import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
-import jalview.util.MappingUtils;
import java.lang.reflect.Method;
import java.net.MalformedURLException;
: "DOWN or unreachable ******************* BAD!"));
}
- /**
- * Tests for the method that computes all peptide variants given codon
- * variants
- */
- @Test(groups = "Functional")
- public void testComputePeptideVariants()
- {
- String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
-
- /*
- * AGT codes for S - this is not included in the variants returned
- */
- List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[]", variants.toString());
-
- // S is reported if it differs from the current value (A):
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
- assertEquals("[S]", variants.toString());
-
- /*
- * synonymous variant is not reported
- */
- codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
- // AGC and AGT both code for S
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
- assertEquals("[]", variants.toString());
-
- /*
- * equivalent variants are only reported once
- */
- codonVariants = new String[][] { { "C" }, { "T" },
- { "A", "C", "G", "T" } };
- // CTA CTC CTG CTT all code for L
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[L]", variants.toString());
-
- /*
- * vary codons 1 and 2; variant products are sorted and non-redundant
- */
- codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
- // aga ata cga cta code for R, I, R, L
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[I, L, R]", variants.toString());
-
- /*
- * vary codons 2 and 3
- */
- codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
- // aga agc ata atc code for R, S, I, I
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[I, R]", variants.toString());
-
- /*
- * vary codons 1 and 3
- */
- codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
- // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[K, N, Y, STOP]", variants.toString());
-
- /*
- * vary codons 1, 2 and 3
- */
- codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
- { "t", "g" } };
- // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[C, R, T, W]", variants.toString());
- }
-
- /**
- * Tests for the method that maps the subset of a dna sequence that has CDS
- * (or subtype) feature.
- */
- @Test(groups = "Functional")
- public void testGetCdsRanges()
- {
- EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
-
- SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
- dnaSeq.createDatasetSequence();
- SequenceI ds = dnaSeq.getDatasetSequence();
-
- // CDS for dna 3-6
- SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
- ds.addSequenceFeature(sf);
- // exon feature should be ignored here
- sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
- ds.addSequenceFeature(sf);
- // CDS for dna 10-12
- sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
- ds.addSequenceFeature(sf);
-
- List<int[]> ranges = testee.getCdsRanges(dnaSeq);
- assertEquals(6, MappingUtils.getLength(ranges));
- assertEquals(2, ranges.size());
- assertEquals(4, ranges.get(0)[0]);
- assertEquals(6, ranges.get(0)[1]);
- assertEquals(10, ranges.get(1)[0]);
- assertEquals(12, ranges.get(1)[1]);
-
- }
-
@Test(groups = "Functional")
public void getGenomicRangesFromFeatures()
{
}
- /**
- * Tests for the method that maps the subset of a dna sequence that has CDS
- * (or subtype) feature - case where the start codon is incomplete.
- */
- @Test(groups = "Functional")
- public void testGetCdsRanges_fivePrimeIncomplete()
- {
- EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
-
- SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
- dnaSeq.createDatasetSequence();
- SequenceI ds = dnaSeq.getDatasetSequence();
-
- // CDS for dna 5-6 (incomplete codon), 7-9
- SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
- sf.setPhase("2"); // skip 2 bases to start of next codon
- ds.addSequenceFeature(sf);
- // CDS for dna 13-15
- sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
- ds.addSequenceFeature(sf);
-
- List<int[]> ranges = testee.getCdsRanges(dnaSeq);
-
- /*
- * check the mapping starts with the first complete codon
- */
- assertEquals(6, MappingUtils.getLength(ranges));
- assertEquals(2, ranges.size());
- assertEquals(7, ranges.get(0)[0]);
- assertEquals(9, ranges.get(0)[1]);
- assertEquals(13, ranges.get(1)[0]);
- assertEquals(15, ranges.get(1)[1]);
- }
-
@Test(groups = "Functional")
public void testIsTranscriptIdentifier()
{
git://source.jalview.org / jalview.git / blobdiff