2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
3 * Copyright (C) 2015 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.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.ColumnSelection;
35 import jalview.datamodel.HiddenSequences;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
41 import jalview.json.binding.biojson.v1.AlignmentPojo;
42 import jalview.json.binding.biojson.v1.AnnotationPojo;
43 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
44 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
45 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
46 import jalview.json.binding.biojson.v1.SequencePojo;
47 import jalview.schemes.ColourSchemeProperty;
48 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
50 import java.awt.Color;
51 import java.io.IOException;
52 import java.io.Reader;
53 import java.util.ArrayList;
54 import java.util.Hashtable;
55 import java.util.Iterator;
56 import java.util.List;
57 import java.util.Vector;
59 import org.json.simple.JSONArray;
60 import org.json.simple.JSONObject;
61 import org.json.simple.parser.JSONParser;
63 public class JSONFile extends AlignFile implements ComplexAlignFile
65 private static String version = new BuildDetails().getVersion();
67 private String webstartUrl = "http://www.jalview.org/services/launchApp";
69 private String application = "Jalview";
71 public static final String FILE_EXT = "json";
73 public static final String FILE_DESC = "JSON";
75 private String globalColourScheme;
77 private boolean showSeqFeatures;
79 private Hashtable<String, Sequence> seqMap;
81 private FeaturesDisplayedI displayedFeatures;
83 private FeatureRenderer fr;
85 private List<int[]> hiddenColumns;
87 private ColumnSelection columnSelection;
89 private List<String> hiddenSeqRefs;
91 private ArrayList<SequenceI> hiddenSequences;
98 public JSONFile(FileParse source) throws IOException
103 public JSONFile(String inFile, String type) throws IOException
109 public void parse() throws IOException
116 public String print()
118 String jsonOutput = null;
121 AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
122 AlignExportSettingI exportSettings = getExportSettings();
124 // if no export settings were supplied use the following with all values
125 // defaulting to true
126 if (exportSettings == null)
128 exportSettings = new AlignExportSettingI()
131 public boolean isExportHiddenSequences()
137 public boolean isExportHiddenColumns()
143 public boolean isExportGroups()
149 public boolean isExportFeatures()
155 public boolean isExportAnnotations()
161 public boolean isCancelled()
169 for (SequenceI seq : seqs)
171 StringBuilder name = new StringBuilder();
172 name.append(seq.getName()).append("/").append(seq.getStart())
173 .append("-").append(seq.getEnd());
174 SequencePojo jsonSeqPojo = new SequencePojo();
175 jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
176 jsonSeqPojo.setOrder(++count);
177 jsonSeqPojo.setEnd(seq.getEnd());
178 jsonSeqPojo.setStart(seq.getStart());
179 jsonSeqPojo.setName(name.toString());
180 jsonSeqPojo.setSeq(seq.getSequenceAsString());
181 jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
183 jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
184 jsonAlignmentPojo.getAppSettings().put("application", application);
185 jsonAlignmentPojo.getAppSettings().put("version", version);
186 jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
187 jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
188 String.valueOf(showSeqFeatures));
190 String[] hiddenSections = getHiddenSections();
191 if (hiddenSections != null)
193 if (hiddenSections[0] != null
194 && exportSettings.isExportHiddenColumns())
196 jsonAlignmentPojo.getAppSettings().put("hiddenCols",
197 String.valueOf(hiddenSections[0]));
199 if (hiddenSections[1] != null
200 && exportSettings.isExportHiddenSequences())
202 jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
203 String.valueOf(hiddenSections[1]));
207 if (exportSettings.isExportAnnotations())
210 .setAlignAnnotation(annotationToJsonPojo(annotations));
214 if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
216 jsonAlignmentPojo.setGlobalColorScheme("None");
220 if (exportSettings.isExportFeatures())
223 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
