenceI> hiddenSequences;
97 private final static String TCOFFEE_SCORE = "TCoffeeScore";
104 public JSONFile(FileParse source) throws IOException
109 public JSONFile(String inFile, String type) throws IOException
115 public void parse() throws IOException
122 public String print()
124 String jsonOutput = null;
127 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
128 AlignExportSettingI exportSettings = getExportSettings();
130 // if no export settings were supplied use the following with all values
131 // defaulting to true
132 if (exportSettings == null)
134 exportSettings = new AlignExportSettingI()
137 public boolean isExportHiddenSequences()
143 public boolean isExportHiddenColumns()
149 public boolean isExportGroups()
155 public boolean isExportFeatures()
161 public boolean isExportAnnotations()
167 public boolean isCancelled()
175 for (SequenceI seq : seqs)
177 StringBuilder name = new StringBuilder();
178 name.append(seq.getName()).append("/").append(seq.getStart())
179 .append("-").append(seq.getEnd());
180 SequencePojo jsonSeqPojo = new SequencePojo();
181 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
182 jsonSeqPojo.setOrder(++count);
183 jsonSeqPojo.setEnd(seq.getEnd());
184 jsonSeqPojo.setStart(seq.getStart());
185 jsonSeqPojo.setName(name.toString());
186 jsonSeqPojo.setSeq(seq.getSequenceAsString());
187 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
189 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
190 jsonAlignmentPojo.getAppSettings().put("application", application);
191 jsonAlignmentPojo.getAppSettings().put("version", version);
192 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
193 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
194 String.valueOf(showSeqFeatures));
196 String[] hiddenSections = getHiddenSections();
197 if (hiddenSections != null)
199 if (hiddenSections[0] != null
200 && exportSettings.isExportHiddenColumns())
202 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
203 String.valueOf(hiddenSections[0]));
205 if (hiddenSections[1] != null
206 && exportSettings.isExportHiddenSequences())
208 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
209 String.valueOf(hiddenSections[1]));
213 if (exportSettings.isExportAnnotations())
216 .setAlignAnnotation(annotationToJsonPojo(annotations));
220 // These color schemes require annotation, disable them if annotations
222 if (globalColourScheme.equalsIgnoreCase("RNA Helices")
223 || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
225 jsonAlignmentPojo.setGlobalColorScheme("None");
229 if (exportSettings.isExportFeatures())
232 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, 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(ColourSchemeProperty
243 .getColourName(seqGrp.cs));
244 seqGrpPojo.setColourText(seqGrp.getColourText());
245 seqGrpPojo.setDescription(seqGrp.getDescription());
246 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
247 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
248 seqGrpPojo.setEndRes(seqGrp.getEndRes());
249 seqGrpPojo.setStartRes(seqGrp.getStartRes());
250 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
251 for (SequenceI seq : seqGrp.getSequences())
253 seqGrpPojo.getSequenceRefs()
254 .add(String.valueOf(seq.hashCode()));
256 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
259 org.json.JSONObject generatedJSon = new org.json.JSONObject(
261 jsonOutput = generatedJSon.toString();
262 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
264 } catch (Exception e)
271 public String[] getHiddenSections()
273 String[] hiddenSections = new String[2];
274 if (getViewport() == null)
279 // hidden column business
280 if (getViewport().hasHiddenColumns())
282 List<int[]> hiddenCols = getViewport().getColumnSelection()
284 StringBuilder hiddenColsBuilder = new StringBuilder();
285 for (int[] range : hiddenCols)
287 hiddenColsBuilder.append(";").append(range[0]).append("-")
291 hiddenColsBuilder.deleteCharAt(0);
292 hiddenSections[0] = hiddenColsBuilder.toString();
295 // hidden rows/seqs business
296 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
297 .getHiddenSequences();
298 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
300 return hiddenSections;
303 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
304 StringBuilder hiddenSeqsBuilder = new StringBuilder();
305 for (SequenceI hiddenSeq : hiddenSeqs)
307 if (hiddenSeq != null)
309 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
312 if (hiddenSeqsBuilder.length() > 0)
314 hiddenSeqsBuilder.deleteCharAt(0);
316 hiddenSections[1] = hiddenSeqsBuilder.toString();
318 return hiddenSections;
321 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
322 List<SequenceI> seqs, FeatureRenderer fr)
324 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
325 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
326 for (SequenceI seq : seqs)
328 SequenceI dataSetSequence = seq.getDatasetSequence();
329 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
