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.FeaturesDisplayedI;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.Annotation;
33 import jalview.datamodel.ColumnSelection;
34 import jalview.datamodel.HiddenSequences;
35 import jalview.datamodel.Sequence;
36 import jalview.datamodel.SequenceFeature;
37 import jalview.datamodel.SequenceGroup;
38 import jalview.datamodel.SequenceI;
39 import jalview.json.binding.v1.AlignmentAnnotationPojo;
40 import jalview.json.binding.v1.AlignmentPojo;
41 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
42 import jalview.json.binding.v1.AnnotationPojo;
43 import jalview.json.binding.v1.SequenceFeaturesPojo;
44 import jalview.json.binding.v1.SequenceGrpPojo;
45 import jalview.json.binding.v1.SequencePojo;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemeProperty;
48 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
50 import java.awt.Color;
51 import java.io.IOException;
52 import java.io.Reader;
53 import java.util.ArrayList;
54 import java.util.Hashtable;
55 import java.util.Iterator;
56 import java.util.List;
57 import java.util.Vector;
59 import org.json.simple.JSONArray;
60 import org.json.simple.JSONObject;
61 import org.json.simple.parser.JSONParser;
63 public class JSONFile extends AlignFile implements ComplexAlignFile
65 private ColourSchemeI colourScheme;
67 private String version = "2.9";
69 private String webstartUrl = "www.jalview.org/services/launchApp";
71 private String application = "Jalview";
73 public static final String FILE_EXT = "json";
75 public static final String FILE_DESC = "JSON";
77 private String globalColorScheme;
79 private boolean showSeqFeatures;
81 private Hashtable<String, Sequence> seqMap;
83 private FeaturesDisplayedI displayedFeatures;
85 private FeatureRenderer fr;
87 private List<int[]> hiddenColumns;
89 private ColumnSelection columnSelection;
91 private List<String> hiddenSeqRefs;
93 private ArrayList<SequenceI> hiddenSequences;
101 public JSONFile(FileParse source) throws IOException
106 public JSONFile(String inFile, String type) throws IOException
112 public void parse() throws IOException
118 public String print()
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()
165 for (SequenceI seq : seqs)
167 StringBuilder name = new StringBuilder();
168 name.append(seq.getName()).append("/").append(seq.getStart())
169 .append("-").append(seq.getEnd());
170 SequencePojo jsonSeqPojo = new SequencePojo();
171 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
172 jsonSeqPojo.setOrder(++count);
173 jsonSeqPojo.setEnd(seq.getEnd());
174 jsonSeqPojo.setStart(seq.getStart());
175 jsonSeqPojo.setName(name.toString());
176 jsonSeqPojo.setSeq(seq.getSequenceAsString());
177 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
180 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
181 jsonAlignmentPojo.getAppSettings().put("application", application);
182 jsonAlignmentPojo.getAppSettings().put("version", version);
183 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
184 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
185 String.valueOf(showSeqFeatures));
187 String[] hiddenSections = getHiddenSections();
188 if (hiddenSections != null)
190 if (hiddenSections[0] != null
192 .isExportHiddenColumns())
194 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
195 String.valueOf(hiddenSections[0]));
197 if (hiddenSections[1] != null
199 .isExportHiddenSequences())
201 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
202 String.valueOf(hiddenSections[1]));
206 if (exportSettings.isExportAnnotations())
209 .setAlignAnnotation(annotationToJsonPojo(annotations));
212 if (exportSettings.isExportFeatures())
215 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
218 if (exportSettings.isExportGroups()
220 && seqGroups.size() > 0)
222 for (SequenceGroup seqGrp : seqGroups)
224 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
225 seqGrpPojo.setGroupName(seqGrp.getName());
226 seqGrpPojo.setColourScheme(ColourSchemeProperty
227 .getColourName(seqGrp.cs));
228 seqGrpPojo.setColourText(seqGrp.getColourText());
229 seqGrpPojo.setDescription(seqGrp.getDescription());
230 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
231 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
232 seqGrpPojo.setEndRes(seqGrp.getEndRes());
233 seqGrpPojo.setStartRes(seqGrp.getStartRes());
234 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
235 for (SequenceI seq : seqGrp.getSequences())
237 seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