226 if (exportSettings.isExportGroups() && seqGroups != null
227 && seqGroups.size() > 0)
229 for (SequenceGroup seqGrp : seqGroups)
231 SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
232 seqGrpPojo.setGroupName(seqGrp.getName());
233 seqGrpPojo.setColourScheme(ColourSchemeProperty
234 .getColourName(seqGrp.cs));
235 seqGrpPojo.setColourText(seqGrp.getColourText());
236 seqGrpPojo.setDescription(seqGrp.getDescription());
237 seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
238 seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
239 seqGrpPojo.setEndRes(seqGrp.getEndRes());
240 seqGrpPojo.setStartRes(seqGrp.getStartRes());
241 seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
242 for (SequenceI seq : seqGrp.getSequences())
244 seqGrpPojo.getSequenceRefs()
245 .add(String.valueOf(seq.hashCode()));
247 jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
250 org.json.JSONObject generatedJSon = new org.json.JSONObject(
252 jsonOutput = generatedJSon.toString();
253 return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
255 } catch (Exception e)
262 public String[] getHiddenSections()
264 String[] hiddenSections = new String[2];
265 if (getViewport() == null)
270 // hidden column business
271 if (getViewport().hasHiddenColumns())
273 List<int[]> hiddenCols = getViewport().getColumnSelection()
275 StringBuilder hiddenColsBuilder = new StringBuilder();
276 for (int[] range : hiddenCols)
278 hiddenColsBuilder.append(";").append(range[0]).append("-")
282 hiddenColsBuilder.deleteCharAt(0);
283 hiddenSections[0] = hiddenColsBuilder.toString();
286 // hidden rows/seqs business
287 HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
288 .getHiddenSequences();
289 if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
291 return hiddenSections;
294 SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
295 StringBuilder hiddenSeqsBuilder = new StringBuilder();
296 for (SequenceI hiddenSeq : hiddenSeqs)
298 if (hiddenSeq != null)
300 hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
303 if (hiddenSeqsBuilder.length() > 0)
305 hiddenSeqsBuilder.deleteCharAt(0);
307 hiddenSections[1] = hiddenSeqsBuilder.toString();
309 return hiddenSections;
312 public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
313 List<SequenceI> seqs, FeatureRenderer fr)
315 displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
316 List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
317 for (SequenceI seq : seqs)
319 SequenceI dataSetSequence = seq.getDatasetSequence();
320 SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
321 : seq.getDatasetSequence().getSequenceFeatures();
323 seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
325 if (seqFeatures == null)
330 for (SequenceFeature sf : seqFeatures)
332 if (displayedFeatures != null
333 && displayedFeatures.isVisible(sf.getType()))
335 SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
336 String.valueOf(seq.hashCode()));
338 String featureColour = (fr == null) ? null : jalview.util.Format
339 .getHexString(fr.findFeatureColour(Color.white, seq,
340 seq.findIndex(sf.getBegin())));
341 jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
342 jsonFeature.setXend(seq.findIndex(sf.getEnd()));
343 jsonFeature.setType(sf.getType());
344 jsonFeature.setDescription(sf.getDescription());
345 jsonFeature.setLinks(sf.links);
346 jsonFeature.setOtherDetails(sf.otherDetails);
347 jsonFeature.setScore(sf.getScore());
348 jsonFeature.setFillColor(featureColour);
349 jsonFeature.setFeatureGroup(sf.getFeatureGroup());
350 sequenceFeaturesPojo.add(jsonFeature);
354 return sequenceFeaturesPojo;
357 public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
358 Vector<AlignmentAnnotation> annotations)
360 List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
361 if (annotations == null)
363 return jsonAnnotations;
365 for (AlignmentAnnotation annot : annotations)
367 AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
368 alignAnnotPojo.setDescription(annot.description);
369 alignAnnotPojo.setLabel(annot.label);
370 for (Annotation annotation : annot.annotations)
372 AnnotationPojo annotationPojo = new AnnotationPojo();
373 if (annotation != null)
375 annotationPojo.setDescription(annotation.description);
376 annotationPojo.setValue(annotation.value);
