X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=f9c2c4b70e4b4e168c166cde07897d75af72115b;hb=6c52cc0b81ae3abdc3c5f6f88a23364a0246351a;hp=5d95a3cb41cea5da6b704ff58dddc9f0229bc095;hpb=b2cedc8371f6624859f107581e6d84e841d4114b;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 5d95a3c..f9c2c4b 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -4,17 +4,15 @@ import static org.testng.AssertJUnit.assertEquals;
 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;
@@ -216,149 +214,12 @@ public class EnsemblSeqProxyTest
                     : "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()
   {