package jalview.io;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
+import jalview.datamodel.AlignExportSettingsAdapter;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
+import jalview.util.Format;
+import jalview.util.JSONUtils;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
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 implements ComplexAlignFile
{
private static String version = new BuildDetails().getVersion();
try
{
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- AlignExportSettingI exportSettings = getExportSettings();
+ AlignExportSettingsI exportSettings = getExportSettings();
- // if no export settings were supplied use the following with all values
- // defaulting to true
+ /*
+ * if no export settings were supplied, provide an 'export all' setting
+ */
if (exportSettings == null)
{
- exportSettings = new AlignExportSettingI()
- {
- @Override
- public boolean isExportHiddenSequences()
- {
- return true;
- }
-
- @Override
- public boolean isExportHiddenColumns()
- {
- return true;
- }
-
- @Override
- public boolean isExportGroups()
- {
- return true;
- }
-
- @Override
- public boolean isExportFeatures()
- {
- return true;
- }
-
- @Override
- public boolean isExportAnnotations()
- {
- return true;
- }
-
- @Override
- public boolean isCancelled()
- {
- return false;
- }
- };
+ exportSettings = new AlignExportSettingsAdapter(true);
}
int count = 0;
if (exportSettings.isExportFeatures())
{
- jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+ jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
}
if (exportSettings.isExportGroups() && seqGroups != null
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
}
- org.json.JSONObject generatedJSon = new org.json.JSONObject(
- jsonAlignmentPojo);
+ org.json.JSONObject generatedJSon = new org.json.JSONObject(jsonAlignmentPojo);
jsonOutput = generatedJSon.toString();
return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
"xEnd");
return hiddenSections;
}
- public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- SequenceI[] sqs, FeatureRenderer fr)
+ protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ SequenceI[] sqs)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
FeatureColourFinder finder = new FeatureColourFinder(fr);
+ String[] visibleFeatureTypes = displayedFeatures == null ? null
+ : displayedFeatures.getVisibleFeatures().toArray(
+ new String[displayedFeatures.getVisibleFeatureCount()]);
+
for (SequenceI seq : sqs)
{
- SequenceI dataSetSequence = seq.getDatasetSequence();
- SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
- : seq.getDatasetSequence().getSequenceFeatures();
-
- seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
- : seqFeatures;
- if (seqFeatures == null)
- {
- continue;
- }
-
+ /*
+ * get all features currently visible (and any non-positional features)
+ */
+ List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
+ visibleFeatureTypes);
for (SequenceFeature sf : seqFeatures)
{
- if (displayedFeatures != null
- && displayedFeatures.isVisible(sf.getType()))
- {
- SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
- String.valueOf(seq.hashCode()));
-
- String featureColour = (fr == null) ? null
- : jalview.util.Format.getHexString(
- finder.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
- 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(featureColour);
- jsonFeature.setFeatureGroup(sf.getFeatureGroup());
- sequenceFeaturesPojo.add(jsonFeature);
- }
+ SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+ String.valueOf(seq.hashCode()));
+
+ String featureColour = (fr == null) ? null : Format
+ .getHexString(finder.findFeatureColour(Color.white, seq,
+ seq.findIndex(sf.getBegin())));
+ int xStart = sf.getBegin() == 0 ? 0
+ : seq.findIndex(sf.getBegin()) - 1;
+ int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
+ jsonFeature.setXstart(xStart);
+ jsonFeature.setXend(xEnd);
+ jsonFeature.setType(sf.getType());
+ jsonFeature.setDescription(sf.getDescription());
+ jsonFeature.setLinks(sf.links);
+ jsonFeature.setOtherDetails(sf.otherDetails);
+ jsonFeature.setScore(sf.getScore());
+ jsonFeature.setFillColor(featureColour);
+ jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+ sequenceFeaturesPojo.add(jsonFeature);
}
}
return sequenceFeaturesPojo;
{
try
{
- JSONParser jsonParser = new JSONParser();
- JSONObject alignmentJsonObj = (JSONObject) jsonParser
- .parse(jsonAlignmentString);
- JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
- JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj
+ Map<String, Object> alignmentJsonObj = (Map<String, Object>) JSONUtils.parse(jsonAlignmentString);
+ List<Object> seqJsonArray = (List<Object>) alignmentJsonObj.get("seqs");
+ List<Object> alAnnotJsonArray = (List<Object>) alignmentJsonObj
.get("alignAnnotation");
- JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj
+ List<Object> jsonSeqArray = (List<Object>) alignmentJsonObj
.get("seqFeatures");
- JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
+ List<Object> seqGrpJsonArray = (List<Object>) alignmentJsonObj
.get("seqGroups");
- JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
+ Map<String, Object> jvSettingsJsonObj = (Map<String, Object>) alignmentJsonObj
.get("appSettings");
if (jvSettingsJsonObj != null)