378 .setSecondaryStructure(annotation.secondaryStructure);
379 annotationPojo.setDisplayCharacter(annotation.displayCharacter);
380 alignAnnotPojo.getAnnotations().add(annotationPojo);
384 alignAnnotPojo.getAnnotations().add(annotationPojo);
387 jsonAnnotations.add(alignAnnotPojo);
389 return jsonAnnotations;
392 @SuppressWarnings("unchecked")
393 public JSONFile parse(Reader jsonAlignmentString)
397 JSONParser jsonParser = new JSONParser();
398 JSONObject alignmentJsonObj = (JSONObject) jsonParser
399 .parse(jsonAlignmentString);
400 JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
401 JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
402 .get("alignAnnotation");
403 JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
405 JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
407 JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
410 if (jvSettingsJsonObj != null)
412 globalColourScheme = (String) jvSettingsJsonObj
413 .get("globalColorScheme");
414 Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
415 "showSeqFeatures").toString());
416 setShowSeqFeatures(showFeatures);
417 parseHiddenSeqRefsAsList(jvSettingsJsonObj);
418 parseHiddenCols(jvSettingsJsonObj);
421 hiddenSequences = new ArrayList<SequenceI>();
422 seqMap = new Hashtable<String, Sequence>();
423 for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
426 JSONObject sequence = sequenceIter.next();
427 String sequcenceString = sequence.get("seq").toString();
428 String sequenceName = sequence.get("name").toString();
429 String seqUniqueId = sequence.get("id").toString();
430 int start = Integer.valueOf(sequence.get("start").toString());
431 int end = Integer.valueOf(sequence.get("end").toString());
432 Sequence seq = new Sequence(sequenceName, sequcenceString, start,
434 if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
436 hiddenSequences.add(seq);
439 seqMap.put(seqUniqueId, seq);
443 parseFeatures(jsonSeqArray);
445 for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
448 JSONObject seqGrpObj = seqGrpIter.next();
449 String grpName = seqGrpObj.get("groupName").toString();
450 String colourScheme = seqGrpObj.get("colourScheme").toString();
451 String description = (seqGrpObj.get("description") == null) ? null
452 : seqGrpObj.get("description").toString();
453 boolean displayBoxes = Boolean.valueOf(seqGrpObj
454 .get("displayBoxes").toString());
455 boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
457 boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
459 boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
460 "showNonconserved").toString());
461 int startRes = Integer
462 .valueOf(seqGrpObj.get("startRes").toString());
463 int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
464 JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
466 ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
467 if (sequenceRefs.size() > 0)
469 Iterator<String> seqHashIter = sequenceRefs.iterator();
470 while (seqHashIter.hasNext())
472 String seqHash = seqHashIter.next();
473 Sequence sequence = seqMap.get(seqHash);
474 if (sequence != null)
476 grpSeqs.add(sequence);
480 SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
481 displayBoxes, displayText, colourText,
483 seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
485 seqGrp.setShowNonconserved(showNonconserved);
486 seqGrp.setDescription(description);
487 this.seqGroups.add(seqGrp);
491 for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
494 JSONObject alAnnot = alAnnotIter.next();
495 JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
496 Annotation[] annotations = new Annotation[annotJsonArray.size()];
498 for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
501 JSONObject annot = annotIter.next();
504 annotations[count] = null;
508 float val = annot.get("value") == null ? null : Float
509 .valueOf(annot.get("value").toString());
510 String desc = annot.get("description") == null ? null : annot
511 .get("description").toString();
512 char ss = annot.get("secondaryStructure") == null
513 || annot.get("secondaryStructure").toString()
514 .equalsIgnoreCase("u0000") ? ' ' : annot
515 .get("secondaryStructure").toString().charAt(0);
516 String displayChar = annot.get("displayCharacter") == null ? ""
517 : annot.get("displayCharacter").toString();
