import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
FileParse fp = proxy.getSequenceReader(Arrays
.asList(new String[] { sq }));
SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
FileParse fp = proxy.getSequenceReader(Arrays
.asList(new String[] { sq }));
SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
SequenceI[] trueSqs = trueRes.getSeqsAsArray();
Assert.assertEquals(sqs.length, trueSqs.length,
"Different number of sequences retrieved for query " + sq);
SequenceI[] trueSqs = trueRes.getSeqsAsArray();
Assert.assertEquals(sqs.length, trueSqs.length,
"Different number of sequences retrieved for query " + sq);
SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
// sort by start position ascending (forward strand)
// sf2 and sf3 tie and should not be reordered by sorting
// sort by start position ascending (forward strand)
// sf2 and sf3 tie and should not be reordered by sorting
- EnsemblSeqProxy.sortFeatures(sfs, true);
- assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertSame(sfs.get(0), sf2);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf1);
+ assertSame(sfs.get(3), sf4);
- EnsemblSeqProxy.sortFeatures(sfs, false);
- assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);