hiddenSequences = new ArrayList<>();
seqMap = new Hashtable<>();
- for (Iterator<JSONObject> sequenceIter = seqJsonArray
- .iterator(); sequenceIter.hasNext();)
+ for (Iterator<Object> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();)
{
- JSONObject sequence = sequenceIter.next();
+ Map<String, Object> sequence = (Map<String, Object>) sequenceIter.next();
String sequcenceString = sequence.get("seq").toString();
String sequenceName = sequence.get("name").toString();
String seqUniqueId = sequence.get("id").toString();
parseFeatures(jsonSeqArray);
- for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
- .iterator(); seqGrpIter.hasNext();)
+ for (Iterator<Object> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter.hasNext();)
{
- JSONObject seqGrpObj = seqGrpIter.next();
+ Map<String, Object> seqGrpObj = (Map<String, Object>)seqGrpIter.next();
String grpName = seqGrpObj.get("groupName").toString();
String colourScheme = seqGrpObj.get("colourScheme").toString();
String description = (seqGrpObj.get("description") == null) ? null
int startRes = Integer
.valueOf(seqGrpObj.get("startRes").toString());
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
- JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
+ List<Object> sequenceRefs = (List<Object>) seqGrpObj.get("sequenceRefs");
ArrayList<SequenceI> grpSeqs = new ArrayList<>();
if (sequenceRefs.size() > 0)
{
- Iterator<String> seqHashIter = sequenceRefs.iterator();
+ Iterator<Object> seqHashIter = sequenceRefs.iterator();
while (seqHashIter.hasNext())
{
- String seqHash = seqHashIter.next();
- Sequence sequence = seqMap.get(seqHash);
+ Sequence sequence = seqMap.get(seqHashIter.next());
if (sequence != null)
{
grpSeqs.add(sequence);
}
- for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
- .iterator(); alAnnotIter.hasNext();)
+ for (Iterator<Object> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter.hasNext();)
{
- JSONObject alAnnot = alAnnotIter.next();
- JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
+ Map<String, Object> alAnnot = (Map<String, Object>) alAnnotIter.next();
+ List<Object> annotJsonArray = (List<Object>) alAnnot.get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
- for (Iterator<JSONObject> annotIter = annotJsonArray
- .iterator(); annotIter.hasNext();)
+ for (Iterator<Object> annotIter = annotJsonArray.iterator(); annotIter.hasNext();)
{
- JSONObject annot = annotIter.next();
+ Map<String, Object> annot = (Map<String, Object>) annotIter.next();
if (annot == null)
{
annotations[count] = null;
alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
: Integer.valueOf(alAnnot.get("graphType").toString());
- JSONObject diplaySettings = (JSONObject) alAnnot
+ Map<String, Object> diplaySettings = (Map<String, Object>) alAnnot
.get("annotationSettings");
if (diplaySettings != null)
{
return this;
}
- public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+ public void parseHiddenSeqRefsAsList(Map<String, Object> jvSettingsJson)
{
hiddenSeqRefs = new ArrayList<>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
}
}
- public void parseHiddenCols(JSONObject jvSettingsJson)
+ public void parseHiddenCols(Map<String, Object> jvSettingsJson)
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
if (hiddenCols != null && !hiddenCols.isEmpty())
}
@SuppressWarnings("unchecked")
- private void parseFeatures(JSONArray jsonSeqFeatures)
+ private void parseFeatures(List<Object> jsonSeqFeatures)
{
if (jsonSeqFeatures != null)
{
displayedFeatures = new FeaturesDisplayed();
- for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
+ for (Iterator<Object> seqFeatureItr = jsonSeqFeatures
.iterator(); seqFeatureItr.hasNext();)
{
- JSONObject jsonFeature = seqFeatureItr.next();
+ Map<String, Object> jsonFeature = (Map<String, Object>) seqFeatureItr.next();
Long begin = (Long) jsonFeature.get("xStart");
Long end = (Long) jsonFeature.get("xEnd");
String type = (String) jsonFeature.get("type");
String featureGrp = (String) jsonFeature.get("featureGroup");
- String descripiton = (String) jsonFeature.get("description");
+ String description = (String) jsonFeature.get("description");
String seqRef = (String) jsonFeature.get("sequenceRef");
Float score = Float.valueOf(jsonFeature.get("score").toString());
Sequence seq = seqMap.get(seqRef);
- SequenceFeature sequenceFeature = new SequenceFeature();
- JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
+
+ /*
+ * begin/end of 0 is for a non-positional feature
+ */
+ int featureBegin = begin.intValue() == 0 ? 0 : seq
+ .findPosition(begin.intValue());
+ int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
+ .intValue()) - 1;
+
+ SequenceFeature sequenceFeature = new SequenceFeature(type,
+ description, featureBegin, featureEnd, score, featureGrp);
+
+ List<Object> linksJsonArray = (List<Object>) jsonFeature.get("links");
if (linksJsonArray != null && linksJsonArray.size() > 0)
{
- Iterator<String> linkList = linksJsonArray.iterator();
+ Iterator<Object> linkList = linksJsonArray.iterator();
while (linkList.hasNext())
{
- String link = linkList.next();
- sequenceFeature.addLink(link);
+ sequenceFeature.addLink((String) linkList.next());
}
}
- 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);
displayedFeatures.setVisible(type);
}