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.AlignmentViewPanel;
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
113 public String print()
115 String jsonOutput = null;
118 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
121 for (SequenceI seq : seqs)
123 StringBuilder name = new StringBuilder();
124 name.append(seq.getName()).append("/").append(seq.getStart())
125 .append("-").append(seq.getEnd());
126 SequencePojo jsonSeqPojo = new SequencePojo();
127 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
128 jsonSeqPojo.setOrder(++count);
129 jsonSeqPojo.setEnd(seq.getEnd());
130 jsonSeqPojo.setStart(seq.getStart());
131 jsonSeqPojo.setName(name.toString());
132 jsonSeqPojo.setSeq(seq.getSequenceAsString());
133 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
136 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
137 jsonAlignmentPojo.getAppSettings().put("application", application);
138 jsonAlignmentPojo.getAppSettings().put("version", version);
139 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
140 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
141 String.valueOf(showSeqFeatures));
143 String[] hiddenSections = getHiddenSections();
144 if (hiddenSections != null)
146 if (hiddenSections[0] != null
147 && getExportSettings()
148 .isExportHiddenColumns())
150 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
151 String.valueOf(hiddenSections[0]));
153 if (hiddenSections[1] != null
154 && getExportSettings()
155 .isExportHiddenSequences())
157 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
158 String.valueOf(hiddenSections[1]));
162 if (getExportSettings().isExportAnnotations())
165 .setAlignAnnotation(annotationToJsonPojo(annotations));
168 if (getExportSettings().isExportFeatures())
171 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
174 if (getExportSettings().isExportGroups()
176 && seqGroups.size() > 0)
178 for (SequenceGroup seqGrp : seqGroups)
180 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
181 seqGrpPojo.setGroupName(seqGrp.getName());
182 seqGrpPojo.setColourScheme(ColourSchemeProperty
183 .getColourName(seqGrp.cs));
184 seqGrpPojo.setColourText(seqGrp.getColourText());
185 seqGrpPojo.setDescription(seqGrp.getDescription());
186 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
187 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
188 seqGrpPojo.setEndRes(seqGrp.getEndRes());
189 seqGrpPojo.setStartRes(seqGrp.getStartRes());
190 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
191 for (SequenceI seq : seqGrp.getSequences())
193 seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
195 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
198 org.json.JSONObject generatedJSon = new org.json.JSONObject(
200 jsonOutput = generatedJSon.toString();
201 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
203 } catch (Exception e)
210 public String[] getHiddenSections()
212 String[] hiddenSections = new String[2];
213 if (getViewport() == null)
218 // hidden column business
219 if (getViewport().hasHiddenColumns())
221 List<int[]> hiddenCols = getViewport().getColumnSelection()
223 StringBuilder hiddenColsBuilder = new StringBuilder();
224 for (int[] range : hiddenCols)
226 hiddenColsBuilder.append(";").append(range[0]).append("-")
230 hiddenColsBuilder.deleteCharAt(0);
231 hiddenSections[0] = hiddenColsBuilder.toString();
234 // hidden rows/seqs business
235 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
236 .getHiddenSequences();
237 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
239 return hiddenSections;
242 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
243 StringBuilder hiddenSeqsBuilder = new StringBuilder();
244 for (SequenceI hiddenSeq : hiddenSeqs)
246 if (hiddenSeq != null)
248 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
251 if (hiddenSeqsBuilder.length() > 0)
253 hiddenSeqsBuilder.deleteCharAt(0);
255 hiddenSections[1] = hiddenSeqsBuilder.toString();
257 return hiddenSections;
260 public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
261 List<SequenceI> seqs, FeatureRenderer fr)
263 FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
264 .getFeaturesDisplayed();
265 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
266 for (SequenceI seq : seqs)
268 SequenceI dataSetSequence = seq.getDatasetSequence();
269 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
270 : seq.getDatasetSequence().getSequenceFeatures();
272 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
274 if (seqFeatures == null)
279 for (SequenceFeature sf : seqFeatures)
281 if (displayedFeatures != null
282 && displayedFeatures.isVisible(sf.getType()))
284 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
285 String.valueOf(seq.hashCode()));
286 String featureColour = (fr == null) ? null : jalview.util.Format
288 .findFeatureColour(Color.white, seq,
289 seq.findIndex(sf.getBegin())));
290 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
291 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
292 jsonFeature.setType(sf.getType());
293 jsonFeature.setDescription(sf.getDescription());
294 jsonFeature.setLinks(sf.links);
295 jsonFeature.setOtherDetails(sf.otherDetails);
296 jsonFeature.setScore(sf.getScore());
297 jsonFeature.setFillColor(featureColour);
298 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
299 sequenceFeaturesPojo.add(jsonFeature);
303 return sequenceFeaturesPojo;
306 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
