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.AlignViewportI;
25 import jalview.api.ComplexAlignFile;
26 import jalview.api.FeatureRenderer;
27 import jalview.api.FeaturesDisplayedI;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenSequences;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.json.binding.v1.AlignmentAnnotationPojo;
37 import jalview.json.binding.v1.AlignmentPojo;
38 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
39 import jalview.json.binding.v1.AnnotationPojo;
40 import jalview.json.binding.v1.SequenceFeaturesPojo;
41 import jalview.json.binding.v1.SequenceGrpPojo;
42 import jalview.json.binding.v1.SequencePojo;
43 import jalview.schemes.ColourSchemeI;
44 import jalview.schemes.ColourSchemeProperty;
46 import java.awt.Color;
47 import java.io.IOException;
48 import java.io.Reader;
49 import java.util.ArrayList;
50 import java.util.Hashtable;
51 import java.util.Iterator;
52 import java.util.List;
53 import java.util.Vector;
55 import org.json.simple.JSONArray;
56 import org.json.simple.JSONObject;
57 import org.json.simple.parser.JSONParser;
59 public class JSONFile extends AlignFile implements ComplexAlignFile
61 private ColourSchemeI colourScheme;
63 private String version = "2.9";
65 private String webstartUrl = "www.jalview.org/services/launchApp";
67 private String application = "Jalview";
69 public static final String FILE_EXT = "json";
71 public static final String FILE_DESC = "JSON";
73 private String globalColorScheme;
75 private boolean showSeqFeatures;
77 private Hashtable<String, Sequence> seqMap;
79 private FeaturesDisplayedI displayedFeatures;
81 private FeatureRenderer fr;
83 private List<int[]> hiddenColumns;
85 private ColumnSelection columnSelection;
87 private List<String> hiddenSeqRefs;
89 private ArrayList<SequenceI> hiddenSequences;
96 public JSONFile(FileParse source) throws IOException
101 public JSONFile(String inFile, String type) throws IOException
107 public void parse() throws IOException
114 public String print()
116 String jsonOutput = null;
119 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
120 if (getViewport() != null)
122 globalColorScheme = ColourSchemeProperty
123 .getColourName(getViewport()
124 .getGlobalColourScheme());
125 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
126 showSeqFeatures = getViewport().isShowSequenceFeatures();
127 fr = getViewport().getFeatureRenderer();
131 for (SequenceI seq : seqs)
133 StringBuilder name = new StringBuilder();
134 name.append(seq.getName()).append("/").append(seq.getStart())
135 .append("-").append(seq.getEnd());
136 SequencePojo jsonSeqPojo = new SequencePojo();
137 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
138 jsonSeqPojo.setOrder(++count);
139 jsonSeqPojo.setEnd(seq.getEnd());
140 jsonSeqPojo.setStart(seq.getStart());
141 jsonSeqPojo.setName(name.toString());
142 jsonSeqPojo.setSeq(seq.getSequenceAsString());
143 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
146 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
147 jsonAlignmentPojo.getAppSettings().put("application", application);
148 jsonAlignmentPojo.getAppSettings().put("version", version);
149 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
150 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
151 String.valueOf(showSeqFeatures));
153 String[] hiddenSections = getHiddenSections();
154 if (hiddenSections != null)
156 if (hiddenSections[0] != null
157 && getViewport().getExportSettings()
158 .isExportHiddenColumns())
160 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
161 String.valueOf(hiddenSections[0]));
163 if (hiddenSections[1] != null
164 && getViewport().getExportSettings()
165 .isExportHiddenSequences())
167 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
168 String.valueOf(hiddenSections[1]));
172 if (getViewport().getExportSettings().isExportAnnotations())
175 .setAlignAnnotation(annotationToJsonPojo(annotations));
178 if (getViewport().getExportSettings().isExportFeatures())
181 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
184 if (getViewport().getExportSettings().isExportGroups()
186 && seqGroups.size() > 0)
188 for (SequenceGroup seqGrp : seqGroups)
190 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
191 seqGrpPojo.setGroupName(seqGrp.getName());
192 seqGrpPojo.setColourScheme(ColourSchemeProperty
193 .getColourName(seqGrp.cs));
194 seqGrpPojo.setColourText(seqGrp.getColourText());
195 seqGrpPojo.setDescription(seqGrp.getDescription());
196 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
197 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
