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.bin.BuildDetails;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Annotation;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.HiddenSequences;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
42 import jalview.json.binding.biojson.v1.AlignmentPojo;
43 import jalview.json.binding.biojson.v1.AnnotationPojo;
44 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
45 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
46 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
47 import jalview.json.binding.biojson.v1.SequencePojo;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.schemes.ColourSchemeProperty;
50 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
52 import java.awt.Color;
53 import java.io.IOException;
54 import java.io.Reader;
55 import java.util.ArrayList;
56 import java.util.Hashtable;
57 import java.util.Iterator;
58 import java.util.List;
59 import java.util.Vector;
61 import org.json.simple.JSONArray;
62 import org.json.simple.JSONObject;
63 import org.json.simple.parser.JSONParser;
65 public class JSONFile extends AlignFile implements ComplexAlignFile
67 private ColourSchemeI colourScheme;
69 private static String version = new BuildDetails().getVersion();
71 private String webstartUrl = "http://www.jalview.org/services/launchApp";
73 private String application = "Jalview";
75 public static final String FILE_EXT = "json";
77 public static final String FILE_DESC = "JSON";
79 private String globalColorScheme;
81 private boolean showSeqFeatures;
83 private Hashtable<String, Sequence> seqMap;
85 private FeaturesDisplayedI displayedFeatures;
87 private FeatureRenderer fr;
89 private List<int[]> hiddenColumns;
91 private ColumnSelection columnSelection;
93 private List<String> hiddenSeqRefs;
95 private ArrayList<SequenceI> hiddenSequences;
102 public JSONFile(FileParse source) throws IOException
107 public JSONFile(String inFile, String type) throws IOException
113 public void parse() throws IOException
120 public String print()
122 String jsonOutput = null;
125 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
126 AlignExportSettingI exportSettings = getExportSettings();
128 // if no export settings were supplied use the following with all values
129 // defaulting to true
130 if (exportSettings == null)
132 exportSettings = new AlignExportSettingI()
135 public boolean isExportHiddenSequences()
141 public boolean isExportHiddenColumns()
147 public boolean isExportGroups()
153 public boolean isExportFeatures()
159 public boolean isExportAnnotations()
165 public boolean isCancelled()
173 for (SequenceI seq : seqs)
175 StringBuilder name = new StringBuilder();
176 name.append(seq.getName()).append("/").append(seq.getStart())
177 .append("-").append(seq.getEnd());
178 SequencePojo jsonSeqPojo = new SequencePojo();
179 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
180 jsonSeqPojo.setOrder(++count);
181 jsonSeqPojo.setEnd(seq.getEnd());
182 jsonSeqPojo.setStart(seq.getStart());
183 jsonSeqPojo.setName(name.toString());
184 jsonSeqPojo.setSeq(seq.getSequenceAsString());
185 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
187 jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
188 jsonAlignmentPojo.getAppSettings().put("application", application);
189 jsonAlignmentPojo.getAppSettings().put("version", version);
190 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
191 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
192 String.valueOf(showSeqFeatures));
194 String[] hiddenSections = getHiddenSections();
195 if (hiddenSections != null)
197 if (hiddenSections[0] != null
198 && exportSettings.isExportHiddenColumns())
200 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
201 String.valueOf(hiddenSections[0]));
203 if (hiddenSections[1] != null
204 && exportSettings.isExportHiddenSequences())
206 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
207 String.valueOf(hiddenSections[1]));
211 if (exportSettings.isExportAnnotations())
214 .setAlignAnnotation(annotationToJsonPojo(annotations));
217 if (exportSettings.isExportFeatures())
220 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
223 if (exportSettings.isExportGroups() && seqGroups != null
224 && seqGroups.size() > 0)
226 for (SequenceGroup seqGrp : seqGroups)
228 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
229 seqGrpPojo.setGroupName(seqGrp.getName());
230 seqGrpPojo.setColourScheme(ColourSchemeProperty
231 .getColourName(seqGrp.cs));
232 seqGrpPojo.setColourText(seqGrp.getColourText());
233 seqGrpPojo.setDescription(seqGrp.getDescription());
234 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
235 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
236 seqGrpPojo.setEndRes(seqGrp.getEndRes());
237 seqGrpPojo.setStartRes(seqGrp.getStartRes());
238 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
239 for (SequenceI seq : seqGrp.getSequences())
241 seqGrpPojo.getSequenceRefs()
242 .add(String.valueOf(seq.hashCode()));
244 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
247 org.json.JSONObject generatedJSon = new org.json.JSONObject(
249 jsonOutput = generatedJSon.toString();
250 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
252 } catch (Exception e)
259 public String[] getHiddenSections()
261 String[] hiddenSections = new String[2];
262 if (getViewport() == null)
267 // hidden column business
268 if (getViewport().hasHiddenColumns())
270 List<int[]> hiddenCols = getViewport().getColumnSelection()
272 StringBuilder hiddenColsBuilder = new StringBuilder();
273 for (int[] range : hiddenCols)
275 hiddenColsBuilder.append(";").append(range[0]).append("-")
279 hiddenColsBuilder.deleteCharAt(0);
280 hiddenSections[0] = hiddenColsBuilder.toString();
