import jalview.gui.Desktop;
import jalview.json.binding.v1.AlignmentAnnotationPojo;
import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
import jalview.json.binding.v1.AnnotationPojo;
-import jalview.json.binding.v1.FeaturePojo;
+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.awt.Color;
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;
public class JSONFile extends AlignFile
{
- private ColourSchemeI cs;
+ private static ColourSchemeI colourScheme;
+
+ private static boolean seqFeaturesEnabled;
private String jalviewVersion;
private String globalColorScheme;
+ private boolean showSeqFeatures;
+
private Hashtable<String, Sequence> seqMap;
private FeaturesDisplayedI displayedFeatures;
super(inFile, type);
}
-
@Override
public void parse() throws IOException
{
@Override
public String print()
{
- AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (Desktop.getCurrentAlignFrame() != null)
+ try
{
- jsonAlignmentPojo.setGlobalColorScheme(ColourSchemeProperty
- .getColourName(Desktop.getCurrentAlignFrame().getViewport()
- .getGlobalColourScheme()));
- this.av = Desktop.getCurrentAlignFrame().getCurrentView();
- this.fr = Desktop.getCurrentAlignFrame().alignPanel
- .cloneFeatureRenderer();
- displayedFeatures = av.getFeaturesDisplayed();
- jsonAlignmentPojo
- .setShowSeqFeatures(Desktop.getCurrentAlignFrame().showSeqFeatures
- .isSelected());
+ 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;
}
- jsonAlignmentPojo.setJalviewVersion(jalviewVersion);
- jsonAlignmentPojo.setWebStartUrl(webStartLaunchServletUrl);
+ }
- if (seqGroups.size() > 0)
+ public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ List<SequenceI> seqs, FeaturesDisplayedI displayedFeatures)
+ {
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+ for (SequenceI seq : seqs)
{
- ArrayList<SequenceGrpPojo> sequenceGroupsPojo = new ArrayList<SequenceGrpPojo>();
- for (SequenceGroup seqGrp : seqGroups)
+ SequenceI dataSetSequence = seq.getDatasetSequence();
+ SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
+ : seq.getDatasetSequence().getSequenceFeatures();
+ for (SequenceFeature sf : seqFeatures)
{
- 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());
+ 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);
}
- jsonAlignmentPojo.getSequenceGroups().add(seqGrpPojo);
}
}
+ 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.getAnnotations().add(annotationPojo);
}
}
- jsonAlignmentPojo.getAlignmentAnnotation().add(alignAnnotPojo);
+ jsonAnnotations.add(alignAnnotPojo);
}
-
- 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 (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getSequenceFeatures() != null)
- {
- ArrayList<FeaturePojo> seqFeaturesPojo = new ArrayList<FeaturePojo>();
- for (SequenceFeature sf : seq.getDatasetSequence()
- .getSequenceFeatures())
- {
-
- 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);
- FeaturePojo jsonFeature = new FeaturePojo();
- 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());
- seqFeaturesPojo.add(jsonFeature);
- }
- }
- jsonSeqPojo.setFeatures(seqFeaturesPojo);
- }
- }
- return new com.json.JSONObject(jsonAlignmentPojo).toString()
- .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
+ return jsonAnnotations;
}
public void parse(String jsonAlignmentString)
JSONObject alignmentJsonObj = (JSONObject) jsonParser
.parse(jsonAlignmentString);
JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
- JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj.get("alignmentAnnotation");
- JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj.get("sequenceGroups");
- String jsColourScheme = (String) alignmentJsonObj
- .get("globalColorScheme");
- Boolean showFeatures = Boolean.valueOf(alignmentJsonObj.get(
- "showSeqFeatures").toString());
- cs = getJalviewColorScheme(jsColourScheme);
+ 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);
- Desktop.setCurrentSeqFeaturesVisible(showFeatures);
+ // Desktop.setCurrentGlobalColourScheme(cs);
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
{
int end = Integer.valueOf(sequence.get("end").toString());
Sequence seq = new Sequence(sequenceName, sequcenceString, start,
end);
- JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
- SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
- jsonSeqArray, seq);
- if (retrievedSeqFeatures != null)
- {
- seq.setSequenceFeatures(retrievedSeqFeatures);
- }
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
}
-
+ parseFeatures(jsonSeqArray);
+
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
.hasNext();)
{
}
-
for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
.hasNext();)
{
JSONObject alAnnot = alAnnotIter.next();
- JSONArray annotJsonArray = (JSONArray) alAnnot
- .get("annotations");
+ JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
}
else
{
- float val = annot.get("value") == null ? null
- : Float.valueOf(annot.get("value")
- .toString());
+ 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();
+ : annot.get("secondaryStructure").toString().charAt(0);
+ String displayChar = annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
}
}
}
- public SequenceFeature[] getJalviewSequenceFeatures(
- JSONArray jsonSeqFeatures, Sequence seq)
+
+ private void parseFeatures(JSONArray jsonSeqFeatures)
{
- SequenceFeature[] seqFeatures = null;
- int count = 0;
if (jsonSeqFeatures != null)
{
- seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
for (@SuppressWarnings("unchecked")
Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
-
- SequenceFeature sequenceFeature = new SequenceFeature();
JSONObject jsonFeature = seqFeatureItr.next();
Long begin = (Long) jsonFeature.get("xStart");
Long end = (Long) jsonFeature.get("xEnd");
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");
- // Vector<String> links = (Vector<String>) jsonFeature.get("links");
-
- // sequenceFeature.links = links;
// 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);
- sequenceFeature.setType(type);
- seqFeatures[count++] = sequenceFeature;
+ seq.addSequenceFeature(sequenceFeature);
}
}
- return seqFeatures;
}
private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
public void LoadAlignmentFeatures(AlignFrame af)
{
- af.setShowSeqFeatures(Desktop.isCurrentSeqFeaturesVisible());
- af.changeColour(Desktop.getCurrentGlobalColourScheme());
+ af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
+ af.changeColour(getColourScheme());
af.setMenusForViewport();
}
{
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;
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff