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();
119 if (getViewport() != null)
121 configureFromViewport();
126 for (SequenceI seq : seqs)
128 StringBuilder name = new StringBuilder();
129 name.append(seq.getName()).append("/").append(seq.getStart())
130 .append("-").append(seq.getEnd());
131 SequencePojo jsonSeqPojo = new SequencePojo();
132 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
133 jsonSeqPojo.setOrder(++count);
134 jsonSeqPojo.setEnd(seq.getEnd());
135 jsonSeqPojo.setStart(seq.getStart());
136 jsonSeqPojo.setName(name.toString());
137 jsonSeqPojo.setSeq(seq.getSequenceAsString());
138 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
141 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
142 jsonAlignmentPojo.getAppSettings().put("application", application);
143 jsonAlignmentPojo.getAppSettings().put("version", version);
144 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
145 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
146 String.valueOf(showSeqFeatures));
148 String[] hiddenSections = getHiddenSections();
149 if (hiddenSections != null)
151 if (hiddenSections[0] != null
152 && getExportSettings()
153 .isExportHiddenColumns())
155 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
156 String.valueOf(hiddenSections[0]));
158 if (hiddenSections[1] != null
159 && getExportSettings()
160 .isExportHiddenSequences())
162 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
163 String.valueOf(hiddenSections[1]));
167 if (getExportSettings().isExportAnnotations())
170 .setAlignAnnotation(annotationToJsonPojo(annotations));
173 if (getExportSettings().isExportFeatures())
176 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
179 if (getExportSettings().isExportGroups()
181 && seqGroups.size() > 0)
183 for (SequenceGroup seqGrp : seqGroups)
185 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
186 seqGrpPojo.setGroupName(seqGrp.getName());
187 seqGrpPojo.setColourScheme(ColourSchemeProperty
188 .getColourName(seqGrp.cs));
189 seqGrpPojo.setColourText(seqGrp.getColourText());
190 seqGrpPojo.setDescription(seqGrp.getDescription());
191 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
192 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
193 seqGrpPojo.setEndRes(seqGrp.getEndRes());
194 seqGrpPojo.setStartRes(seqGrp.getStartRes());
195 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
196 for (SequenceI seq : seqGrp.getSequences())
198 seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
200 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
203 org.json.JSONObject generatedJSon = new org.json.JSONObject(
205 jsonOutput = generatedJSon.toString();
206 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
208 } catch (Exception e)
215 public String[] getHiddenSections()
217 String[] hiddenSections = new String[2];
218 if (getViewport() == null)
223 // hidden column business
224 if (getViewport().hasHiddenColumns())
226 List<int[]> hiddenCols = getViewport().getColumnSelection()
228 StringBuilder hiddenColsBuilder = new StringBuilder();
229 for (int[] range : hiddenCols)
231 hiddenColsBuilder.append(";").append(range[0]).append("-")
235 hiddenColsBuilder.deleteCharAt(0);
236 hiddenSections[0] = hiddenColsBuilder.toString();
239 // hidden rows/seqs business
240 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
241 .getHiddenSequences();
242 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
244 return hiddenSections;
247 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
248 StringBuilder hiddenSeqsBuilder = new StringBuilder();
249 for (SequenceI hiddenSeq : hiddenSeqs)
251 if (hiddenSeq != null)
253 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
256 if (hiddenSeqsBuilder.length() > 0)
258 hiddenSeqsBuilder.deleteCharAt(0);
260 hiddenSections[1] = hiddenSeqsBuilder.toString();
262 return hiddenSections;
265 public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
266 List<SequenceI> seqs, FeatureRenderer fr)
268 FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
269 .getFeaturesDisplayed();
270 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
271 for (SequenceI seq : seqs)
273 SequenceI dataSetSequence = seq.getDatasetSequence();
274 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
275 : seq.getDatasetSequence().getSequenceFeatures();
277 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
279 if (seqFeatures == null)
284 for (SequenceFeature sf : seqFeatures)
286 if (displayedFeatures != null
287 && displayedFeatures.isVisible(sf.getType()))
289 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
290 String.valueOf(seq.hashCode()));
291 String featureColour = (fr == null) ? null : jalview.util.Format
293 .findFeatureColour(Color.white, seq,
294 seq.findIndex(sf.getBegin())));
295 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
296 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
297 jsonFeature.setType(sf.getType());
298 jsonFeature.setDescription(sf.getDescription());
299 jsonFeature.setLinks(sf.links);
300 jsonFeature.setOtherDetails(sf.otherDetails);
301 jsonFeature.setScore(sf.getScore());
302 jsonFeature.setFillColor(featureColour);
303 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
304 sequenceFeaturesPojo.add(jsonFeature);
308 return sequenceFeaturesPojo;
311 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
312 Vector<AlignmentAnnotation> annotations)
314 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
