+package jalview.io;
+
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.json.binding.v1.AlignmentAnnotationPojo;
+import jalview.json.binding.v1.AlignmentPojo;
+import jalview.json.binding.v1.AnnotationPojo;
+import jalview.json.binding.v1.JalviewSettingsPojo;
+import jalview.json.binding.v1.JalviewSettingsPojo.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.v1.SequenceFeaturesPojo;
+import jalview.json.binding.v1.SequenceGrpPojo;
+import jalview.json.binding.v1.SequencePojo;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
+public class JSONFile extends AlignFile
+{
+ private static ColourSchemeI colourScheme;
+
+ private static boolean seqFeaturesEnabled;
+
+ private String jalviewVersion;
+
+ private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+
+ public static final String FILE_EXT = "json";
+
+ public static final String FILE_DESC = "JSON";
+
+ private String globalColorScheme;
+
+ private boolean showSeqFeatures;
+
+ private Hashtable<String, Sequence> seqMap;
+
+ private FeaturesDisplayedI displayedFeatures;
+
+ private AlignmentViewport av;
+
+ private jalview.api.FeatureRenderer fr;
+
+ public JSONFile()
+ {
+ super();
+ }
+
+ public JSONFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public JSONFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ @Override
+ public void parse() throws IOException
+ {
+ StringBuilder jsonStringBuilder = new StringBuilder();
+ String currentLine;
+ while ((currentLine = nextLine()) != null)
+ {
+ jsonStringBuilder.append(currentLine);
+ }
+ parse(jsonStringBuilder.toString());
+
+ }
+
+ @Override
+ public String print()
+ {
+ try
+ {
+ JSONExportSettings exportSettings = new JSONExportSettings();
+ exportSettings.setExportAnnotations(true);
+ exportSettings.setExportGroups(true);
+ exportSettings.setExportJalviewSettings(true);
+ exportSettings.setExportSequenceFeatures(true);
+
+ AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
+ if (Desktop.getCurrentAlignFrame() != null)
+ {
+ globalColorScheme = ColourSchemeProperty.getColourName(Desktop
+ .getCurrentAlignFrame().getViewport()
+ .getGlobalColourScheme());
+ this.av = Desktop.getCurrentAlignFrame().getCurrentView();
+ this.fr = Desktop.getCurrentAlignFrame().alignPanel
+ .cloneFeatureRenderer();
+ displayedFeatures = av.getFeaturesDisplayed();
+ showSeqFeatures = Desktop.getCurrentAlignFrame().showSeqFeatures
+ .isSelected();
+ }
+
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ StringBuilder name = new StringBuilder();
+ name.append(seq.getName()).append("/").append(seq.getStart())
+ .append("-").append(seq.getEnd());
+ SequencePojo jsonSeqPojo = new SequencePojo();
+ jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode());
+ jsonSeqPojo.setOrder(++count);
+ jsonSeqPojo.setEnd(seq.getEnd());
+ jsonSeqPojo.setStart(seq.getStart());
+ jsonSeqPojo.setName(name.toString());
+ jsonSeqPojo.setSeq(seq.getSequenceAsString());
+ jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
+ }
+
+ if (exportSettings.isExportJalviewSettings())
+ {
+ JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
+ jvSettings.setGlobalColorScheme(globalColorScheme);
+ jvSettings.setJalviewVersion(jalviewVersion);
+ jvSettings.setWebStartUrl(webStartLaunchServletUrl);
+ jvSettings.setShowSeqFeatures(showSeqFeatures);
+ jsonAlignmentPojo.setJalviewSettings(jvSettings);
+ }
+
+ if (exportSettings.isExportAnnotations())
+ {
+ jsonAlignmentPojo
+ .setAlignAnnotation(annotationToJsonPojo(annotations));
+ }
+
+ if (exportSettings.isExportSequenceFeatures())
+ {
+ jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(seqs,
+ displayedFeatures));
+ }
+
+ if (exportSettings.isExportGroups() && seqGroups.size() > 0)
+ {
+ ArrayList<SequenceGrpPojo> sequenceGroupsPojo = new ArrayList<SequenceGrpPojo>();