330 : seq.getDatasetSequence().getSequenceFeatures();
332 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
334 if (seqFeatures == null)
339 for (SequenceFeature sf : seqFeatures)
341 if (displayedFeatures != null
342 && displayedFeatures.isVisible(sf.getType()))
344 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
345 String.valueOf(seq.hashCode()));
347 String featureColour = (fr == null) ? null : jalview.util.Format
348 .getHexString(fr.findFeatureColour(Colour.white, seq,
349 seq.findIndex(sf.getBegin())));
350 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
351 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
352 jsonFeature.setType(sf.getType());
353 jsonFeature.setDescription(sf.getDescription());
354 jsonFeature.setLinks(sf.links);
355 jsonFeature.setOtherDetails(sf.otherDetails);
356 jsonFeature.setScore(sf.getScore());
357 jsonFeature.setFillColor(featureColour);
358 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
359 sequenceFeaturesPojo.add(jsonFeature);
363 return sequenceFeaturesPojo;
366 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
367 Vector<AlignmentAnnotation> annotations)
369 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
370 if (annotations == null)
372 return jsonAnnotations;
374 for (AlignmentAnnotation annot : annotations)
376 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
377 alignAnnotPojo.setDescription(annot.description);
378 alignAnnotPojo.setLabel(annot.label);
379 if (!Double.isNaN(annot.score))
381 alignAnnotPojo.setScore(annot.score);
383 alignAnnotPojo.setCalcId(annot.getCalcId());
384 alignAnnotPojo.setGraphType(annot.graph);
386 AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
387 annotSetting.setBelowAlignment(annot.belowAlignment);
388 annotSetting.setCentreColLabels(annot.centreColLabels);
389 annotSetting.setScaleColLabel(annot.scaleColLabel);
390 annotSetting.setShowAllColLabels(annot.showAllColLabels);
391 annotSetting.setVisible(annot.visible);
392 annotSetting.setHasIcon(annot.hasIcons);
393 alignAnnotPojo.setAnnotationSettings(annotSetting);
394 SequenceI refSeq = annot.sequenceRef;
397 alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
399 for (Annotation annotation : annot.annotations)
401 AnnotationPojo annotationPojo = new AnnotationPojo();
402 if (annotation != null)
404 annotationPojo.setDescription(annotation.description);
405 annotationPojo.setValue(annotation.value);
407 .setSecondaryStructure(annotation.secondaryStructure);
408 String displayChar = annotation.displayCharacter == null ? null
409 : annotation.displayCharacter;
410 // System.out.println("--------------------->[" + displayChar + "]");
411 annotationPojo.setDisplayCharacter(displayChar);
412 if (annotation.colour != null)
414 annotationPojo.setColour(jalview.util.Format
415 .getHexString(annotation.colour));
417 alignAnnotPojo.getAnnotations().add(annotationPojo);
421 if (annot.getCalcId() != null
422 && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
428 alignAnnotPojo.getAnnotations().add(annotationPojo);
432 jsonAnnotations.add(alignAnnotPojo);
434 return jsonAnnotations;
437 @SuppressWarnings("unchecked")
438 public JSONFile parse(Reader jsonAlignmentString)
442 JSONParser jsonParser = new JSONParser();
443 JSONObject alignmentJsonObj = (JSONObject) jsonParser
444 .parse(jsonAlignmentString);
445 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
446 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
447 .get("alignAnnotation");
448 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
450 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
452 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
455 if (jvSettingsJsonObj != null)
457 globalColourScheme = (String) jvSettingsJsonObj
458 .get("globalColorScheme");
459 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
460 "showSeqFeatures").toString());
461 setShowSeqFeatures(showFeatures);
462 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
463 parseHiddenCols(jvSettingsJsonObj);
466 hiddenSequences = new ArrayList<SequenceI>();
467 seqMap = new Hashtable<String, Sequence>();
468 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
471 JSONObject sequence = sequenceIter.next();
472 String sequcenceString = sequence.get("seq").toString();
473 String sequenceName = sequence.get("name").toString();
474 String seqUniqueId = sequence.get("id").toString();
475 int start = Integer.valueOf(sequence.get("start").toString());
476 int end = Integer.valueOf(sequence.get("end").toString());
477 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
479 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
481 hiddenSequences.add(seq);
484 seqMap.put(seqUniqueId, seq);
487 parseFeatures(jsonSeqArray);
489 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
492 JSONObject seqGrpObj = seqGrpIter.next();
493 String grpName = seqGrpObj.get("groupName").toString();
494 String colourScheme = seqGrpObj.get("colourScheme").toString();