198 seqGrpPojo.setEndRes(seqGrp.getEndRes());
199 seqGrpPojo.setStartRes(seqGrp.getStartRes());
200 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
201 for (SequenceI seq : seqGrp.getSequences())
203 seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
205 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
208 org.json.JSONObject generatedJSon = new org.json.JSONObject(
210 jsonOutput = generatedJSon.toString();
211 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
213 } catch (Exception e)
220 public String[] getHiddenSections()
222 String[] hiddenSections = new String[2];
223 if (getViewport() == null)
228 // hidden column business
229 if (getViewport().hasHiddenColumns())
231 List<int[]> hiddenCols = getViewport().getColumnSelection()
233 StringBuilder hiddenColsBuilder = new StringBuilder();
234 for (int[] range : hiddenCols)
236 hiddenColsBuilder.append(";").append(range[0]).append("-")
240 hiddenColsBuilder.deleteCharAt(0);
241 hiddenSections[0] = hiddenColsBuilder.toString();
244 // hidden rows/seqs business
245 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
246 .getHiddenSequences();
247 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
249 return hiddenSections;
252 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
253 StringBuilder hiddenSeqsBuilder = new StringBuilder();
254 for (SequenceI hiddenSeq : hiddenSeqs)
256 if (hiddenSeq != null)
258 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
261 if (hiddenSeqsBuilder.length() > 0)
263 hiddenSeqsBuilder.deleteCharAt(0);
265 hiddenSections[1] = hiddenSeqsBuilder.toString();
267 return hiddenSections;
270 public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
271 List<SequenceI> seqs, FeatureRenderer fr)
273 FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
274 .getFeaturesDisplayed();
275 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
276 for (SequenceI seq : seqs)
278 SequenceI dataSetSequence = seq.getDatasetSequence();
279 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
280 : seq.getDatasetSequence().getSequenceFeatures();
282 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
284 if (seqFeatures == null)
289 for (SequenceFeature sf : seqFeatures)
291 if (displayedFeatures != null
292 && displayedFeatures.isVisible(sf.getType()))
294 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
295 String.valueOf(seq.hashCode()));
296 String featureColour = (fr == null) ? null : jalview.util.Format
298 .findFeatureColour(Color.white, seq,
299 seq.findIndex(sf.getBegin())));
300 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
301 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
302 jsonFeature.setType(sf.getType());
303 jsonFeature.setDescription(sf.getDescription());
304 jsonFeature.setLinks(sf.links);
305 jsonFeature.setOtherDetails(sf.otherDetails);
306 jsonFeature.setScore(sf.getScore());
307 jsonFeature.setFillColor(featureColour);
308 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
309 sequenceFeaturesPojo.add(jsonFeature);
313 return sequenceFeaturesPojo;
316 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
317 Vector<AlignmentAnnotation> annotations)
319 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
320 if (annotations == null)
322 return jsonAnnotations;
324 for (AlignmentAnnotation annot : annotations)
326 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
327 alignAnnotPojo.setDescription(annot.description);
328 alignAnnotPojo.setLabel(annot.label);
329 for (Annotation annotation : annot.annotations)
331 AnnotationPojo annotationPojo = new AnnotationPojo();
332 if (annotation != null)
334 annotationPojo.setDescription(annotation.description);
335 annotationPojo.setValue(annotation.value);
337 .setSecondaryStructure(annotation.secondaryStructure);
338 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
339 alignAnnotPojo.getAnnotations().add(annotationPojo);
343 alignAnnotPojo.getAnnotations().add(annotationPojo);
346 jsonAnnotations.add(alignAnnotPojo);
348 return jsonAnnotations;
351 @SuppressWarnings("unchecked")
352 public JSONFile parse(Reader jsonAlignmentString)
356 JSONParser jsonParser = new JSONParser();
357 JSONObject alignmentJsonObj = (JSONObject) jsonParser
358 .parse(jsonAlignmentString);
359 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
360 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
361 .get("alignAnnotation");
362 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
364 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
366 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