315 if (annotations == null)
317 return jsonAnnotations;
319 for (AlignmentAnnotation annot : annotations)
321 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
322 alignAnnotPojo.setDescription(annot.description);
323 alignAnnotPojo.setLabel(annot.label);
324 for (Annotation annotation : annot.annotations)
326 AnnotationPojo annotationPojo = new AnnotationPojo();
327 if (annotation != null)
329 annotationPojo.setDescription(annotation.description);
330 annotationPojo.setValue(annotation.value);
332 .setSecondaryStructure(annotation.secondaryStructure);
333 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
334 alignAnnotPojo.getAnnotations().add(annotationPojo);
338 alignAnnotPojo.getAnnotations().add(annotationPojo);
341 jsonAnnotations.add(alignAnnotPojo);
343 return jsonAnnotations;
346 @SuppressWarnings("unchecked")
347 public JSONFile parse(Reader jsonAlignmentString)
351 JSONParser jsonParser = new JSONParser();
352 JSONObject alignmentJsonObj = (JSONObject) jsonParser
353 .parse(jsonAlignmentString);
354 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
355 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
356 .get("alignAnnotation");
357 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
359 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
361 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
364 if (jvSettingsJsonObj != null)
366 String jsColourScheme = (String) jvSettingsJsonObj
367 .get("globalColorScheme");
368 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
369 "showSeqFeatures").toString());
370 setColourScheme(getJalviewColorScheme(jsColourScheme));
371 setShowSeqFeatures(showFeatures);
372 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
373 parseHiddenCols(jvSettingsJsonObj);
376 hiddenSequences = new ArrayList<SequenceI>();
377 seqMap = new Hashtable<String, Sequence>();
378 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
381 JSONObject sequence = sequenceIter.next();
382 String sequcenceString = sequence.get("seq").toString();
383 String sequenceName = sequence.get("name").toString();
384 String seqUniqueId = sequence.get("id").toString();
385 int start = Integer.valueOf(sequence.get("start").toString());
386 int end = Integer.valueOf(sequence.get("end").toString());
387 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
389 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
391 hiddenSequences.add(seq);
394 seqMap.put(seqUniqueId, seq);
396 parseFeatures(jsonSeqArray);
398 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
401 JSONObject seqGrpObj = seqGrpIter.next();
402 String grpName = seqGrpObj.get("groupName").toString();
403 String colourScheme = seqGrpObj.get("colourScheme").toString();
404 String description = (seqGrpObj.get("description") == null) ? null
405 : seqGrpObj.get("description").toString();
406 boolean displayBoxes = Boolean.valueOf(seqGrpObj
407 .get("displayBoxes").toString());
408 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
410 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
412 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
413 "showNonconserved").toString());
414 int startRes = Integer
415 .valueOf(seqGrpObj.get("startRes").toString());
416 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
417 JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
419 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
420 if (seqsHashArray.size() > 0)
422 Iterator<String> seqHashIter = seqsHashArray.iterator();
423 while (seqHashIter.hasNext())
425 String seqHash = seqHashIter.next();
426 Sequence sequence = seqMap.get(seqHash);
427 if (sequence != null)
429 grpSeqs.add(sequence);
433 ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
434 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
435 displayBoxes, displayText, colourText, startRes, endRes);
436 seqGrp.setShowNonconserved(showNonconserved);
437 seqGrp.setDescription(description);
438 this.seqGroups.add(seqGrp);
442 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
445 JSONObject alAnnot = alAnnotIter.next();
446 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
447 Annotation[] annotations = new Annotation[annotJsonArray.size()];
449 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
452 JSONObject annot = annotIter.next();
455 annotations[count] = null;
459 float val = annot.get("value") == null ? null : Float
460 .valueOf(annot.get("value").toString());
461 String desc = annot.get("description") == null ? null : annot
462 .get("description").toString();
464 char ss = annot.get("secondaryStructure") == null ? ' '
465 : annot.get("secondaryStructure").toString().charAt(0);
466 String displayChar = annot.get("displayCharacter").toString();
468 annotations[count] = new Annotation(displayChar, desc, ss, val);
473 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
474 .get("label").toString(), alAnnot.get("description")
475 .toString(), annotations);
476 this.annotations.add(alignAnnot);
479 } catch (Exception e)
486 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
488 hiddenSeqRefs = new ArrayList<String>();
489 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
490 if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
491 String[] seqRefs = hiddenSeqs.split(";");
492 for(String seqRef : seqRefs){
493 hiddenSeqRefs.add(seqRef);
498 public void parseHiddenCols(JSONObject jvSettingsJson)
500 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
501 if(hiddenCols != null && !hiddenCols.isEmpty()){