307 Vector<AlignmentAnnotation> annotations)
309 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
310 if (annotations == null)
312 return jsonAnnotations;
314 for (AlignmentAnnotation annot : annotations)
316 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
317 alignAnnotPojo.setDescription(annot.description);
318 alignAnnotPojo.setLabel(annot.label);
319 for (Annotation annotation : annot.annotations)
321 AnnotationPojo annotationPojo = new AnnotationPojo();
322 if (annotation != null)
324 annotationPojo.setDescription(annotation.description);
325 annotationPojo.setValue(annotation.value);
327 .setSecondaryStructure(annotation.secondaryStructure);
328 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
329 alignAnnotPojo.getAnnotations().add(annotationPojo);
333 alignAnnotPojo.getAnnotations().add(annotationPojo);
336 jsonAnnotations.add(alignAnnotPojo);
338 return jsonAnnotations;
341 @SuppressWarnings("unchecked")
342 public JSONFile parse(Reader jsonAlignmentString)
346 JSONParser jsonParser = new JSONParser();
347 JSONObject alignmentJsonObj = (JSONObject) jsonParser
348 .parse(jsonAlignmentString);
349 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
350 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
351 .get("alignAnnotation");
352 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
354 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
356 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
359 if (jvSettingsJsonObj != null)
361 String jsColourScheme = (String) jvSettingsJsonObj
362 .get("globalColorScheme");
363 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
364 "showSeqFeatures").toString());
365 setColourScheme(getJalviewColorScheme(jsColourScheme));
366 setShowSeqFeatures(showFeatures);
367 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
368 parseHiddenCols(jvSettingsJsonObj);
371 hiddenSequences = new ArrayList<SequenceI>();
372 seqMap = new Hashtable<String, Sequence>();
373 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
376 JSONObject sequence = sequenceIter.next();
377 String sequcenceString = sequence.get("seq").toString();
378 String sequenceName = sequence.get("name").toString();
379 String seqUniqueId = sequence.get("id").toString();
380 int start = Integer.valueOf(sequence.get("start").toString());
381 int end = Integer.valueOf(sequence.get("end").toString());
382 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
384 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
386 hiddenSequences.add(seq);
389 seqMap.put(seqUniqueId, seq);
391 parseFeatures(jsonSeqArray);
393 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
396 JSONObject seqGrpObj = seqGrpIter.next();
397 String grpName = seqGrpObj.get("groupName").toString();
398 String colourScheme = seqGrpObj.get("colourScheme").toString();
399 String description = (seqGrpObj.get("description") == null) ? null
400 : seqGrpObj.get("description").toString();
401 boolean displayBoxes = Boolean.valueOf(seqGrpObj
402 .get("displayBoxes").toString());
403 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
405 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
407 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
408 "showNonconserved").toString());
409 int startRes = Integer
410 .valueOf(seqGrpObj.get("startRes").toString());
411 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
412 JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
414 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
415 if (seqsHashArray.size() > 0)
417 Iterator<String> seqHashIter = seqsHashArray.iterator();
418 while (seqHashIter.hasNext())
420 String seqHash = seqHashIter.next();
421 Sequence sequence = seqMap.get(seqHash);
422 if (sequence != null)
424 grpSeqs.add(sequence);
428 ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
429 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
430 displayBoxes, displayText, colourText, startRes, endRes);
431 seqGrp.setShowNonconserved(showNonconserved);
432 seqGrp.setDescription(description);
433 this.seqGroups.add(seqGrp);
437 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
440 JSONObject alAnnot = alAnnotIter.next();
441 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
442 Annotation[] annotations = new Annotation[annotJsonArray.size()];
444 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
447 JSONObject annot = annotIter.next();
450 annotations[count] = null;
454 float val = annot.get("value") == null ? null : Float
455 .valueOf(annot.get("value").toString());
456 String desc = annot.get("description") == null ? null : annot
457 .get("description").toString();
459 char ss = annot.get("secondaryStructure") == null ? ' '
460 : annot.get("secondaryStructure").toString().charAt(0);
461 String displayChar = annot.get("displayCharacter").toString();
463 annotations[count] = new Annotation(displayChar, desc, ss, val);
468 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
469 .get("label").toString(), alAnnot.get("description")
470 .toString(), annotations);
471 this.annotations.add(alignAnnot);
474 } catch (Exception e)
481 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
483 hiddenSeqRefs = new ArrayList<String>();
484 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
485 if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
486 String[] seqRefs = hiddenSeqs.split(";");
487 for(String seqRef : seqRefs){
488 hiddenSeqRefs.add(seqRef);
493 public void parseHiddenCols(JSONObject jvSettingsJson)
