String.valueOf(showSeqFeatures));
String[] hiddenSections = exportHiddenSections();
- if (hiddenSections != null)
+ if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
{
- jsonAlignmentPojo.getAppSettings().put("hiddenCols",
- String.valueOf(hiddenSections[0]));
- jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
- String.valueOf(hiddenSections[1]));
+ if (hiddenSections[0] != null)
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+ String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null)
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+ String.valueOf(hiddenSections[1]));
+ }
}
}
// 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 : ");
+ // 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;
}
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
: seq.getDatasetSequence().getSequenceFeatures();
+ seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+ : seqFeatures;
if (seqFeatures == null)
{
continue;
int end = Integer.valueOf(sequence.get("end").toString());
Sequence seq = new Sequence(sequenceName, sequcenceString, start,
end);
- if (hiddenSeqRefs.contains(seqUniqueId))
+ if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
{
seq.setHidden(true);
}