495 String description = (seqGrpObj.get("description") == null) ? null
496 : seqGrpObj.get("description").toString();
497 boolean displayBoxes = Boolean.valueOf(seqGrpObj
498 .get("displayBoxes").toString());
499 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
501 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
503 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
504 "showNonconserved").toString());
505 int startRes = Integer
506 .valueOf(seqGrpObj.get("startRes").toString());
507 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
508 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
510 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
511 if (sequenceRefs.size() > 0)
513 Iterator<String> seqHashIter = sequenceRefs.iterator();
514 while (seqHashIter.hasNext())
516 String seqHash = seqHashIter.next();
517 Sequence sequence = seqMap.get(seqHash);
518 if (sequence != null)
520 grpSeqs.add(sequence);
524 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
525 displayBoxes, displayText, colourText, startRes, endRes);
526 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
528 seqGrp.setShowNonconserved(showNonconserved);
529 seqGrp.setDescription(description);
530 this.seqGroups.add(seqGrp);
534 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
537 JSONObject alAnnot = alAnnotIter.next();
538 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
539 Annotation[] annotations = new Annotation[annotJsonArray.size()];
541 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
544 JSONObject annot = annotIter.next();
547 annotations[count] = null;
551 float val = annot.get("value") == null ? null : Float
552 .valueOf(annot.get("value").toString());
553 String desc = annot.get("description") == null ? null : annot
554 .get("description").toString();
555 char ss = annot.get("secondaryStructure") == null
556 || annot.get("secondaryStructure").toString()
557 .equalsIgnoreCase("u0000") ? ' ' : annot
558 .get("secondaryStructure").toString().charAt(0);
559 String displayChar = annot.get("displayCharacter") == null ? ""
560 : annot.get("displayCharacter").toString();
562 annotations[count] = new Annotation(displayChar, desc, ss, val);
563 if (annot.get("colour") != null)
565 Color color = UserColourScheme.getColourFromString(annot.get(
566 "colour").toString());
567 annotations[count].colour = color;
573 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
574 .get("label").toString(), alAnnot.get("description")
575 .toString(), annotations);
576 alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
577 .valueOf(alAnnot.get("graphType").toString());
579 JSONObject diplaySettings = (JSONObject) alAnnot
580 .get("annotationSettings");
581 if (diplaySettings != null)
584 alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
585 : Boolean.valueOf(diplaySettings.get("scaleColLabel")
587 alignAnnot.showAllColLabels = (diplaySettings
588 .get("showAllColLabels") == null) ? true : Boolean
589 .valueOf(diplaySettings.get("showAllColLabels")
591 alignAnnot.centreColLabels = (diplaySettings
592 .get("centreColLabels") == null) ? true
593 : Boolean.valueOf(diplaySettings.get("centreColLabels")
595 alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
596 : Boolean.valueOf(diplaySettings.get("belowAlignment")
598 alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
599 : Boolean.valueOf(diplaySettings.get("visible")
601 alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
602 : Boolean.valueOf(diplaySettings.get("hasIcon")
606 if (alAnnot.get("score") != null)
608 alignAnnot.score = Double
609 .valueOf(alAnnot.get("score").toString());
612 String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
613 "calcId").toString();
614 alignAnnot.setCalcId(calcId);
615 String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
616 .get("sequenceRef").toString() : null;
618 Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
619 if (sequence != null)
621 alignAnnot.sequenceRef = sequence;
622 sequence.addAlignmentAnnotation(alignAnnot);
623 if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
625 alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
627 sequence.addAlignmentAnnotation(alignAnnot);
628 alignAnnot.adjustForAlignment();
631 alignAnnot.validateRangeAndDisplay();
632 this.annotations.add(alignAnnot);
635 } catch (Exception e)
642 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
644 hiddenSeqRefs = new ArrayList<String>();
645 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
646 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
648 String[] seqRefs = hiddenSeqs.split(";");
649 for (String seqRef : seqRefs)
651 hiddenSeqRefs.add(seqRef);
656 public void parseHiddenCols(JSONObject jvSettingsJson)
658 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
659 if (hiddenCols != null && !hiddenCols.isEmpty())
661 columnSelection = new ColumnSelection();
662 String[] rangeStrings = hiddenCols.split(";");
663 for (String rangeString : rangeStrings)