495 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
496 if(hiddenCols != null && !hiddenCols.isEmpty()){
497 columnSelection = new ColumnSelection();
498 String[] rangeStrings = hiddenCols.split(";");
499 for(String rangeString : rangeStrings){
500 String[] range = rangeString.split("-");
501 columnSelection.hideColumns(Integer.valueOf(range[0]),
502 Integer.valueOf(range[1]));
507 @SuppressWarnings("unchecked")
508 private void parseFeatures(JSONArray jsonSeqFeatures)
510 if (jsonSeqFeatures != null)
512 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
515 JSONObject jsonFeature = seqFeatureItr.next();
516 Long begin = (Long) jsonFeature.get("xStart");
517 Long end = (Long) jsonFeature.get("xEnd");
518 String type = (String) jsonFeature.get("type");
519 String featureGrp = (String) jsonFeature.get("featureGroup");
520 String descripiton = (String) jsonFeature.get("description");
521 String seqRef = (String) jsonFeature.get("sequenceRef");
522 Float score = Float.valueOf(jsonFeature.get("score").toString());
524 Sequence seq = seqMap.get(seqRef);
525 SequenceFeature sequenceFeature = new SequenceFeature();
526 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
527 if (linksJsonArray != null && linksJsonArray.size() > 0)
529 Iterator<String> linkList = linksJsonArray.iterator();
530 while (linkList.hasNext())
532 String link = linkList.next();
533 sequenceFeature.addLink(link);
536 sequenceFeature.setFeatureGroup(featureGrp);
537 sequenceFeature.setScore(score);
538 sequenceFeature.setDescription(descripiton);
539 sequenceFeature.setType(type);
540 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
541 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
542 seq.addSequenceFeature(sequenceFeature);
547 public static ColourSchemeI getJalviewColorScheme(
548 String bioJsColourSchemeName)
550 ColourSchemeI jalviewColor = null;
551 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
554 if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
556 jalviewColor = cs.getJvColourScheme();
563 public String getGlobalColorScheme()
565 return globalColorScheme;
568 public void setGlobalColorScheme(String globalColorScheme)
570 this.globalColorScheme = globalColorScheme;
573 public ColourSchemeI getColourScheme()
578 public void setColourScheme(ColourSchemeI colourScheme)
580 this.colourScheme = colourScheme;
583 public FeaturesDisplayedI getDisplayedFeatures()
585 return displayedFeatures;
588 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
590 this.displayedFeatures = displayedFeatures;
594 public void configureForView(AlignmentViewPanel avpanel)
596 super.configureForView(avpanel);
599 setViewport(avpanel.getAlignViewport());
600 seqGroups = avpanel.getAlignment().getGroups();
601 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
602 fr = avpanel.cloneFeatureRenderer();
604 for (SequenceI seq : getViewport().getAlignment().getSequences())
609 // Add non auto calculated annotation to AlignFile
610 for (AlignmentAnnotation annot : getViewport().getAlignment()
611 .getAlignmentAnnotation())
613 if (annot != null && !annot.autoCalculated)
615 if (annot.label.equals("PDB.CATempFactor"))
619 annotations.add(annot);
623 globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
624 .getGlobalColourScheme());
625 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
626 showSeqFeatures = getViewport().isShowSequenceFeatures();
631 public static String getJSONData(AlignmentViewPanel av)
633 JSONFile jsonFile = new JSONFile();
634 jsonFile.configureForView(av);
635 String jsonString = jsonFile.print();
639 public boolean isShowSeqFeatures()
641 return showSeqFeatures;
644 public void setShowSeqFeatures(boolean showSeqFeatures)
646 this.showSeqFeatures = showSeqFeatures;
649 public Vector<AlignmentAnnotation> getAnnotations()
654 public List<int[]> getHiddenColumns()
656 return hiddenColumns;
659 public ColumnSelection getColumnSelection()
661 return columnSelection;
664 public void setColumnSelection(ColumnSelection columnSelection)
666 this.columnSelection = columnSelection;
669 public SequenceI[] getHiddenSequences()
671 if (hiddenSequences == null || hiddenSequences.isEmpty())
673 return new SequenceI[]
676 synchronized (hiddenSequences)
678 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
682 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
684 this.hiddenSequences = hiddenSequences;
687 public class JSONExportSettings
689 private boolean exportSequence;
691 private boolean exportSequenceFeatures;
693 private boolean exportAnnotations;
695 private boolean exportGroups;
697 private boolean exportJalviewSettings;
699 public boolean isExportSequence()
701 return exportSequence;
704 public void setExportSequence(boolean exportSequence)
706 this.exportSequence = exportSequence;
709 public boolean isExportSequenceFeatures()
711 return exportSequenceFeatures;
714 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
716 this.exportSequenceFeatures = exportSequenceFeatures;
719 public boolean isExportAnnotations()
721 return exportAnnotations;
724 public void setExportAnnotations(boolean exportAnnotations)
726 this.exportAnnotations = exportAnnotations;
729 public boolean isExportGroups()
734 public void setExportGroups(boolean exportGroups)
736 this.exportGroups = exportGroups;
739 public boolean isExportJalviewSettings()
741 return exportJalviewSettings;
744 public void setExportJalviewSettings(boolean exportJalviewSettings)
746 this.exportJalviewSettings = exportJalviewSettings;