import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Map;
import uk.ac.vamsas.objects.core.Sequence;
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Map;
import uk.ac.vamsas.objects.core.Sequence;
uk.ac.vamsas.objects.core.Sequence sequence = null;
DataSet ds;
public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
uk.ac.vamsas.objects.core.Sequence sequence = null;
DataSet ds;
public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
- jalview.datamodel.SequenceI sq2,
- uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
+ SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2,
+ DataSet dataset)
{
super(datastore, dbentry, DbRef.class);
// initialise object specific attributes
{
super(datastore, dbentry, DbRef.class);
// initialise object specific attributes
public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
SequenceI dsseq)
{
public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
SequenceI dsseq)
{
{
log.info("Performing updateMapTo remove this message when we know what we're doing.");
// TODO determine how sequences associated with database mappings are stored
{
log.info("Performing updateMapTo remove this message when we know what we're doing.");
// TODO determine how sequences associated with database mappings are stored
- : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
- : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
+ : ((mp.getMappedWidth() == 3) ? SymbolDictionary.STANDARD_NA
+ : SymbolDictionary.STANDARD_AA),
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
.toString(), vobj.getVersion().toString(), vobj
.getAccessionId().toString()));
if (vobj.getMapCount() > 0)
.toString(), vobj.getVersion().toString(), vobj
.getAccessionId().toString()));
if (vobj.getMapCount() > 0)
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}