369 if (jvSettingsJsonObj != null)
371 String jsColourScheme = (String) jvSettingsJsonObj
372 .get("globalColorScheme");
373 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
374 "showSeqFeatures").toString());
375 setColourScheme(getJalviewColorScheme(jsColourScheme));
376 setShowSeqFeatures(showFeatures);
377 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
378 parseHiddenCols(jvSettingsJsonObj);
381 hiddenSequences = new ArrayList<SequenceI>();
382 seqMap = new Hashtable<String, Sequence>();
383 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
386 JSONObject sequence = sequenceIter.next();
387 String sequcenceString = sequence.get("seq").toString();
388 String sequenceName = sequence.get("name").toString();
389 String seqUniqueId = sequence.get("id").toString();
390 int start = Integer.valueOf(sequence.get("start").toString());
391 int end = Integer.valueOf(sequence.get("end").toString());
392 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
394 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
396 hiddenSequences.add(seq);
399 seqMap.put(seqUniqueId, seq);
401 parseFeatures(jsonSeqArray);
403 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
406 JSONObject seqGrpObj = seqGrpIter.next();
407 String grpName = seqGrpObj.get("groupName").toString();
408 String colourScheme = seqGrpObj.get("colourScheme").toString();
409 String description = (seqGrpObj.get("description") == null) ? null
410 : seqGrpObj.get("description").toString();
411 boolean displayBoxes = Boolean.valueOf(seqGrpObj
412 .get("displayBoxes").toString());
413 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
415 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
417 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
418 "showNonconserved").toString());
419 int startRes = Integer
420 .valueOf(seqGrpObj.get("startRes").toString());
421 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
422 JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
424 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
425 if (seqsHashArray.size() > 0)
427 Iterator<String> seqHashIter = seqsHashArray.iterator();
428 while (seqHashIter.hasNext())
430 String seqHash = seqHashIter.next();
431 Sequence sequence = seqMap.get(seqHash);
432 if (sequence != null)
434 grpSeqs.add(sequence);
438 ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
439 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
440 displayBoxes, displayText, colourText, startRes, endRes);
441 seqGrp.setShowNonconserved(showNonconserved);
442 seqGrp.setDescription(description);
443 this.seqGroups.add(seqGrp);
447 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
450 JSONObject alAnnot = alAnnotIter.next();
451 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
452 Annotation[] annotations = new Annotation[annotJsonArray.size()];
454 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
457 JSONObject annot = annotIter.next();
460 annotations[count] = null;
464 float val = annot.get("value") == null ? null : Float
465 .valueOf(annot.get("value").toString());
466 String desc = annot.get("description") == null ? null : annot
467 .get("description").toString();
469 char ss = annot.get("secondaryStructure") == null ? ' '
470 : annot.get("secondaryStructure").toString().charAt(0);
471 String displayChar = annot.get("displayCharacter").toString();
473 annotations[count] = new Annotation(displayChar, desc, ss, val);
478 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
479 .get("label").toString(), alAnnot.get("description")
480 .toString(), annotations);
481 this.annotations.add(alignAnnot);
484 } catch (Exception e)
491 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
493 hiddenSeqRefs = new ArrayList<String>();
494 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
495 if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
496 String[] seqRefs = hiddenSeqs.split(";");
497 for(String seqRef : seqRefs){
498 hiddenSeqRefs.add(seqRef);
503 public void parseHiddenCols(JSONObject jvSettingsJson)
505 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
506 if(hiddenCols != null && !hiddenCols.isEmpty()){
507 columnSelection = new ColumnSelection();
508 String[] rangeStrings = hiddenCols.split(";");
509 for(String rangeString : rangeStrings){
510 String[] range = rangeString.split("-");
511 columnSelection.hideColumns(Integer.valueOf(range[0]),
512 Integer.valueOf(range[1]));
517 @SuppressWarnings("unchecked")
518 private void parseFeatures(JSONArray jsonSeqFeatures)
520 if (jsonSeqFeatures != null)