502 columnSelection = new ColumnSelection();
503 String[] rangeStrings = hiddenCols.split(";");
504 for(String rangeString : rangeStrings){
505 String[] range = rangeString.split("-");
506 columnSelection.hideColumns(Integer.valueOf(range[0]),
507 Integer.valueOf(range[1]));
512 @SuppressWarnings("unchecked")
513 private void parseFeatures(JSONArray jsonSeqFeatures)
515 if (jsonSeqFeatures != null)
517 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
520 JSONObject jsonFeature = seqFeatureItr.next();
521 Long begin = (Long) jsonFeature.get("xStart");
522 Long end = (Long) jsonFeature.get("xEnd");
523 String type = (String) jsonFeature.get("type");
524 String featureGrp = (String) jsonFeature.get("featureGroup");
525 String descripiton = (String) jsonFeature.get("description");
526 String seqRef = (String) jsonFeature.get("sequenceRef");
527 Float score = Float.valueOf(jsonFeature.get("score").toString());
529 Sequence seq = seqMap.get(seqRef);
530 SequenceFeature sequenceFeature = new SequenceFeature();
531 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
532 if (linksJsonArray != null && linksJsonArray.size() > 0)
534 Iterator<String> linkList = linksJsonArray.iterator();
535 while (linkList.hasNext())
537 String link = linkList.next();
538 sequenceFeature.addLink(link);
541 sequenceFeature.setFeatureGroup(featureGrp);
542 sequenceFeature.setScore(score);
543 sequenceFeature.setDescription(descripiton);
544 sequenceFeature.setType(type);
545 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
546 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
547 seq.addSequenceFeature(sequenceFeature);
552 public static ColourSchemeI getJalviewColorScheme(
553 String bioJsColourSchemeName)
555 ColourSchemeI jalviewColor = null;
556 for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
559 if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
561 jalviewColor = cs.getJvColourScheme();
568 public String getGlobalColorScheme()
570 return globalColorScheme;
573 public void setGlobalColorScheme(String globalColorScheme)
575 this.globalColorScheme = globalColorScheme;
578 public ColourSchemeI getColourScheme()
583 public void setColourScheme(ColourSchemeI colourScheme)
585 this.colourScheme = colourScheme;
588 public FeaturesDisplayedI getDisplayedFeatures()
590 return displayedFeatures;
593 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
595 this.displayedFeatures = displayedFeatures;
598 public void configureForView(AlignmentViewPanel avpanel)
601 setViewport(avpanel.getAlignViewport());
602 seqGroups = avpanel.getAlignment().getGroups();
603 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
604 fr = avpanel.cloneFeatureRenderer();
606 for (SequenceI seq : getViewport().getAlignment().getSequences())
611 // Add non auto calculated annotation to AlignFile
612 for (AlignmentAnnotation annot : getViewport().getAlignment()
613 .getAlignmentAnnotation())
615 if (annot != null && !annot.autoCalculated)
617 if (annot.label.equals("PDB.CATempFactor"))
621 annotations.add(annot);
626 public void configureFromViewport()
628 if (getViewport() == null)
632 globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
633 .getGlobalColourScheme());
634 setDisplayedFeatures(getViewport().getFeaturesDisplayed());
635 showSeqFeatures = getViewport().isShowSequenceFeatures();
638 public static String getJSONData(AlignmentViewPanel av)
640 JSONFile jsonFile = new JSONFile();
641 jsonFile.configureForView(av);
642 String jsonString = jsonFile.print();
646 public boolean isShowSeqFeatures()
648 return showSeqFeatures;
651 public void setShowSeqFeatures(boolean showSeqFeatures)
653 this.showSeqFeatures = showSeqFeatures;
656 public Vector<AlignmentAnnotation> getAnnotations()
661 public List<int[]> getHiddenColumns()
663 return hiddenColumns;
666 public ColumnSelection getColumnSelection()
668 return columnSelection;
671 public void setColumnSelection(ColumnSelection columnSelection)
673 this.columnSelection = columnSelection;
676 public SequenceI[] getHiddenSequences()
678 if (hiddenSequences == null || hiddenSequences.isEmpty())
680 return new SequenceI[]
683 synchronized (hiddenSequences)
685 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
689 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
691 this.hiddenSequences = hiddenSequences;
694 public class JSONExportSettings
696 private boolean exportSequence;
698 private boolean exportSequenceFeatures;
700 private boolean exportAnnotations;
702 private boolean exportGroups;
704 private boolean exportJalviewSettings;
706 public boolean isExportSequence()
708 return exportSequence;
711 public void setExportSequence(boolean exportSequence)
713 this.exportSequence = exportSequence;
716 public boolean isExportSequenceFeatures()
718 return exportSequenceFeatures;
721 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
723 this.exportSequenceFeatures = exportSequenceFeatures;
726 public boolean isExportAnnotations()
728 return exportAnnotations;
731 public void setExportAnnotations(boolean exportAnnotations)
733 this.exportAnnotations = exportAnnotations;
736 public boolean isExportGroups()
741 public void setExportGroups(boolean exportGroups)
743 this.exportGroups = exportGroups;
746 public boolean isExportJalviewSettings()
748 return exportJalviewSettings;
751 public void setExportJalviewSettings(boolean exportJalviewSettings)
753 this.exportJalviewSettings = exportJalviewSettings;