239 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
242 org.json.JSONObject generatedJSon = new org.json.JSONObject(
244 jsonOutput = generatedJSon.toString();
245 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
247 } catch (Exception e)
254 public String[] getHiddenSections()
256 String[] hiddenSections = new String[2];
257 if (getViewport() == null)
262 // hidden column business
263 if (getViewport().hasHiddenColumns())
265 List<int[]> hiddenCols = getViewport().getColumnSelection()
267 StringBuilder hiddenColsBuilder = new StringBuilder();
268 for (int[] range : hiddenCols)
270 hiddenColsBuilder.append(";").append(range[0]).append("-")
274 hiddenColsBuilder.deleteCharAt(0);
275 hiddenSections[0] = hiddenColsBuilder.toString();
278 // hidden rows/seqs business
279 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
280 .getHiddenSequences();
281 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
283 return hiddenSections;
286 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
287 StringBuilder hiddenSeqsBuilder = new StringBuilder();
288 for (SequenceI hiddenSeq : hiddenSeqs)
290 if (hiddenSeq != null)
292 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
295 if (hiddenSeqsBuilder.length() > 0)
297 hiddenSeqsBuilder.deleteCharAt(0);
299 hiddenSections[1] = hiddenSeqsBuilder.toString();
301 return hiddenSections;
304 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
305 List<SequenceI> seqs, FeatureRenderer fr)
307 displayedFeatures = (fr == null) ? null : fr
308 .getFeaturesDisplayed();
309 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
310 for (SequenceI seq : seqs)
312 SequenceI dataSetSequence = seq.getDatasetSequence();
313 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
314 : seq.getDatasetSequence().getSequenceFeatures();
316 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
318 if (seqFeatures == null)
323 for (SequenceFeature sf : seqFeatures)
325 if (displayedFeatures != null
326 && displayedFeatures.isVisible(sf.getType()))
328 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
329 String.valueOf(seq.hashCode()));
331 String featureColour = (fr == null) ? null : jalview.util.Format
333 .findFeatureColour(Color.white, seq,
334 seq.findIndex(sf.getBegin())));
335 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
336 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
337 jsonFeature.setType(sf.getType());
338 jsonFeature.setDescription(sf.getDescription());
339 jsonFeature.setLinks(sf.links);
340 jsonFeature.setOtherDetails(sf.otherDetails);
341 jsonFeature.setScore(sf.getScore());
342 jsonFeature.setFillColor(featureColour);
343 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
344 sequenceFeaturesPojo.add(jsonFeature);
348 return sequenceFeaturesPojo;
351 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
352 Vector<AlignmentAnnotation> annotations)
354 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
355 if (annotations == null)
357 return jsonAnnotations;
359 for (AlignmentAnnotation annot : annotations)
361 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
362 alignAnnotPojo.setDescription(annot.description);
363 alignAnnotPojo.setLabel(annot.label);
364 for (Annotation annotation : annot.annotations)
366 AnnotationPojo annotationPojo = new AnnotationPojo();
367 if (annotation != null)
369 annotationPojo.setDescription(annotation.description);
370 annotationPojo.setValue(annotation.value);
372 .setSecondaryStructure(annotation.secondaryStructure);
373 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
374 alignAnnotPojo.getAnnotations().add(annotationPojo);
378 alignAnnotPojo.getAnnotations().add(annotationPojo);
381 jsonAnnotations.add(alignAnnotPojo);
383 return jsonAnnotations;
386 @SuppressWarnings("unchecked")
387 public JSONFile parse(Reader jsonAlignmentString)
391 JSONParser jsonParser = new JSONParser();
392 JSONObject alignmentJsonObj = (JSONObject) jsonParser
393 .parse(jsonAlignmentString);
394 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
395 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
396 .get("alignAnnotation");
397 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
399 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
401 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
404 if (jvSettingsJsonObj != null)
406 String jsColourScheme = (String) jvSettingsJsonObj
407 .get("globalColorScheme");
408 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
409 "showSeqFeatures").toString());
410 setColourScheme(getJalviewColorScheme(jsColourScheme));
