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 java.awt.Color;
25 import java.io.IOException;
26 import java.util.ArrayList;
27 import java.util.Hashtable;
28 import java.util.Iterator;
29 import java.util.List;
30 import java.util.Vector;
32 import org.json.simple.JSONArray;
33 import org.json.simple.JSONObject;
34 import org.json.simple.parser.JSONParser;
36 import jalview.api.AlignViewportI;
37 import jalview.api.ComplexAlignFile;
38 import jalview.api.FeatureRenderer;
39 import jalview.api.FeaturesDisplayedI;
40 import jalview.datamodel.AlignmentAnnotation;
41 import jalview.datamodel.Annotation;
42 import jalview.datamodel.ColumnSelection;
43 import jalview.datamodel.HiddenSequences;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceFeature;
46 import jalview.datamodel.SequenceGroup;
47 import jalview.datamodel.SequenceI;
48 import jalview.json.binding.v1.AlignmentAnnotationPojo;
49 import jalview.json.binding.v1.AlignmentPojo;
50 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
51 import jalview.json.binding.v1.AnnotationPojo;
52 import jalview.json.binding.v1.SequenceFeaturesPojo;
53 import jalview.json.binding.v1.SequenceGrpPojo;
54 import jalview.json.binding.v1.SequencePojo;
55 import jalview.schemes.ColourSchemeI;
56 import jalview.schemes.ColourSchemeProperty;
58 public class JSONFile extends AlignFile implements ComplexAlignFile
60 private ColourSchemeI colourScheme;
62 private String version = "2.9";
64 private String webstartUrl = "www.jalview.org/services/launchApp";
66 private String application = "Jalview";
68 public static final String FILE_EXT = "json";
70 public static final String FILE_DESC = "JSON";
72 private String globalColorScheme;
74 private boolean showSeqFeatures;
76 private Hashtable<String, Sequence> seqMap;
78 private FeaturesDisplayedI displayedFeatures;
80 private FeatureRenderer fr;
82 private JSONExportSettings jsonExportSettings;
84 private List<int[]> hiddenColumns;
86 private ColumnSelection columnSelection;
88 private List<String> hiddenSeqRefs;
90 private ArrayList<SequenceI> hiddenSequences;
97 public JSONFile(FileParse source) throws IOException
102 public JSONFile(String inFile, String type) throws IOException
108 public void parse() throws IOException
110 StringBuilder jsonStringBuilder = new StringBuilder();
112 while ((currentLine = nextLine()) != null)
114 jsonStringBuilder.append(currentLine);
116 parse(jsonStringBuilder.toString());
121 public String print()
123 String jsonOutput = null;
126 if (getJsonExportSettings() == null)
128 jsonExportSettings = new JSONExportSettings();
129 jsonExportSettings.setExportAnnotations(true);
130 jsonExportSettings.setExportGroups(true);
131 jsonExportSettings.setExportJalviewSettings(true);
132 jsonExportSettings.setExportSequenceFeatures(true);
135 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
136 if (getViewport() != null)
138 globalColorScheme = ColourSchemeProperty
139 .getColourName(getViewport()
140 .getGlobalColourScheme());
141 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
142 showSeqFeatures = getViewport().isShowSequenceFeatures();
143 fr = getViewport().getFeatureRenderer();
147 for (SequenceI seq : seqs)
149 StringBuilder name = new StringBuilder();
150 name.append(seq.getName()).append("/").append(seq.getStart())
151 .append("-").append(seq.getEnd());
152 SequencePojo jsonSeqPojo = new SequencePojo();
153 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
154 jsonSeqPojo.setOrder(++count);
155 jsonSeqPojo.setEnd(seq.getEnd());
156 jsonSeqPojo.setStart(seq.getStart());
157 jsonSeqPojo.setName(name.toString());
158 jsonSeqPojo.setSeq(seq.getSequenceAsString());
159 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
162 if (jsonExportSettings.isExportJalviewSettings())
164 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
165 jsonAlignmentPojo.getAppSettings().put("application", application);
166 jsonAlignmentPojo.getAppSettings().put("version", version);
167 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
168 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
169 String.valueOf(showSeqFeatures));
171 String[] hiddenSections = exportHiddenSections();
172 if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
174 if (hiddenSections[0] != null)
176 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
177 String.valueOf(hiddenSections[0]));
179 if (hiddenSections[1] != null)
181 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
182 String.valueOf(hiddenSections[1]));
187 if (jsonExportSettings.isExportAnnotations())
190 .setAlignAnnotation(annotationToJsonPojo(annotations));
193 if (jsonExportSettings.isExportSequenceFeatures())
196 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
199 if (jsonExportSettings.isExportGroups() && seqGroups != null
