package jalview.io;
-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;
-import org.json.simple.parser.JSONParser;
-
-import jalview.api.AlignViewControllerGuiI;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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 jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-public class JSONFile extends AlignFile
+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 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 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()
{
super();
@Override
public void parse() throws IOException
{
- StringBuilder jsonStringBuilder = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- jsonStringBuilder.append(currentLine);
- }
- parse(jsonStringBuilder.toString());
+ parse(getReader());
}
-
@Override
public String print()
{
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)
- {
- globalColorScheme = ColourSchemeProperty
- .getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
- fr = getViewport().getFeatureRenderer();
- }
int count = 0;
for (SequenceI seq : seqs)
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 && getViewport().isIncludeHiddenRegion())
+ if (hiddenSections[0] != null
+ && getExportSettings()
+ .isExportHiddenColumns())
{
- if (hiddenSections[0] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenCols",
- String.valueOf(hiddenSections[0]));
- }
- if (hiddenSections[1] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
- String.valueOf(hiddenSections[1]));
- }
+ jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+ String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null
+ && getExportSettings()
+ .isExportHiddenSequences())
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+ String.valueOf(hiddenSections[1]));
}
}
- if (jsonExportSettings.isExportAnnotations())
+ if (getExportSettings().isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (getExportSettings().isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (jsonExportSettings.isExportGroups() && seqGroups != null
+ if (getExportSettings().isExportGroups()
+ && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
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
}
SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
- System.out.print("Hidden Seqs : ");
- // if(hiddenSeqs != null){
StringBuilder hiddenSeqsBuilder = new StringBuilder();
for (SequenceI hiddenSeq : hiddenSeqs)
{
}
}
if (hiddenSeqsBuilder.length() > 0)
- {
+ {
hiddenSeqsBuilder.deleteCharAt(0);
- }
+ }
hiddenSections[1] = hiddenSeqsBuilder.toString();
- System.out.println(hiddenSections[1]);
- // }
return hiddenSections;
}
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
parseHiddenCols(jvSettingsJsonObj);
}
+ hiddenSequences = new ArrayList<SequenceI>();
seqMap = new Hashtable<String, Sequence>();
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
end);
if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
{
- seq.setHidden(true);
+ hiddenSequences.add(seq);
}
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
public void parseHiddenCols(JSONObject jvSettingsJson)
{
- hiddenColumns = new ArrayList<int[]>();
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("-");
- hiddenColumns.add(new int[]
- { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
+ columnSelection.hideColumns(Integer.valueOf(range[0]),
+ Integer.valueOf(range[1]));
}
}
}
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 applySettingsToAlignmentView(AlignViewControllerGuiI avc)
- {
- avc.setShowSeqFeatures(isShowSeqFeatures());
- avc.changeColour(getColourScheme());
- avc.setMenusForViewport();
- avc.hideColumns(hiddenColumns);
- avc.syncHiddenSequences();
- }
-
public String getGlobalColorScheme()
{
return globalColorScheme;
this.displayedFeatures = displayedFeatures;
}
- public JSONExportSettings getJsonExportSettings()
- {
- return jsonExportSettings;
- }
-
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ @Override
+ public void configureForView(AlignmentViewPanel avpanel)
{
- this.jsonExportSettings = jsonExportSettings;
- }
+ super.configureForView(avpanel);
+ if (isExporting())
+ {
+ setViewport(avpanel.getAlignViewport());
+ seqGroups = avpanel.getAlignment().getGroups();
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ fr = avpanel.cloneFeatureRenderer();
- public static String getJSONData(AlignViewportI av)
- {
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+ for (SequenceI seq : getViewport().getAlignment().getSequences())
+ {
+ seqs.add(seq);
+ }
- for (SequenceI seq : av.getAlignment().getSequences())
- {
- jsonFile.seqs.add(seq);
- }
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : getViewport().getAlignment()
+ .getAlignmentAnnotation())
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ annotations.add(annot);
}
- jsonFile.annotations.add(annot);
}
+
+ globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+ .getGlobalColourScheme());
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ showSeqFeatures = getViewport().isShowSequenceFeatures();
}
+ }
+
+
+ public static String getJSONData(AlignmentViewPanel av)
+ {
+ JSONFile jsonFile = new JSONFile();
+ jsonFile.configureForView(av);
String jsonString = jsonFile.print();
return jsonString;
}
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;