package jalview.io.vamsas;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
+import java.util.List;
+
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Sequence;
// private AlignmentI jvdset;
public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
- SequenceI sq, String dict, DataSet dataset)
+ SequenceI sq, String theDict, DataSet theDataset)
{
super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
- this.dataset = dataset;
+ this.dataset = theDataset;
// this.jvdset = jvdset;
- this.dict = dict;
+ this.dict = theDict;
doSync();
}
doJvUpdate();
}
+ @Override
public void addFromDocument()
{
Sequence vseq = (Sequence) vobj;
modified = true;
}
+ @Override
public void updateFromDoc()
{
Sequence sq = (Sequence) vobj;
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
{
*/
private boolean updateSqFeatures()
{
- boolean modified = false;
+ boolean changed = false;
SequenceI sq = (SequenceI) jvobj;
// add or update any new features/references on dataset sequence
- if (sq.getSequenceFeatures() != null)
+ List<SequenceFeature> sfs = sq.getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- int sfSize = sq.getSequenceFeatures().length;
-
- for (int sf = 0; sf < sfSize; sf++)
- {
- modified |= new jalview.io.vamsas.Sequencefeature(datastore,
- (jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf], dataset,
- (Sequence) vobj).docWasUpdated();
- }
+ changed |= new jalview.io.vamsas.Sequencefeature(datastore, sf,
+ dataset, (Sequence) vobj).docWasUpdated();
}
- return modified;
+
+ return changed;
}
+ @Override
public void addToDocument()
{
SequenceI sq = (SequenceI) jvobj;
if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
{
// only sync database references for dataset sequences
- DBRefEntry[] entries = sq.getDBRefs();
+ List<DBRefEntry> entries = sq.getDBRefs();
// jalview.datamodel.DBRefEntry dbentry;
- for (int db = 0; db < entries.length; db++)
+ for (int db = 0, dn = entries.size(); db < dn; db++)
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
- entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
+ // dbentry =
+ entries.get(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();
}
}
return modifiedtheseq;
}
+ @Override
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();
}
boolean modified = false;
+ @Override
public void updateToDoc()
{
SequenceI sq = (SequenceI) jvobj;