519 annotations[count] = new Annotation(displayChar, desc, ss, val);
524 AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
525 .get("label").toString(), alAnnot.get("description")
526 .toString(), annotations);
527 this.annotations.add(alignAnnot);
529 } catch (Exception e)
536 public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
538 hiddenSeqRefs = new ArrayList<String>();
539 String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
540 if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
542 String[] seqRefs = hiddenSeqs.split(";");
543 for (String seqRef : seqRefs)
545 hiddenSeqRefs.add(seqRef);
550 public void parseHiddenCols(JSONObject jvSettingsJson)
552 String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
553 if (hiddenCols != null && !hiddenCols.isEmpty())
555 columnSelection = new ColumnSelection();
556 String[] rangeStrings = hiddenCols.split(";");
557 for (String rangeString : rangeStrings)
559 String[] range = rangeString.split("-");
560 columnSelection.hideColumns(Integer.valueOf(range[0]),
561 Integer.valueOf(range[1]));
566 @SuppressWarnings("unchecked")
567 private void parseFeatures(JSONArray jsonSeqFeatures)
569 if (jsonSeqFeatures != null)
571 displayedFeatures = new FeaturesDisplayed();
572 for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
575 JSONObject jsonFeature = seqFeatureItr.next();
576 Long begin = (Long) jsonFeature.get("xStart");
577 Long end = (Long) jsonFeature.get("xEnd");
578 String type = (String) jsonFeature.get("type");
579 String featureGrp = (String) jsonFeature.get("featureGroup");
580 String descripiton = (String) jsonFeature.get("description");
581 String seqRef = (String) jsonFeature.get("sequenceRef");
582 Float score = Float.valueOf(jsonFeature.get("score").toString());
584 Sequence seq = seqMap.get(seqRef);
585 SequenceFeature sequenceFeature = new SequenceFeature();
586 JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
587 if (linksJsonArray != null && linksJsonArray.size() > 0)
589 Iterator<String> linkList = linksJsonArray.iterator();
590 while (linkList.hasNext())
592 String link = linkList.next();
593 sequenceFeature.addLink(link);
596 sequenceFeature.setFeatureGroup(featureGrp);
597 sequenceFeature.setScore(score);
598 sequenceFeature.setDescription(descripiton);
599 sequenceFeature.setType(type);
600 sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
601 sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
602 seq.addSequenceFeature(sequenceFeature);
603 displayedFeatures.setVisible(type);
608 public String getGlobalColourScheme()
610 return globalColourScheme;
613 public void setGlobalColorScheme(String globalColourScheme)
615 this.globalColourScheme = globalColourScheme;
619 public FeaturesDisplayedI getDisplayedFeatures()
621 return displayedFeatures;
624 public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
626 this.displayedFeatures = displayedFeatures;
629 public void configureForView(AlignmentViewPanel avpanel)
631 super.configureForView(avpanel);
632 AlignViewportI viewport = avpanel.getAlignViewport();
633 AlignmentI alignment = viewport.getAlignment();
634 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
636 seqGroups = alignment.getGroups();
637 fr = avpanel.cloneFeatureRenderer();
639 // Add non auto calculated annotation to AlignFile
640 for (AlignmentAnnotation annot : annots)
642 if (annot != null && !annot.autoCalculated)
648 annotations.add(annot);
651 globalColourScheme = ColourSchemeProperty.getColourName(viewport
652 .getGlobalColourScheme());
653 setDisplayedFeatures(viewport.getFeaturesDisplayed());
654 showSeqFeatures = viewport.isShowSequenceFeatures();
658 public boolean isShowSeqFeatures()
660 return showSeqFeatures;
663 public void setShowSeqFeatures(boolean showSeqFeatures)
665 this.showSeqFeatures = showSeqFeatures;
668 public Vector<AlignmentAnnotation> getAnnotations()
673 public List<int[]> getHiddenColumns()
675 return hiddenColumns;
678 public ColumnSelection getColumnSelection()
680 return columnSelection;
683 public void setColumnSelection(ColumnSelection columnSelection)
685 this.columnSelection = columnSelection;
688 public SequenceI[] getHiddenSequences()
690 if (hiddenSequences == null || hiddenSequences.isEmpty())
692 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;