import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.DasSourceBrowser;
import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
import java.util.Vector;
import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
/**
* Implements a runnable for validating a sequence against external databases
/**
* picr client instance
*/
- uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
+ AccessionMapperInterface picrClient = null;
// /This will be a collection of Vectors of sequenceI refs.
// The key will be the seq name or accession id of the seq
{
alseqs[i] = seqs[i];
if (seqs[i].getDatasetSequence() != null)
+ {
ds[i] = seqs[i].getDatasetSequence();
+ }
else
+ {
ds[i] = seqs[i];
+ }
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
{
// af.featureSettings_actionPerformed(null);
String[] defdb = null, otherdb = sfetcher
- .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ .getDbInstances(DasSequenceSource.class);
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
- .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+ .getSelectedSources() : new DasSourceBrowser()
.getSelectedSources();
Enumeration<jalviewSourceI> en = dasselsrc.elements();
while (en.hasMoreElements())
}
// append additional sources
DbSourceProxy[] otherdb = sfetcher
- .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ .getDbSourceProxyInstances(DasSequenceSource.class);
if (otherdb != null && otherdb.length > 0)
{
DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+ picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
}
} catch (Exception e)
int seqIndex = 0;
- jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+ DbSourceProxy dbsource = dbSources[db];
{
// for moment, we dumbly iterate over all retrieval sources for a
// particular database
AlignmentI retrieved = null;
try
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Querying "
+ Cache.log.debug("Querying "
+ dbsource.getDbName() + " with : '"
+ queryString.toString() + "'");
}
for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
{
SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+ DBRefEntry[] uprefs = DBRefUtils.selectRefs(
sequence.getDBRef(), new String[]
{ dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// taking into account all accessionIds and names in the file
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+ DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
entry.getDBRef(), new String[]
{ dbSource });
if (entryRefs == null)
int absStart = entrySeq.indexOf(nonGapped);
int mapStart = entry.getStart();
- jalview.datamodel.Mapping mp;
+ Mapping mp;
if (absStart == -1)
{
{
nseq.addElement(sequencesArray[i]);
DBRefEntry dbr[] = sequencesArray[i].getDBRef();
- jalview.datamodel.Mapping map = null;
+ Mapping map = null;
for (int r = 0; (dbr != null) && r < dbr.length; r++)
{
if ((map = dbr[r].getMap()) != null)