+ for (SequenceGroup seqGrp : seqGroups)
+ {
+ SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
+ seqGrpPojo.setGroupName(seqGrp.getName());
+ seqGrpPojo.setColourScheme(ColourSchemeProperty
+ .getColourName(seqGrp.cs));
+ seqGrpPojo.setColourText(seqGrp.getColourText());
+ seqGrpPojo.setDescription(seqGrp.getDescription());
+ seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
+ seqGrpPojo.setDisplayText(seqGrp.getDisplayText());
+ seqGrpPojo.setEndRes(seqGrp.getEndRes());
+ seqGrpPojo.setStartRes(seqGrp.getStartRes());
+ seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
+ for (SequenceI seq : seqGrp.getSequences())
+ {
+ seqGrpPojo.getSeqsHash().add(
+ seq.getName() + "_" + seq.hashCode());
+ }
+ jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
+ }
+ }
+ com.json.JSONObject generatedJSon = new com.json.JSONObject(
+ jsonAlignmentPojo);
+ String jsonOutput = generatedJSon.toString();
+ return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
+ "xEnd");
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ List<SequenceI> seqs, FeaturesDisplayedI displayedFeatures)
+ {
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+ for (SequenceI seq : seqs)
+ {
+ SequenceI dataSetSequence = seq.getDatasetSequence();
+ SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
+ : seq.getDatasetSequence().getSequenceFeatures();
+ for (SequenceFeature sf : seqFeatures)
+ {
+ if (displayedFeatures != null
+ && displayedFeatures.isVisible(sf.getType()))
+ {
+ // String fillColor = ((fr != null) ? jalview.util.Format
+ // .getHexString(fr.findFeatureColour(Color.white, seq,
+ // seq.findIndex(sf.getBegin()))) : null);
+ SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+ seq.getName() + "_" + seq.hashCode());
+ jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
+ jsonFeature.setXend(seq.findIndex(sf.getEnd()));
+ jsonFeature.setType(sf.getType());
+ jsonFeature.setDescription(sf.getDescription());
+ jsonFeature.setLinks(sf.links);
+ jsonFeature.setOtherDetails(sf.otherDetails);
+ jsonFeature.setScore(sf.getScore());
+ // jsonFeature.setFillColor(fillColor);
+ jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+ sequenceFeaturesPojo.add(jsonFeature);
+ }
+ }
+ }
+ return sequenceFeaturesPojo;
+ }
+
+ public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
+ Vector<AlignmentAnnotation> annotations)
+ {
+ List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+ for (AlignmentAnnotation annot : annotations)
+ {
+ AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
+ alignAnnotPojo.setDescription(annot.description);
+ alignAnnotPojo.setLabel(annot.label);
+ for (Annotation annotation : annot.annotations)
+ {
+ AnnotationPojo annotationPojo = new AnnotationPojo();
+ if (annotation != null)
+ {
+ annotationPojo.setDescription(annotation.description);
+ annotationPojo.setValue(annotation.value);
+ annotationPojo
+ .setSecondaryStructure(annotation.secondaryStructure);
+ annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
+ else
+ {
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
+ }
+ jsonAnnotations.add(alignAnnotPojo);
+ }
+ return jsonAnnotations;
+ }
+
+ public void parse(String jsonAlignmentString)
+ {
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject alignmentJsonObj = (JSONObject) jsonParser
+ .parse(jsonAlignmentString);
+ JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
+ JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
+ .get("alignAnnotation");
+ JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
+ .get("seqFeatures");
+ JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
+ .get("seqGroups");
+ JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
+ .get("jalviewSettings");
+
+ if (jvSettingsJsonObj != null)