283 // hidden rows/seqs business
284 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
285 .getHiddenSequences();
286 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
288 return hiddenSections;
291 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
292 StringBuilder hiddenSeqsBuilder = new StringBuilder();
293 for (SequenceI hiddenSeq : hiddenSeqs)
295 if (hiddenSeq != null)
297 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
300 if (hiddenSeqsBuilder.length() > 0)
302 hiddenSeqsBuilder.deleteCharAt(0);
304 hiddenSections[1] = hiddenSeqsBuilder.toString();
306 return hiddenSections;
309 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
310 List<SequenceI> seqs, FeatureRenderer fr)
312 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
313 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
314 for (SequenceI seq : seqs)
316 SequenceI dataSetSequence = seq.getDatasetSequence();
317 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
318 : seq.getDatasetSequence().getSequenceFeatures();
320 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
322 if (seqFeatures == null)
327 for (SequenceFeature sf : seqFeatures)
329 if (displayedFeatures != null
330 && displayedFeatures.isVisible(sf.getType()))
332 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
333 String.valueOf(seq.hashCode()));
335 String featureColour = (fr == null) ? null : jalview.util.Format
336 .getHexString(fr.findFeatureColour(Color.white, seq,
337 seq.findIndex(sf.getBegin())));
338 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
339 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
340 jsonFeature.setType(sf.getType());
341 jsonFeature.setDescription(sf.getDescription());
342 jsonFeature.setLinks(sf.links);
343 jsonFeature.setOtherDetails(sf.otherDetails);
344 jsonFeature.setScore(sf.getScore());
345 jsonFeature.setFillColor(featureColour);
346 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
347 sequenceFeaturesPojo.add(jsonFeature);
351 return sequenceFeaturesPojo;
354 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
355 Vector<AlignmentAnnotation> annotations)
357 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
358 if (annotations == null)
360 return jsonAnnotations;
362 for (AlignmentAnnotation annot : annotations)
364 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
365 alignAnnotPojo.setDescription(annot.description);
366 alignAnnotPojo.setLabel(annot.label);
367 for (Annotation annotation : annot.annotations)
369 AnnotationPojo annotationPojo = new AnnotationPojo();
370 if (annotation != null)
372 annotationPojo.setDescription(annotation.description);
373 annotationPojo.setValue(annotation.value);
375 .setSecondaryStructure(annotation.secondaryStructure);
376 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
377 alignAnnotPojo.getAnnotations().add(annotationPojo);
381 alignAnnotPojo.getAnnotations().add(annotationPojo);
384 jsonAnnotations.add(alignAnnotPojo);
386 return jsonAnnotations;
389 @SuppressWarnings("unchecked")
390 public JSONFile parse(Reader jsonAlignmentString)
392 String jsColourScheme = null;
395 JSONParser jsonParser = new JSONParser();
396 JSONObject alignmentJsonObj = (JSONObject) jsonParser
397 .parse(jsonAlignmentString);
398 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
399 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
400 .get("alignAnnotation");
401 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
403 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
405 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
408 if (jvSettingsJsonObj != null)
410 jsColourScheme = (String) jvSettingsJsonObj
411 .get("globalColorScheme");
412 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
413 "showSeqFeatures").toString());
414 setShowSeqFeatures(showFeatures);
415 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
416 parseHiddenCols(jvSettingsJsonObj);
419 hiddenSequences = new ArrayList<SequenceI>();
420 seqMap = new Hashtable<String, Sequence>();
421 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
424 JSONObject sequence = sequenceIter.next();
425 String sequcenceString = sequence.get("seq").toString();
426 String sequenceName = sequence.get("name").toString();
427 String seqUniqueId = sequence.get("id").toString();
428 int start = Integer.valueOf(sequence.get("start").toString());
429 int end = Integer.valueOf(sequence.get("end").toString());
430 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
432 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
434 hiddenSequences.add(seq);
437 seqMap.put(seqUniqueId, seq);
440 if (jsColourScheme != null)
442 setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
444 new Alignment(seqs.toArray(new SequenceI[0]))));
446 parseFeatures(jsonSeqArray);
448 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
451 JSONObject seqGrpObj = seqGrpIter.next();
452 String grpName = seqGrpObj.get("groupName").toString();
453 String colourScheme = seqGrpObj.get("colourScheme").toString();
454 String description = (seqGrpObj.get("description") == null) ? null
455 : seqGrpObj.get("description").toString();
456 boolean displayBoxes = Boolean.valueOf(seqGrpObj
457 .get("displayBoxes").toString());
458 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
460 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
462 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
463 "showNonconserved").toString());
464 int startRes = Integer
465 .valueOf(seqGrpObj.get("startRes").toString());
466 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
467 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
469 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
470 if (sequenceRefs.size() > 0)