522 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
525 JSONObject jsonFeature = seqFeatureItr.next();
526 Long begin = (Long) jsonFeature.get("xStart");
527 Long end = (Long) jsonFeature.get("xEnd");
528 String type = (String) jsonFeature.get("type");
529 String featureGrp = (String) jsonFeature.get("featureGroup");
530 String descripiton = (String) jsonFeature.get("description");
531 String seqRef = (String) jsonFeature.get("sequenceRef");
532 Float score = Float.valueOf(jsonFeature.get("score").toString());
534 Sequence seq = seqMap.get(seqRef);
535 SequenceFeature sequenceFeature = new SequenceFeature();
536 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
537 if (linksJsonArray != null && linksJsonArray.size() > 0)
539 Iterator<String> linkList = linksJsonArray.iterator();
540 while (linkList.hasNext())
542 String link = linkList.next();
543 sequenceFeature.addLink(link);
546 sequenceFeature.setFeatureGroup(featureGrp);
547 sequenceFeature.setScore(score);
548 sequenceFeature.setDescription(descripiton);
549 sequenceFeature.setType(type);
550 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
551 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
552 seq.addSequenceFeature(sequenceFeature);
557 public static ColourSchemeI getJalviewColorScheme(
558 String bioJsColourSchemeName)
560 ColourSchemeI jalviewColor = null;
561 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
564 if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
566 jalviewColor = cs.getJvColourScheme();
573 public String getGlobalColorScheme()
575 return globalColorScheme;
578 public void setGlobalColorScheme(String globalColorScheme)
580 this.globalColorScheme = globalColorScheme;
583 public ColourSchemeI getColourScheme()
588 public void setColourScheme(ColourSchemeI colourScheme)
590 this.colourScheme = colourScheme;
593 public FeaturesDisplayedI getDisplayedFeatures()
595 return displayedFeatures;
598 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
600 this.displayedFeatures = displayedFeatures;
604 public static String getJSONData(AlignViewportI av)
606 JSONFile jsonFile = new JSONFile();
607 jsonFile.setViewport(av);
608 jsonFile.seqGroups = av.getAlignment().getGroups();
609 jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
611 for (SequenceI seq : av.getAlignment().getSequences())
613 jsonFile.seqs.add(seq);
616 // Add non auto calculated annotation to AlignFile
617 for (AlignmentAnnotation annot : av.getAlignment()
618 .getAlignmentAnnotation())
620 if (annot != null && !annot.autoCalculated)
622 if (annot.label.equals("PDB.CATempFactor"))
626 jsonFile.annotations.add(annot);
629 String jsonString = jsonFile.print();
633 public boolean isShowSeqFeatures()
635 return showSeqFeatures;
638 public void setShowSeqFeatures(boolean showSeqFeatures)
640 this.showSeqFeatures = showSeqFeatures;
643 public Vector<AlignmentAnnotation> getAnnotations()
648 public List<int[]> getHiddenColumns()
650 return hiddenColumns;
653 public ColumnSelection getColumnSelection()
655 return columnSelection;
658 public void setColumnSelection(ColumnSelection columnSelection)
660 this.columnSelection = columnSelection;
663 public SequenceI[] getHiddenSequences()
665 if (hiddenSequences == null || hiddenSequences.isEmpty())
667 return new SequenceI[]
670 synchronized (hiddenSequences)
672 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
676 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
678 this.hiddenSequences = hiddenSequences;
681 public class JSONExportSettings
683 private boolean exportSequence;
685 private boolean exportSequenceFeatures;
687 private boolean exportAnnotations;
689 private boolean exportGroups;
691 private boolean exportJalviewSettings;
693 public boolean isExportSequence()
695 return exportSequence;
698 public void setExportSequence(boolean exportSequence)
700 this.exportSequence = exportSequence;
703 public boolean isExportSequenceFeatures()
705 return exportSequenceFeatures;
708 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
710 this.exportSequenceFeatures = exportSequenceFeatures;
713 public boolean isExportAnnotations()
715 return exportAnnotations;
718 public void setExportAnnotations(boolean exportAnnotations)
720 this.exportAnnotations = exportAnnotations;
723 public boolean isExportGroups()
728 public void setExportGroups(boolean exportGroups)
730 this.exportGroups = exportGroups;
733 public boolean isExportJalviewSettings()
735 return exportJalviewSettings;
738 public void setExportJalviewSettings(boolean exportJalviewSettings)
740 this.exportJalviewSettings = exportJalviewSettings;