200 && seqGroups.size() > 0)
202 for (SequenceGroup seqGrp : seqGroups)
204 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
205 seqGrpPojo.setGroupName(seqGrp.getName());
206 seqGrpPojo.setColourScheme(ColourSchemeProperty
207 .getColourName(seqGrp.cs));
208 seqGrpPojo.setColourText(seqGrp.getColourText());
209 seqGrpPojo.setDescription(seqGrp.getDescription());
210 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
211 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
212 seqGrpPojo.setEndRes(seqGrp.getEndRes());
213 seqGrpPojo.setStartRes(seqGrp.getStartRes());
214 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
215 for (SequenceI seq : seqGrp.getSequences())
217 seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
219 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
222 org.json.JSONObject generatedJSon = new org.json.JSONObject(
224 jsonOutput = generatedJSon.toString();
225 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
227 } catch (Exception e)
234 public String[] exportHiddenSections()
236 String[] hiddenSections = new String[2];
237 if (getViewport() == null)
242 // hidden column business
243 if (getViewport().hasHiddenColumns())
245 List<int[]> hiddenCols = getViewport().getColumnSelection()
247 StringBuilder hiddenColsBuilder = new StringBuilder();
248 for (int[] range : hiddenCols)
250 hiddenColsBuilder.append(";").append(range[0]).append("-")
254 hiddenColsBuilder.deleteCharAt(0);
255 hiddenSections[0] = hiddenColsBuilder.toString();
258 // hidden rows/seqs business
259 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
260 .getHiddenSequences();
261 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
263 return hiddenSections;
266 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
267 StringBuilder hiddenSeqsBuilder = new StringBuilder();
268 for (SequenceI hiddenSeq : hiddenSeqs)
270 if (hiddenSeq != null)
272 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
275 if (hiddenSeqsBuilder.length() > 0)
277 hiddenSeqsBuilder.deleteCharAt(0);
279 hiddenSections[1] = hiddenSeqsBuilder.toString();
281 return hiddenSections;
284 public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
285 List<SequenceI> seqs, FeatureRenderer fr)
287 FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
288 .getFeaturesDisplayed();
289 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
290 for (SequenceI seq : seqs)
292 SequenceI dataSetSequence = seq.getDatasetSequence();
293 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
294 : seq.getDatasetSequence().getSequenceFeatures();
296 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
298 if (seqFeatures == null)
303 for (SequenceFeature sf : seqFeatures)
305 if (displayedFeatures != null
306 && displayedFeatures.isVisible(sf.getType()))
308 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
309 String.valueOf(seq.hashCode()));
310 String featureColour = (fr == null) ? null : jalview.util.Format
312 .findFeatureColour(Color.white, seq,
313 seq.findIndex(sf.getBegin())));
314 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
315 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
316 jsonFeature.setType(sf.getType());
317 jsonFeature.setDescription(sf.getDescription());
318 jsonFeature.setLinks(sf.links);
319 jsonFeature.setOtherDetails(sf.otherDetails);
320 jsonFeature.setScore(sf.getScore());
321 jsonFeature.setFillColor(featureColour);
322 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
323 sequenceFeaturesPojo.add(jsonFeature);
327 return sequenceFeaturesPojo;
330 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
331 Vector<AlignmentAnnotation> annotations)
333 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
334 if (annotations == null)
336 return jsonAnnotations;
338 for (AlignmentAnnotation annot : annotations)
340 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
341 alignAnnotPojo.setDescription(annot.description);
342 alignAnnotPojo.setLabel(annot.label);
343 for (Annotation annotation : annot.annotations)
345 AnnotationPojo annotationPojo = new AnnotationPojo();
346 if (annotation != null)
348 annotationPojo.setDescription(annotation.description);
349 annotationPojo.setValue(annotation.value);
351 .setSecondaryStructure(annotation.secondaryStructure);
352 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
353 alignAnnotPojo.getAnnotations().add(annotationPojo);
357 alignAnnotPojo.getAnnotations().add(annotationPojo);
360 jsonAnnotations.add(alignAnnotPojo);
362 return jsonAnnotations;
365 @SuppressWarnings("unchecked")
366 public JSONFile parse(String jsonAlignmentString)
370 JSONParser jsonParser = new JSONParser();
371 JSONObject alignmentJsonObj = (JSONObject) jsonParser
372 .parse(jsonAlignmentString);
373 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
