package jalview.io;
-import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewportI;
+import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import java.awt.Color;
import java.io.IOException;
+import java.io.Reader;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
-public class JSONFile extends AlignFile
+public class JSONFile extends AlignFile implements ComplexAlignFile
{
private ColourSchemeI colourScheme;
private FeatureRenderer fr;
- private JSONExportSettings jsonExportSettings;
+ private List<int[]> hiddenColumns;
+
+ private ColumnSelection columnSelection;
+
+ private List<String> hiddenSeqRefs;
+
+ private ArrayList<SequenceI> hiddenSequences;
public JSONFile()
{
@Override
public void parse() throws IOException
{
- StringBuilder jsonStringBuilder = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- jsonStringBuilder.append(currentLine);
- }
- parse(jsonStringBuilder.toString());
+ parse(getReader());
}
String jsonOutput = null;
try
{
- if (getJsonExportSettings() == null)
- {
- jsonExportSettings = new JSONExportSettings();
- jsonExportSettings.setExportAnnotations(true);
- jsonExportSettings.setExportGroups(true);
- jsonExportSettings.setExportJalviewSettings(true);
- jsonExportSettings.setExportSequenceFeatures(true);
- }
-
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
if (getViewport() != null)
{
name.append(seq.getName()).append("/").append(seq.getStart())
.append("-").append(seq.getEnd());
SequencePojo jsonSeqPojo = new SequencePojo();
- jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode());
+ jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
jsonSeqPojo.setOrder(++count);
jsonSeqPojo.setEnd(seq.getEnd());
jsonSeqPojo.setStart(seq.getStart());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- if (jsonExportSettings.isExportJalviewSettings())
+ jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.getAppSettings().put("application", application);
+ jsonAlignmentPojo.getAppSettings().put("version", version);
+ jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+ jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+ String.valueOf(showSeqFeatures));
+
+ String[] hiddenSections = getHiddenSections();
+ if (hiddenSections != null)
{
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
- jsonAlignmentPojo.getAppSettings().put("application", application);
- jsonAlignmentPojo.getAppSettings().put("version", version);
- jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
- jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
- String.valueOf(showSeqFeatures));
-
- String[] hiddenSections = exportHiddenSections();
- if (hiddenSections != null)
+ if (hiddenSections[0] != null
+ && getViewport().getExportSettings()
+ .isExportHiddenColumns())
{
jsonAlignmentPojo.getAppSettings().put("hiddenCols",
String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null
+ && getViewport().getExportSettings()
+ .isExportHiddenSequences())
+ {
jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
String.valueOf(hiddenSections[1]));
}
}
- if (jsonExportSettings.isExportAnnotations())
+ if (getViewport().getExportSettings().isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (getViewport().getExportSettings().isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (jsonExportSettings.isExportGroups() && seqGroups != null
+ if (getViewport().getExportSettings().isExportGroups()
+ && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
for (SequenceI seq : seqGrp.getSequences())
{
- seqGrpPojo.getSeqsHash().add(
- seq.getName() + "_" + seq.hashCode());
+ seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
}
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
return jsonOutput;
}
- public String[] exportHiddenSections()
+ public String[] getHiddenSections()
{
String[] hiddenSections = new String[2];
if (getViewport() == null)
return null;
}
- System.out.println("--- Hidden Sections ---");
// hidden column business
if (getViewport().hasHiddenColumns())
{
- System.out.print("Hidden Cols : ");
List<int[]> hiddenCols = getViewport().getColumnSelection()
.getHiddenColumns();
StringBuilder hiddenColsBuilder = new StringBuilder();
hiddenColsBuilder.deleteCharAt(0);
hiddenSections[0] = hiddenColsBuilder.toString();
- System.out.println(hiddenSections[0]);
}
// hidden rows/seqs business
HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
.getHiddenSequences();
- if (hiddenSeqsObj == null)
+ if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
{
return hiddenSections;
}
SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
- System.out.print("Hidden Seqs : ");
StringBuilder hiddenSeqsBuilder = new StringBuilder();
for (SequenceI hiddenSeq : hiddenSeqs)
{
hiddenSeqsBuilder.deleteCharAt(0);
}
hiddenSections[1] = hiddenSeqsBuilder.toString();
- System.out.println(hiddenSections[1]);
+
return hiddenSections;
}
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
: seq.getDatasetSequence().getSequenceFeatures();
+ seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+ : seqFeatures;
if (seqFeatures == null)
{
continue;
&& displayedFeatures.isVisible(sf.getType()))
{
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
- seq.getName() + "_" + seq.hashCode());
+ String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
.getHexString(fr
.findFeatureColour(Color.white, seq,
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
"showSeqFeatures").toString());
setColourScheme(getJalviewColorScheme(jsColourScheme));
setShowSeqFeatures(showFeatures);
+ parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+ parseHiddenCols(jvSettingsJsonObj);
}
+ hiddenSequences = new ArrayList<SequenceI>();
seqMap = new Hashtable<String, Sequence>();
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
int end = Integer.valueOf(sequence.get("end").toString());
Sequence seq = new Sequence(sequenceName, sequcenceString, start,
end);
+ if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
+ {
+ hiddenSequences.add(seq);
+ }
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
}
return this;
}
+ public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+ {
+ hiddenSeqRefs = new ArrayList<String>();
+ String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
+ if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+ String[] seqRefs = hiddenSeqs.split(";");
+ for(String seqRef : seqRefs){
+ hiddenSeqRefs.add(seqRef);
+ }
+ }
+ }
+
+ public void parseHiddenCols(JSONObject jvSettingsJson)
+ {
+ String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
+ if(hiddenCols != null && !hiddenCols.isEmpty()){
+ columnSelection = new ColumnSelection();
+ String[] rangeStrings = hiddenCols.split(";");
+ for(String rangeString : rangeStrings){
+ String[] range = rangeString.split("-");
+ columnSelection.hideColumns(Integer.valueOf(range[0]),
+ Integer.valueOf(range[1]));
+ }
+ }
+ }
@SuppressWarnings("unchecked")
private void parseFeatures(JSONArray jsonSeqFeatures)
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();
return jalviewColor;
}
- public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
- {
- af.setShowSeqFeatures(isShowSeqFeatures());
- af.changeColour(getColourScheme());
- af.setMenusForViewport();
- }
-
public String getGlobalColorScheme()
{
return globalColorScheme;
this.displayedFeatures = displayedFeatures;
}
- public JSONExportSettings getJsonExportSettings()
- {
- return jsonExportSettings;
- }
-
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
- {
- this.jsonExportSettings = jsonExportSettings;
- }
public static String getJSONData(AlignViewportI av)
{
return annotations;
}
+ public List<int[]> getHiddenColumns()
+ {
+ return hiddenColumns;
+ }
+
+ public ColumnSelection getColumnSelection()
+ {
+ return columnSelection;
+ }
+
+ public void setColumnSelection(ColumnSelection columnSelection)
+ {
+ this.columnSelection = columnSelection;
+ }
+
+ public SequenceI[] getHiddenSequences()
+ {
+ if (hiddenSequences == null || hiddenSequences.isEmpty())
+ {
+ return new SequenceI[]
+ {};
+ }
+ synchronized (hiddenSequences)
+ {
+ return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
+ }
+ }
+
+ public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
+ {
+ this.hiddenSequences = hiddenSequences;
+ }
+
public class JSONExportSettings
{
private boolean exportSequence;
git://source.jalview.org / jalview.git / blobdiff