import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.Uniprot;
import java.util.ArrayList;
List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
SequenceFetcher sfetcher = new SequenceFetcher();
boolean pdbFound = false;
List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
SequenceFetcher sfetcher = new SequenceFetcher();
boolean pdbFound = false;
SequenceI seq = alsq.getSequenceAt(0);
assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+ retrievalId, seq.getName());
SequenceI seq = alsq.getSequenceAt(0);
assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+ retrievalId, seq.getName());
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- assertNotNull("Sequence features missing", sfs);
+ List<SequenceFeature> sfs = seq.getSequenceFeatures();
+ assertFalse("Sequence features missing", sfs.isEmpty());
- sfs[0].getType()));
- assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
- DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
- new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
- DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+ sfs.get(0).getType()));
+ assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
+ DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[] { DBRefSource.UNIPROT });
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
assertEquals("Expected cross reference map to be one amino acid", dr[0]
.getMap().getMappedWidth(), 1);
assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
.getMap().getWidth(), 3);
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
assertEquals("Expected cross reference map to be one amino acid", dr[0]
.getMap().getMappedWidth(), 1);
assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
.getMap().getWidth(), 3);
- AlignmentI sprods = CrossRef.findXrefSequences(
- alsq.getSequencesArray(), true, dr[0].getSource(),
- alsq.getDataset());
+ AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+ .findXrefSequences(dr[0].getSource(), true);