374 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
375 .get("alignAnnotation");
376 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
378 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
380 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
383 if (jvSettingsJsonObj != null)
385 String jsColourScheme = (String) jvSettingsJsonObj
386 .get("globalColorScheme");
387 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
388 "showSeqFeatures").toString());
389 setColourScheme(getJalviewColorScheme(jsColourScheme));
390 setShowSeqFeatures(showFeatures);
391 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
392 parseHiddenCols(jvSettingsJsonObj);
395 hiddenSequences = new ArrayList<SequenceI>();
396 seqMap = new Hashtable<String, Sequence>();
397 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
400 JSONObject sequence = sequenceIter.next();
401 String sequcenceString = sequence.get("seq").toString();
402 String sequenceName = sequence.get("name").toString();
403 String seqUniqueId = sequence.get("id").toString();
404 int start = Integer.valueOf(sequence.get("start").toString());
405 int end = Integer.valueOf(sequence.get("end").toString());
406 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
408 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
410 hiddenSequences.add(seq);
413 seqMap.put(seqUniqueId, seq);
415 parseFeatures(jsonSeqArray);
417 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
420 JSONObject seqGrpObj = seqGrpIter.next();
421 String grpName = seqGrpObj.get("groupName").toString();
422 String colourScheme = seqGrpObj.get("colourScheme").toString();
423 String description = (seqGrpObj.get("description") == null) ? null
424 : seqGrpObj.get("description").toString();
425 boolean displayBoxes = Boolean.valueOf(seqGrpObj
426 .get("displayBoxes").toString());
427 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
429 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
431 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
432 "showNonconserved").toString());
433 int startRes = Integer
434 .valueOf(seqGrpObj.get("startRes").toString());
435 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
436 JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
438 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
439 if (seqsHashArray.size() > 0)
441 Iterator<String> seqHashIter = seqsHashArray.iterator();
442 while (seqHashIter.hasNext())
444 String seqHash = seqHashIter.next();
445 Sequence sequence = seqMap.get(seqHash);
446 if (sequence != null)
448 grpSeqs.add(sequence);
452 ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
453 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
454 displayBoxes, displayText, colourText, startRes, endRes);
455 seqGrp.setShowNonconserved(showNonconserved);
456 seqGrp.setDescription(description);
457 this.seqGroups.add(seqGrp);
461 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
464 JSONObject alAnnot = alAnnotIter.next();
465 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
466 Annotation[] annotations = new Annotation[annotJsonArray.size()];
468 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
471 JSONObject annot = annotIter.next();
474 annotations[count] = null;
478 float val = annot.get("value") == null ? null : Float
479 .valueOf(annot.get("value").toString());
480 String desc = annot.get("description") == null ? null : annot
481 .get("description").toString();
483 char ss = annot.get("secondaryStructure") == null ? ' '
484 : annot.get("secondaryStructure").toString().charAt(0);
485 String displayChar = annot.get("displayCharacter").toString();
487 annotations[count] = new Annotation(displayChar, desc, ss, val);
492 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
493 .get("label").toString(), alAnnot.get("description")
494 .toString(), annotations);
495 this.annotations.add(alignAnnot);
498 } catch (Exception e)
505 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
507 hiddenSeqRefs = new ArrayList<String>();
508 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
509 if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
510 String[] seqRefs = hiddenSeqs.split(";");
511 for(String seqRef : seqRefs){
512 hiddenSeqRefs.add(seqRef);
517 public void parseHiddenCols(JSONObject jvSettingsJson)
519 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
520 if(hiddenCols != null && !hiddenCols.isEmpty()){
521 columnSelection = new ColumnSelection();
522 String[] rangeStrings = hiddenCols.split(";");
523 for(String rangeString : rangeStrings){
524 String[] range = rangeString.split("-");
525 columnSelection.hideColumns(Integer.valueOf(range[0]),
526 Integer.valueOf(range[1]));
531 @SuppressWarnings("unchecked")
532 private void parseFeatures(JSONArray jsonSeqFeatures)
534 if (jsonSeqFeatures != null)
