import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-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.SequenceFeaturesPojo;
-import jalview.json.binding.v1.SequenceGrpPojo;
-import jalview.json.binding.v1.SequencePojo;
+import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
+import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationPojo;
+import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
+import jalview.json.binding.biojson.v1.SequenceGrpPojo;
+import jalview.json.binding.biojson.v1.SequencePojo;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
private ArrayList<SequenceI> hiddenSequences;
-
public JSONFile()
{
super();
parse(getReader());
}
+
@Override
public String print()
{
if (hiddenSections != null)
{
if (hiddenSections[0] != null
- && exportSettings
- .isExportHiddenColumns())
+ && exportSettings.isExportHiddenColumns())
{
jsonAlignmentPojo.getAppSettings().put("hiddenCols",
String.valueOf(hiddenSections[0]));
}
if (hiddenSections[1] != null
- && exportSettings
- .isExportHiddenSequences())
+ && exportSettings.isExportHiddenSequences())
{
jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
String.valueOf(hiddenSections[1]));
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (exportSettings.isExportGroups()
- && seqGroups != null
+ if (exportSettings.isExportGroups() && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
List<SequenceI> seqs, FeatureRenderer fr)
{
- displayedFeatures = (fr == null) ? null : fr
- .getFeaturesDisplayed();
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
for (SequenceI seq : seqs)
{
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr
- .findFeatureColour(Color.white, seq,
+ .getHexString(fr.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
}
ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
- grpColourScheme,
- displayBoxes, displayText, colourText, startRes, endRes);
+ grpColourScheme, displayBoxes, displayText, colourText,
+ startRes, endRes);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
String desc = annot.get("description") == null ? null : annot
.get("description").toString();
- char ss = annot.get("secondaryStructure") == null ? ' '
- : annot.get("secondaryStructure").toString().charAt(0);
- String displayChar = annot.get("displayCharacter").toString();
+ char ss = annot.get("secondaryStructure") == null ? ' ' : annot
+ .get("secondaryStructure").toString().charAt(0);
+ String displayChar = annot.get("displayCharacter") == null ? ""
+ : annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
}
{
hiddenSeqRefs = new ArrayList<String>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
- if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+ if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
+ {
String[] seqRefs = hiddenSeqs.split(";");
- for(String seqRef : seqRefs){
+ for (String seqRef : seqRefs)
+ {
hiddenSeqRefs.add(seqRef);
}
}
public void parseHiddenCols(JSONObject jvSettingsJson)
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
- if(hiddenCols != null && !hiddenCols.isEmpty()){
+ if (hiddenCols != null && !hiddenCols.isEmpty())
+ {
columnSelection = new ColumnSelection();
String[] rangeStrings = hiddenCols.split(";");
- for(String rangeString : rangeStrings){
+ for (String rangeString : rangeStrings)
+ {
String[] range = rangeString.split("-");
columnSelection.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
this.displayedFeatures = displayedFeatures;
}
-
public void configureForView(AlignmentViewPanel avpanel)
{
super.configureForView(avpanel);
{
if (hiddenSequences == null || hiddenSequences.isEmpty())
{
- return new SequenceI[]
- {};
+ return new SequenceI[] {};
}
synchronized (hiddenSequences)
{