private String application = "Jalview";
- public static final String FILE_EXT = "json";
-
- public static final String FILE_DESC = "JSON";
-
private String globalColourScheme;
private boolean showSeqFeatures;
super(source);
}
- public JSONFile(String inFile, String type) throws IOException
+ public JSONFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
@Override
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
String jsonOutput = null;
try
}
int count = 0;
- for (SequenceI seq : seqs)
+ for (SequenceI seq : sqs)
{
StringBuilder name = new StringBuilder();
name.append(seq.getName()).append("/").append(seq.getStart())
if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+ .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
}
if (exportSettings.isExportGroups() && seqGroups != null
}
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- List<SequenceI> seqs, FeatureRenderer fr)
+ SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
- for (SequenceI seq : seqs)
+ if (sqs == null)
+ {
+ return sequenceFeaturesPojo;
+ }
+
+ for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null