536 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
539 JSONObject jsonFeature = seqFeatureItr.next();
540 Long begin = (Long) jsonFeature.get("xStart");
541 Long end = (Long) jsonFeature.get("xEnd");
542 String type = (String) jsonFeature.get("type");
543 String featureGrp = (String) jsonFeature.get("featureGroup");
544 String descripiton = (String) jsonFeature.get("description");
545 String seqRef = (String) jsonFeature.get("sequenceRef");
546 Float score = Float.valueOf(jsonFeature.get("score").toString());
548 Sequence seq = seqMap.get(seqRef);
549 SequenceFeature sequenceFeature = new SequenceFeature();
550 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
551 if (linksJsonArray != null && linksJsonArray.size() > 0)
553 Iterator<String> linkList = linksJsonArray.iterator();
554 while (linkList.hasNext())
556 String link = linkList.next();
557 sequenceFeature.addLink(link);
560 sequenceFeature.setFeatureGroup(featureGrp);
561 sequenceFeature.setScore(score);
562 sequenceFeature.setDescription(descripiton);
563 sequenceFeature.setType(type);
564 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
565 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
566 seq.addSequenceFeature(sequenceFeature);
571 public static ColourSchemeI getJalviewColorScheme(
572 String bioJsColourSchemeName)
574 ColourSchemeI jalviewColor = null;
575 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
578 if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
580 jalviewColor = cs.getJvColourScheme();
587 public String getGlobalColorScheme()
589 return globalColorScheme;
592 public void setGlobalColorScheme(String globalColorScheme)
594 this.globalColorScheme = globalColorScheme;
597 public ColourSchemeI getColourScheme()
602 public void setColourScheme(ColourSchemeI colourScheme)
604 this.colourScheme = colourScheme;
607 public FeaturesDisplayedI getDisplayedFeatures()
609 return displayedFeatures;
612 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
614 this.displayedFeatures = displayedFeatures;
617 public JSONExportSettings getJsonExportSettings()
619 return jsonExportSettings;
622 public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
624 this.jsonExportSettings = jsonExportSettings;
628 public static String getJSONData(AlignViewportI av)
630 JSONFile jsonFile = new JSONFile();
631 jsonFile.setViewport(av);
632 jsonFile.seqGroups = av.getAlignment().getGroups();
633 jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
635 for (SequenceI seq : av.getAlignment().getSequences())
637 jsonFile.seqs.add(seq);
640 // Add non auto calculated annotation to AlignFile
641 for (AlignmentAnnotation annot : av.getAlignment()
642 .getAlignmentAnnotation())
644 if (annot != null && !annot.autoCalculated)
646 if (annot.label.equals("PDB.CATempFactor"))
650 jsonFile.annotations.add(annot);
653 String jsonString = jsonFile.print();
657 public boolean isShowSeqFeatures()
659 return showSeqFeatures;
662 public void setShowSeqFeatures(boolean showSeqFeatures)
664 this.showSeqFeatures = showSeqFeatures;
667 public Vector<AlignmentAnnotation> getAnnotations()
672 public List<int[]> getHiddenColumns()
674 return hiddenColumns;
677 public ColumnSelection getColumnSelection()
679 return columnSelection;
682 public void setColumnSelection(ColumnSelection columnSelection)
684 this.columnSelection = columnSelection;
687 public SequenceI[] getHiddenSequences()
689 if (hiddenSequences == null || hiddenSequences.isEmpty())
691 return new SequenceI[]
694 synchronized (hiddenSequences)
696 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
700 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
702 this.hiddenSequences = hiddenSequences;
705 public class JSONExportSettings
707 private boolean exportSequence;
709 private boolean exportSequenceFeatures;
711 private boolean exportAnnotations;
713 private boolean exportGroups;
715 private boolean exportJalviewSettings;
717 public boolean isExportSequence()
719 return exportSequence;
722 public void setExportSequence(boolean exportSequence)
724 this.exportSequence = exportSequence;
727 public boolean isExportSequenceFeatures()
729 return exportSequenceFeatures;
732 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
734 this.exportSequenceFeatures = exportSequenceFeatures;
737 public boolean isExportAnnotations()
739 return exportAnnotations;
742 public void setExportAnnotations(boolean exportAnnotations)
744 this.exportAnnotations = exportAnnotations;
747 public boolean isExportGroups()
752 public void setExportGroups(boolean exportGroups)
754 this.exportGroups = exportGroups;
757 public boolean isExportJalviewSettings()
759 return exportJalviewSettings;
762 public void setExportJalviewSettings(boolean exportJalviewSettings)
764 this.exportJalviewSettings = exportJalviewSettings;