472 Iterator<String> seqHashIter = sequenceRefs.iterator();
473 while (seqHashIter.hasNext())
475 String seqHash = seqHashIter.next();
476 Sequence sequence = seqMap.get(seqHash);
477 if (sequence != null)
479 grpSeqs.add(sequence);
483 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
484 displayBoxes, displayText, colourText,
486 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
488 seqGrp.setShowNonconserved(showNonconserved);
489 seqGrp.setDescription(description);
490 this.seqGroups.add(seqGrp);
494 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
497 JSONObject alAnnot = alAnnotIter.next();
498 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
499 Annotation[] annotations = new Annotation[annotJsonArray.size()];
501 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
504 JSONObject annot = annotIter.next();
507 annotations[count] = null;
511 float val = annot.get("value") == null ? null : Float
512 .valueOf(annot.get("value").toString());
513 String desc = annot.get("description") == null ? null : annot
514 .get("description").toString();
515 char ss = annot.get("secondaryStructure") == null
516 || annot.get("secondaryStructure").toString()
517 .equalsIgnoreCase("u0000") ? ' ' : annot
518 .get("secondaryStructure").toString().charAt(0);
519 String displayChar = annot.get("displayCharacter") == null ? ""
520 : annot.get("displayCharacter").toString();
522 annotations[count] = new Annotation(displayChar, desc, ss, val);
527 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
528 .get("label").toString(), alAnnot.get("description")
529 .toString(), annotations);
530 this.annotations.add(alignAnnot);
533 } catch (Exception e)
540 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
542 hiddenSeqRefs = new ArrayList<String>();
543 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
544 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
546 String[] seqRefs = hiddenSeqs.split(";");
547 for (String seqRef : seqRefs)
549 hiddenSeqRefs.add(seqRef);
554 public void parseHiddenCols(JSONObject jvSettingsJson)
556 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
557 if (hiddenCols != null && !hiddenCols.isEmpty())
559 columnSelection = new ColumnSelection();
560 String[] rangeStrings = hiddenCols.split(";");
561 for (String rangeString : rangeStrings)
563 String[] range = rangeString.split("-");
564 columnSelection.hideColumns(Integer.valueOf(range[0]),
565 Integer.valueOf(range[1]));
570 @SuppressWarnings("unchecked")
571 private void parseFeatures(JSONArray jsonSeqFeatures)
573 if (jsonSeqFeatures != null)
575 displayedFeatures = new FeaturesDisplayed();
576 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
579 JSONObject jsonFeature = seqFeatureItr.next();
580 Long begin = (Long) jsonFeature.get("xStart");
581 Long end = (Long) jsonFeature.get("xEnd");
582 String type = (String) jsonFeature.get("type");
583 String featureGrp = (String) jsonFeature.get("featureGroup");
584 String descripiton = (String) jsonFeature.get("description");
585 String seqRef = (String) jsonFeature.get("sequenceRef");
586 Float score = Float.valueOf(jsonFeature.get("score").toString());
588 Sequence seq = seqMap.get(seqRef);
589 SequenceFeature sequenceFeature = new SequenceFeature();
590 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
591 if (linksJsonArray != null && linksJsonArray.size() > 0)
593 Iterator<String> linkList = linksJsonArray.iterator();
594 while (linkList.hasNext())
596 String link = linkList.next();
597 sequenceFeature.addLink(link);
600 sequenceFeature.setFeatureGroup(featureGrp);
601 sequenceFeature.setScore(score);
602 sequenceFeature.setDescription(descripiton);
603 sequenceFeature.setType(type);
604 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
605 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
606 seq.addSequenceFeature(sequenceFeature);
607 displayedFeatures.setVisible(type);
612 public String getGlobalColorScheme()
614 return globalColorScheme;
617 public void setGlobalColorScheme(String globalColorScheme)
619 this.globalColorScheme = globalColorScheme;
622 public ColourSchemeI getColourScheme()
627 public void setColourScheme(ColourSchemeI colourScheme)
629 this.colourScheme = colourScheme;
633 public FeaturesDisplayedI getDisplayedFeatures()
635 return displayedFeatures;
638 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
640 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[] {};
708 synchronized (hiddenSequences)
710 return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
714 public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
716 this.hiddenSequences = hiddenSequences;
719 public class JSONExportSettings
721 private boolean exportSequence;
723 private boolean exportSequenceFeatures;
725 private boolean exportAnnotations;
727 private boolean exportGroups;
729 private boolean exportJalviewSettings;
731 public boolean isExportSequence()
733 return exportSequence;
736 public void setExportSequence(boolean exportSequence)
738 this.exportSequence = exportSequence;
741 public boolean isExportSequenceFeatures()
743 return exportSequenceFeatures;
746 public void setExportSequenceFeatures(boolean exportSequenceFeatures)
748 this.exportSequenceFeatures = exportSequenceFeatures;
751 public boolean isExportAnnotations()
753 return exportAnnotations;
756 public void setExportAnnotations(boolean exportAnnotations)
758 this.exportAnnotations = exportAnnotations;
761 public boolean isExportGroups()
766 public void setExportGroups(boolean exportGroups)
768 this.exportGroups = exportGroups;
771 public boolean isExportJalviewSettings()
773 return exportJalviewSettings;
776 public void setExportJalviewSettings(boolean exportJalviewSettings)
778 this.exportJalviewSettings = exportJalviewSettings;