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.AlignExportSettingI;
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.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
import jalview.json.binding.v1.SequencePojo;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+
+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 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()
{
try
{
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (getViewport() != null)
+ AlignExportSettingI exportSettings = getExportSettings();
+
+ // if no export settings were supplied use the following with all values
+ // defaulting to true
+ if (exportSettings == null)
{
- globalColorScheme = ColourSchemeProperty
- .getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
- fr = getViewport().getFeatureRenderer();
+ 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;
+ }
+ };
}
int count = 0;
if (hiddenSections != null)
{
if (hiddenSections[0] != null
- && getViewport().getExportSettings()
+ && exportSettings
.isExportHiddenColumns())
{
jsonAlignmentPojo.getAppSettings().put("hiddenCols",
String.valueOf(hiddenSections[0]));
}
if (hiddenSections[1] != null
- && getViewport().getExportSettings()
+ && exportSettings
.isExportHiddenSequences())
{
jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
}
}
- if (getViewport().getExportSettings().isExportAnnotations())
+ if (exportSettings.isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (getViewport().getExportSettings().isExportFeatures())
+ if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (getViewport().getExportSettings().isExportGroups()
+ if (exportSettings.isExportGroups()
&& seqGroups != null
&& seqGroups.size() > 0)
{
return hiddenSections;
}
- public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
List<SequenceI> seqs, FeatureRenderer fr)
{
- FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
+ displayedFeatures = (fr == null) ? null : fr
.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
for (SequenceI seq : seqs)
{
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
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
{
}
}
}
- ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
+ ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
+ grpColourScheme,
displayBoxes, displayText, colourText, startRes, endRes);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
{
if (jsonSeqFeatures != null)
{
+ displayedFeatures = new FeaturesDisplayed();
for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
seq.addSequenceFeature(sequenceFeature);
+ displayedFeatures.setVisible(type);
}
}
}
this.colourScheme = colourScheme;
}
+ @Override
public FeaturesDisplayedI getDisplayedFeatures()
{
return displayedFeatures;
}
- public static String getJSONData(AlignViewportI av)
+ public void configureForView(AlignmentViewPanel avpanel)
{
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+ super.configureForView(avpanel);
+ AlignViewportI viewport = avpanel.getAlignViewport();
+ AlignmentI alignment = viewport.getAlignment();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+
+ seqGroups = alignment.getGroups();
+ fr = avpanel.cloneFeatureRenderer();
- for (SequenceI seq : av.getAlignment().getSequences())
- {
- jsonFile.seqs.add(seq);
- }
-
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
+ for (AlignmentAnnotation annot : annots)
{
if (annot != null && !annot.autoCalculated)
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (!annot.visible)
{
continue;
}
- jsonFile.annotations.add(annot);
+ annotations.add(annot);
}
}
- String jsonString = jsonFile.print();
- return jsonString;
+ globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
+ setDisplayedFeatures(viewport.getFeaturesDisplayed());
+ showSeqFeatures = viewport.isShowSequenceFeatures();
+
}
public boolean isShowSeqFeatures()
git://source.jalview.org / jalview.git / blobdiff