import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.CutAndPasteTransfer;
-import jalview.gui.DasSourceBrowser;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
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;
{
private static final String NEWLINE = System.lineSeparator();
+ public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
public interface FetchFinishedListenerI
{
void finished();
DbSourceProxy[] sources, FeatureSettings featureSettings,
boolean isNucleotide)
{
- listeners = new ArrayList<FetchFinishedListenerI>();
+ listeners = new ArrayList<>();
this.progressWindow = progressIndicatorFrame;
alseqs = new SequenceI[seqs.length];
SequenceI[] ds = new SequenceI[seqs.length];
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(progressIndicatorFrame);
+ sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
// set default behaviour for transferring excess sequence data to the
// dataset
- trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+ trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
if (sources == null)
{
setDatabaseSources(featureSettings, isNucleotide);
{
// af.featureSettings_actionPerformed(null);
String[] defdb = null;
- List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
- ? featureSettings.getSelectedSources()
- : new DasSourceBrowser().getSelectedSources();
-
- for (jalviewSourceI src : dasselsrc)
- {
- List<DbSourceProxy> sp = src.getSequenceSourceProxies();
- if (sp != null)
- {
- selsources.addAll(sp);
- if (sp.size() > 1)
- {
- Cache.log.debug("Added many Db Sources for :" + src.getTitle());
- }
- }
- }
+ List<DbSourceProxy> selsources = new ArrayList<>();
// select appropriate databases based on alignFrame context.
if (forNucleotide)
{
{
defdb = DBRefSource.PROTEINDBS;
}
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ List<DbSourceProxy> srces = new ArrayList<>();
for (String ddb : defdb)
{
List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
}
/**
- * retrieve all the das sequence sources and add them to the list of db
- * sources to retrieve from
- */
- public void appendAllDasSources()
- {
- if (dbSources == null)
- {
- dbSources = new DbSourceProxy[0];
- }
- // append additional sources
- DbSourceProxy[] otherdb = sfetcher
- .getDbSourceProxyInstances(DasSequenceSource.class);
- if (otherdb != null && otherdb.length > 0)
- {
- DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
- + otherdb.length];
- System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
- System.arraycopy(otherdb, 0, newsrc, dbSources.length,
- otherdb.length);
- dbSources = newsrc;
- }
- }
-
- /**
* start the fetcher thread
*
* @param waitTillFinished
}
else if (seqs == null)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
seqs.addElement(seq);
}
}
else
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
seqs.addElement(seq);
}
e.printStackTrace();
}
- Vector<SequenceI> sdataset = new Vector<SequenceI>(
+ Vector<SequenceI> sdataset = new Vector<>(
Arrays.asList(dataset));
- List<String> warningMessages = new ArrayList<String>();
+ List<String> warningMessages = new ArrayList<>();
int db = 0;
while (sdataset.size() > 0 && db < dbSources.length)
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
sdataset.copyInto(currSeqs);// seqs that are to be validated against
// dbSources[db]
- Vector<String> queries = new Vector<String>(); // generated queries curSeq
- seqRefs = new Hashtable<String, Vector<SequenceI>>();
+ Vector<String> queries = new Vector<>(); // generated queries curSeq
+ seqRefs = new Hashtable<>();
int seqIndex = 0;
{
// Work out which sequences this sequence matches,
// taking into account all accessionIds and names in the file
- Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
+ Vector<SequenceI> sequenceMatches = new Vector<>();
// look for corresponding accession ids
DBRefEntry[] entryRefs = DBRefUtils
.selectRefs(retrievedSeq.getDBRefs(), new String[]
if (updateRefFrame)
{
- SequenceFeature[] sfs = sequence.getSequenceFeatures();
- if (sfs != null)
+ /*
+ * relocate existing sequence features by offset
+ */
+ int startShift = absStart - sequenceStart + 1;
+ if (startShift != 0)
{
- /*
- * relocate existing sequence features by offset
- */
- int start = sequenceStart;
- int end = sequence.getEnd();
- int startShift = 1 - absStart - start;
-
- if (startShift != 0)
- {
- for (SequenceFeature sf : sfs)
- {
- if (sf.getBegin() >= start && sf.getEnd() <= end)
- {
- sf.setBegin(sf.getBegin() + startShift);
- sf.setEnd(sf.getEnd() + startShift);
- modified = true;
- }
- }
- }
+ modified |= sequence.getFeatures().shiftFeatures(1,
+ startShift);
}
}
}
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector<SequenceI> nseq = new Vector<SequenceI>();
+ Vector<SequenceI> nseq = new Vector<>();
for (int i = 0; sequencesArray != null
&& i < sequencesArray.length; i++)
{