411 setShowSeqFeatures(showFeatures);
412 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
413 parseHiddenCols(jvSettingsJsonObj);
416 hiddenSequences = new ArrayList<SequenceI>();
417 seqMap = new Hashtable<String, Sequence>();
418 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
421 JSONObject sequence = sequenceIter.next();
422 String sequcenceString = sequence.get("seq").toString();
423 String sequenceName = sequence.get("name").toString();
424 String seqUniqueId = sequence.get("id").toString();
425 int start = Integer.valueOf(sequence.get("start").toString());
426 int end = Integer.valueOf(sequence.get("end").toString());
427 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
429 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
431 hiddenSequences.add(seq);
434 seqMap.put(seqUniqueId, seq);
436 parseFeatures(jsonSeqArray);
438 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
441 JSONObject seqGrpObj = seqGrpIter.next();
442 String grpName = seqGrpObj.get("groupName").toString();
443 String colourScheme = seqGrpObj.get("colourScheme").toString();
444 String description = (seqGrpObj.get("description") == null) ? null
445 : seqGrpObj.get("description").toString();
446 boolean displayBoxes = Boolean.valueOf(seqGrpObj
447 .get("displayBoxes").toString());
448 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
450 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
452 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
453 "showNonconserved").toString());
454 int startRes = Integer
455 .valueOf(seqGrpObj.get("startRes").toString());
456 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
457 JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
459 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
460 if (seqsHashArray.size() > 0)
462 Iterator<String> seqHashIter = seqsHashArray.iterator();
463 while (seqHashIter.hasNext())
465 String seqHash = seqHashIter.next();
466 Sequence sequence = seqMap.get(seqHash);
467 if (sequence != null)
469 grpSeqs.add(sequence);
473 ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
474 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
476 displayBoxes, displayText, colourText, startRes, endRes);
477 seqGrp.setShowNonconserved(showNonconserved);
478 seqGrp.setDescription(description);
479 this.seqGroups.add(seqGrp);
483 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
486 JSONObject alAnnot = alAnnotIter.next();
487 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
488 Annotation[] annotations = new Annotation[annotJsonArray.size()];
490 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
493 JSONObject annot = annotIter.next();
496 annotations[count] = null;
500 float val = annot.get("value") == null ? null : Float
501 .valueOf(annot.get("value").toString());
502 String desc = annot.get("description") == null ? null : annot
503 .get("description").toString();
505 char ss = annot.get("secondaryStructure") == null ? ' '
506 : annot.get("secondaryStructure").toString().charAt(0);
507 String displayChar = annot.get("displayCharacter").toString();
509 annotations[count] = new Annotation(displayChar, desc, ss, val);
514 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
515 .get("label").toString(), alAnnot.get("description")
516 .toString(), annotations);
517 this.annotations.add(alignAnnot);
520 } catch (Exception e)
527 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
529 hiddenSeqRefs = new ArrayList<String>();
530 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
531 if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
532 String[] seqRefs = hiddenSeqs.split(";");
533 for(String seqRef : seqRefs){
534 hiddenSeqRefs.add(seqRef);
539 public void parseHiddenCols(JSONObject jvSettingsJson)
541 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
542 if(hiddenCols != null && !hiddenCols.isEmpty()){
543 columnSelection = new ColumnSelection();
544 String[] rangeStrings = hiddenCols.split(";");
545 for(String rangeString : rangeStrings){
546 String[] range = rangeString.split("-");
547 columnSelection.hideColumns(Integer.valueOf(range[0]),
548 Integer.valueOf(range[1]));
553 @SuppressWarnings("unchecked")
554 private void parseFeatures(JSONArray jsonSeqFeatures)
556 if (jsonSeqFeatures != null)
558 displayedFeatures = new FeaturesDisplayed();
559 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
562 JSONObject jsonFeature = seqFeatureItr.next();
563 Long begin = (Long) jsonFeature.get("xStart");
564 Long end = (Long) jsonFeature.get("xEnd");