665 String[] range = rangeString.split("-");
666 columnSelection.hideColumns(Integer.valueOf(range[0]),
667 Integer.valueOf(range[1]));
672 @SuppressWarnings("unchecked")
673 private void parseFeatures(JSONArray jsonSeqFeatures)
675 if (jsonSeqFeatures != null)
677 displayedFeatures = new FeaturesDisplayed();
678 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
681 JSONObject jsonFeature = seqFeatureItr.next();
682 Long begin = (Long) jsonFeature.get("xStart");
683 Long end = (Long) jsonFeature.get("xEnd");
684 String type = (String) jsonFeature.get("type");
685 String featureGrp = (String) jsonFeature.get("featureGroup");
686 String descripiton = (String) jsonFeature.get("description");
687 String seqRef = (String) jsonFeature.get("sequenceRef");
688 Float score = Float.valueOf(jsonFeature.get("score").toString());
690 Sequence seq = seqMap.get(seqRef);
691 SequenceFeature sequenceFeature = new SequenceFeature();
692 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
693 if (linksJsonArray != null && linksJsonArray.size() > 0)
695 Iterator<String> linkList = linksJsonArray.iterator();
696 while (linkList.hasNext())
698 String link = linkList.next();
699 sequenceFeature.addLink(link);
702 sequenceFeature.setFeatureGroup(featureGrp);
703 sequenceFeature.setScore(score);
704 sequenceFeature.setDescription(descripiton);
705 sequenceFeature.setType(type);
706 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
707 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
708 seq.addSequenceFeature(sequenceFeature);
709 displayedFeatures.setVisible(type);
715 public String getGlobalColourScheme()
717 return globalColourScheme;
720 public void setGlobalColorScheme(String globalColourScheme)
722 this.globalColourScheme = globalColourScheme;
726 public FeaturesDisplayedI getDisplayedFeatures()
728 return displayedFeatures;
731 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
733 this.displayedFeatures = displayedFeatures;
737 public void configureForView(AlignmentViewPanel avpanel)
739 super.configureForView(avpanel);
740 AlignViewportI viewport = avpanel.getAlignViewport();
741 AlignmentI alignment = viewport.getAlignment();
742 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
744 seqGroups = alignment.getGroups();
745 fr = avpanel.cloneFeatureRenderer();
747 // Add non auto calculated annotation to AlignFile
748 for (AlignmentAnnotation annot : annots)
750 if (annot != null && !annot.autoCalculated)
752 annotations.add(annot);
755 globalColourScheme = ColourSchemeProperty.getColourName(viewport
756 .getGlobalColourScheme());
757 setDisplayedFeatures(viewport.getFeaturesDisplayed());
758 showSeqFeatures = viewport.isShowSequenceFeatures();
763 public boolean isShowSeqFeatures()
765 return showSeqFeatures;
768 public void setShowSeqFeatures(boolean showSeqFeatures)
770 this.showSeqFeatures = showSeqFeatures;
773 public Vector<AlignmentAnnotation> getAnnotations()
778 public List<int[]> getHiddenColumns()
780 return hiddenColumns;
784 public ColumnSelection getColumnSelection()
786 return columnSelection;
789 public void setColumnSelection(ColumnSelection columnSelection)
791 this.columnSelection = columnSelection;
795 public SequenceI[] getHiddenSequences()
797 if (hiddenSequences == null || hiddenSequences.isEmpty())
799 return new SequenceI[] {};
801 synchronized (hiddenSequences)
803 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
807 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
809 this.hiddenSequences = hiddenSequences;
812 public class JSONExportSettings
814 private boolean exportSequence;
816 private boolean exportSequenceFeatures;
818 private boolean exportAnnotations;
820 private boolean exportGroups;
822 private boolean exportJalviewSettings;
824 public boolean isExportSequence()
826 return exportSequence;
829 public void setExportSequence(boolean exportSequence)
831 this.exportSequence = exportSequence;
834 public boolean isExportSequenceFeatures()
836 return exportSequenceFeatures;
839 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
841 this.exportSequenceFeatures = exportSequenceFeatures;
844 public boolean isExportAnnotations()
846 return exportAnnotations;
849 public void setExportAnnotations(boolean exportAnnotations)
851 this.exportAnnotations = exportAnnotations;
854 public boolean isExportGroups()
859 public void setExportGroups(boolean exportGroups)
861 this.exportGroups = exportGroups;
864 public boolean isExportJalviewSettings()
866 return exportJalviewSettings;
869 public void setExportJalviewSettings(boolean exportJalviewSettings)
871 this.exportJalviewSettings = exportJalviewSettings;
876 * Returns a descriptor for suitable feature display settings with
878 * <li>ResNums or insertions features visible</li>
879 * <li>insertions features coloured red</li>
880 * <li>ResNum features coloured by label</li>
881 * <li>Insertions displayed above (on top of) ResNums</li>
885 public FeatureSettingsModelI getFeatureColourScheme()
887 return new PDBFeatureSettings();