+ {
+ String jsColourScheme = (String) jvSettingsJsonObj
+ .get("globalColorScheme");
+ Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
+ "showSeqFeatures").toString());
+ setColourScheme(getJalviewColorScheme(jsColourScheme));
+ JSONFile.setSeqFeaturesEnabled(showFeatures);
+ // Desktop.setCurrentSeqFeaturesVisible(showFeatures);
+ }
+
+ seqMap = new Hashtable<String, Sequence>();
+ // Desktop.setCurrentGlobalColourScheme(cs);
+ for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
+ .hasNext();)
+ {
+ JSONObject sequence = sequenceIter.next();
+ String sequcenceString = sequence.get("seq").toString();
+ String sequenceName = sequence.get("name").toString();
+ String seqUniqueId = sequence.get("id").toString();
+ int start = Integer.valueOf(sequence.get("start").toString());
+ int end = Integer.valueOf(sequence.get("end").toString());
+ Sequence seq = new Sequence(sequenceName, sequcenceString, start,
+ end);
+ seqs.add(seq);
+ seqMap.put(seqUniqueId, seq);
+ }
+ parseFeatures(jsonSeqArray);
+
+ for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
+ .hasNext();)
+ {
+ JSONObject seqGrpObj = seqGrpIter.next();
+ String grpName = seqGrpObj.get("groupName").toString();
+ String colourScheme = seqGrpObj.get("colourScheme").toString();
+ String description = (seqGrpObj.get("description") == null) ? null
+ : seqGrpObj.get("description").toString();
+ boolean displayBoxes = Boolean.valueOf(seqGrpObj
+ .get("displayBoxes").toString());
+ boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
+ .toString());
+ boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
+ .toString());
+ boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
+ "showNonconserved").toString());
+ int startRes = Integer
+ .valueOf(seqGrpObj.get("startRes").toString());
+ int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
+ JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
+
+ ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ if (seqsHashArray.size() > 0)
+ {
+ Iterator<String> seqHashIter = seqsHashArray.iterator();
+ while (seqHashIter.hasNext())
+ {
+ String seqHash = seqHashIter.next();
+ Sequence sequence = seqMap.get(seqHash);
+ if (sequence != null)
+ {
+ grpSeqs.add(sequence);
+ }
+ }
+ }
+ ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
+ displayBoxes, displayText, colourText, startRes, endRes);
+ seqGrp.setShowNonconserved(showNonconserved);
+ seqGrp.setDescription(description);
+ this.seqGroups.add(seqGrp);
+
+ }
+
+ for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
+ .hasNext();)
+ {
+ JSONObject alAnnot = alAnnotIter.next();
+ JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
+ Annotation[] annotations = new Annotation[annotJsonArray.size()];
+ int count = 0;
+ for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
+ .hasNext();)
+ {
+ JSONObject annot = annotIter.next();
+ if (annot == null)
+ {
+ annotations[count] = null;
+ }
+ else
+ {
+ float val = annot.get("value") == null ? null : Float
+ .valueOf(annot.get("value").toString());
+ String desc = annot.get("description") == null ? null : annot
+ .get("description").toString();
+
+ char ss = annot.get("secondaryStructure") == null ? null
+ : annot.get("secondaryStructure").toString().charAt(0);
+ String displayChar = annot.get("displayCharacter").toString();
+
+ annotations[count] = new Annotation(displayChar, desc, ss, val);
+ }
+ ++count;
+ }
+
+ AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
+ .get("label").toString(), alAnnot.get("description")
+ .toString(), annotations);
+ this.annotations.add(alignAnnot);
+ }
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+
+ private void parseFeatures(JSONArray jsonSeqFeatures)
+ {
+ if (jsonSeqFeatures != null)
+ {
+ for (@SuppressWarnings("unchecked")
+ Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
+ .hasNext();)
+ {
+ JSONObject jsonFeature = seqFeatureItr.next();
+ Long begin = (Long) jsonFeature.get("xStart");
+ Long end = (Long) jsonFeature.get("xEnd");
+ String type = (String) jsonFeature.get("type");
+ String color = (String) jsonFeature.get("fillColor");
+ String featureGrp = (String) jsonFeature.get("featureGroup");
+ String descripiton = (String) jsonFeature.get("description");
+ String seqRef = (String) jsonFeature.get("sequenceRef");
+ Float score = Float.valueOf(jsonFeature.get("score").toString());
+ // Hashtable otherDetails = (Hashtable) jsonFeature
+ // .get("otherDetails");
+ // sequenceFeature.otherDetails = otherDetails;
+
+ Sequence seq = seqMap.get(seqRef);
+ SequenceFeature sequenceFeature = new SequenceFeature();
+ JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
+ if (linksJsonArray != null && linksJsonArray.size() > 0)
+ {
+ Iterator<String> linkList = linksJsonArray.iterator();
+ while (linkList.hasNext())
+ {
+ String link = linkList.next();
+ sequenceFeature.addLink(link);
+ }
+ }
+ sequenceFeature.setFeatureGroup(featureGrp);
+ sequenceFeature.setScore(score);
+ sequenceFeature.setDescription(descripiton);
+ sequenceFeature.setType(type);
+ sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
+ sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
+ seq.addSequenceFeature(sequenceFeature);
+ }
+ }
+ }
+
+ private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+ {
+ ColourSchemeI jalviewColor = null;
+ for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+ .values())
+ {
+ if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
+ {
+ jalviewColor = cs.getJvColourScheme();
+ break;
+ }
+ }
+ return jalviewColor;
+ }
+
+ public void LoadAlignmentFeatures(AlignFrame af)
+ {
+ af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
+ af.changeColour(getColourScheme());
+ af.setMenusForViewport();
+ }
+
+ public String getGlobalColorScheme()
+ {
+ return globalColorScheme;
+ }
+
+ public void setGlobalColorScheme(String globalColorScheme)
+ {
+ this.globalColorScheme = globalColorScheme;
+ }
+
+ public static ColourSchemeI getColourScheme()
+ {
+ return colourScheme;
+ }
+
+ public static void setColourScheme(ColourSchemeI colourScheme)
+ {
+ JSONFile.colourScheme = colourScheme;
+ }
+
+ public static boolean isSeqFeaturesEnabled()
+ {
+ return seqFeaturesEnabled;
+ }
+
+ public static void setSeqFeaturesEnabled(boolean seqFeaturesEnabled)
+ {
+ JSONFile.seqFeaturesEnabled = seqFeaturesEnabled;
+ }
+
+ public class JSONExportSettings
+ {
+ private boolean exportSequence;
+
+ private boolean exportSequenceFeatures;
+
+ private boolean exportAnnotations;
+
+ private boolean exportGroups;
+
+ private boolean exportJalviewSettings;
+
+ public boolean isExportSequence()
+ {
+ return exportSequence;
+ }
+
+ public void setExportSequence(boolean exportSequence)
+ {
+ this.exportSequence = exportSequence;
+ }
+
+ public boolean isExportSequenceFeatures()
+ {
+ return exportSequenceFeatures;
+ }
+
+ public void setExportSequenceFeatures(boolean exportSequenceFeatures)
+ {
+ this.exportSequenceFeatures = exportSequenceFeatures;
+ }
+
+ public boolean isExportAnnotations()
+ {
+ return exportAnnotations;
+ }
+
+ public void setExportAnnotations(boolean exportAnnotations)
+ {
+ this.exportAnnotations = exportAnnotations;
+ }
+
+ public boolean isExportGroups()
+ {
+ return exportGroups;
+ }
+
+ public void setExportGroups(boolean exportGroups)
+ {
+ this.exportGroups = exportGroups;
+ }
+
+ public boolean isExportJalviewSettings()
+ {
+ return exportJalviewSettings;
+ }
+
+ public void setExportJalviewSettings(boolean exportJalviewSettings)
+ {
+ this.exportJalviewSettings = exportJalviewSettings;
+ }
+ }
+}