565 String type = (String) jsonFeature.get("type");
566 String featureGrp = (String) jsonFeature.get("featureGroup");
567 String descripiton = (String) jsonFeature.get("description");
568 String seqRef = (String) jsonFeature.get("sequenceRef");
569 Float score = Float.valueOf(jsonFeature.get("score").toString());
571 Sequence seq = seqMap.get(seqRef);
572 SequenceFeature sequenceFeature = new SequenceFeature();
573 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
574 if (linksJsonArray != null && linksJsonArray.size() > 0)
576 Iterator<String> linkList = linksJsonArray.iterator();
577 while (linkList.hasNext())
579 String link = linkList.next();
580 sequenceFeature.addLink(link);
583 sequenceFeature.setFeatureGroup(featureGrp);
584 sequenceFeature.setScore(score);
585 sequenceFeature.setDescription(descripiton);
586 sequenceFeature.setType(type);
587 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
588 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
589 seq.addSequenceFeature(sequenceFeature);
590 displayedFeatures.setVisible(type);
595 public static ColourSchemeI getJalviewColorScheme(
596 String bioJsColourSchemeName)
598 ColourSchemeI jalviewColor = null;
599 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
602 if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
604 jalviewColor = cs.getJvColourScheme();
611 public String getGlobalColorScheme()
613 return globalColorScheme;
616 public void setGlobalColorScheme(String globalColorScheme)
618 this.globalColorScheme = globalColorScheme;
621 public ColourSchemeI getColourScheme()
626 public void setColourScheme(ColourSchemeI colourScheme)
628 this.colourScheme = colourScheme;
632 public FeaturesDisplayedI getDisplayedFeatures()
634 return displayedFeatures;
637 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
639 this.displayedFeatures = displayedFeatures;
643 public void configureForView(AlignmentViewPanel avpanel)
645 super.configureForView(avpanel);
646 AlignViewportI viewport = avpanel.getAlignViewport();
647 AlignmentI alignment = viewport.getAlignment();
648 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
650 seqGroups = alignment.getGroups();
651 fr = avpanel.cloneFeatureRenderer();
653 // Add non auto calculated annotation to AlignFile
654 for (AlignmentAnnotation annot : annots)
656 if (annot != null && !annot.autoCalculated)
662 annotations.add(annot);
665 globalColorScheme = ColourSchemeProperty.getColourName(viewport
666 .getGlobalColourScheme());
667 setDisplayedFeatures(viewport.getFeaturesDisplayed());
668 showSeqFeatures = viewport.isShowSequenceFeatures();
672 public boolean isShowSeqFeatures()
674 return showSeqFeatures;
677 public void setShowSeqFeatures(boolean showSeqFeatures)
679 this.showSeqFeatures = showSeqFeatures;
682 public Vector<AlignmentAnnotation> getAnnotations()
687 public List<int[]> getHiddenColumns()
689 return hiddenColumns;
692 public ColumnSelection getColumnSelection()
694 return columnSelection;
697 public void setColumnSelection(ColumnSelection columnSelection)
699 this.columnSelection = columnSelection;
702 public SequenceI[] getHiddenSequences()
704 if (hiddenSequences == null || hiddenSequences.isEmpty())
706 return new SequenceI[]
709 synchronized (hiddenSequences)
711 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
715 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
717 this.hiddenSequences = hiddenSequences;
720 public class JSONExportSettings
722 private boolean exportSequence;
724 private boolean exportSequenceFeatures;
726 private boolean exportAnnotations;
728 private boolean exportGroups;
730 private boolean exportJalviewSettings;
732 public boolean isExportSequence()
734 return exportSequence;
737 public void setExportSequence(boolean exportSequence)
739 this.exportSequence = exportSequence;
742 public boolean isExportSequenceFeatures()
744 return exportSequenceFeatures;
747 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
749 this.exportSequenceFeatures = exportSequenceFeatures;
752 public boolean isExportAnnotations()
754 return exportAnnotations;
757 public void setExportAnnotations(boolean exportAnnotations)
759 this.exportAnnotations = exportAnnotations;
762 public boolean isExportGroups()
767 public void setExportGroups(boolean exportGroups)
769 this.exportGroups = exportGroups;
772 public boolean isExportJalviewSettings()
774 return exportJalviewSettings;
777 public void setExportJalviewSettings(boolean exportJalviewSettings)
779 this.exportJalviewSettings = exportJalviewSettings;