/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
SequenceI sequence = (SequenceI) jvobj;
if (!sequence.getSequenceAsString().equals(sq.getSequence()))
{
- log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
+ log.warn(
+ "Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
}
else
{
{
modified |= new jalview.io.vamsas.Sequencefeature(datastore,
(jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf], dataset,
- (Sequence) vobj).docWasUpdated();
+ .getSequenceFeatures()[sf],
+ dataset, (Sequence) vobj).docWasUpdated();
}
}
return modified;
boolean modifiedthedoc = false;
SequenceI sq = (SequenceI) jvobj;
- if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
+ if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
{
// only sync database references for dataset sequences
- DBRefEntry[] entries = sq.getDBRef();
+ DBRefEntry[] entries = sq.getDBRefs();
// jalview.datamodel.DBRefEntry dbentry;
for (int db = 0; db < entries.length; db++)
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
+ // dbentry =
entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
}
for (int db = 0; db < entries.length; db++)
{
modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
+ // dbentry =
entries[db], vsq, sq).jvWasUpdated();
}
}
public void conflict()
{
- log.warn("Conflict in dataset sequence update to document. Overwriting document");
+ log.warn(
+ "Conflict in dataset sequence update to document. Overwriting document");
// TODO: could try to import from document data to jalview first. and then
updateToDoc();
}