X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=a4d6d92b98964e6ab8afc925a1b9e5b9f8dee7e1;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=42afa82e1de0f95f4096b77059878d5f9275f776;hpb=d38847f4c9170385c3b4c8fbc5e6f5c95a15a196;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 42afa82..a4d6d92 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -21,22 +21,17 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertSame;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
-import jalview.io.FileParse;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
-import java.util.Arrays;
-import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
@@ -125,7 +120,11 @@ public class EnsemblSeqProxyTest
                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
-                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
+                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
+                  // ? insertion added in ENSP00000288602.11, not in P15056
+                  + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
+                  // end insertion
+                  + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
@@ -136,13 +135,13 @@ public class EnsemblSeqProxyTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+    SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
   }
 
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    SequenceOntologyFactory.setInstance(null);
+    SequenceOntologyFactory.setSequenceOntology(null);
   }
 
   @DataProvider(name = "ens_seqs")
@@ -153,22 +152,21 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+  public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
           String fastasq) throws Exception
   {
-    FileParse fp = proxy.getSequenceReader(Arrays
-            .asList(new String[] { sq }));
-    SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
-    SequenceI[] trueSqs = trueRes.getSeqsAsArray();
-    Assert.assertEquals(sqs.length, trueSqs.length,
+    SequenceI[] expected = trueRes.getSeqsAsArray();
+    AlignmentI retrieved = proxy.getSequenceRecords(sq);
+
+    Assert.assertEquals(retrieved.getHeight(), expected.length,
             "Different number of sequences retrieved for query " + sq);
-    Alignment ral = new Alignment(sqs);
-    for (SequenceI tr : trueSqs)
+
+    for (SequenceI tr : expected)
     {
       SequenceI[] rseq;
       Assert.assertNotNull(
-              rseq = ral.findSequenceMatch(tr.getName()),
+              rseq = retrieved.findSequenceMatch(tr.getName()),
               "Couldn't find sequences matching expected sequence "
                       + tr.getName());
       Assert.assertEquals(rseq.length, 1,
@@ -179,7 +177,6 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-
     }
   }
 
@@ -222,7 +219,6 @@ public class EnsemblSeqProxyTest
     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
             1, 2, 0f, null);
     sf.setValue("alleles", alleles);
-    sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 
     EnsemblSeqProxy.reverseComplementAlleles(sf);
     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
@@ -230,33 +226,5 @@ public class EnsemblSeqProxyTest
     assertEquals(revcomp, sf.getDescription());
     // verify alleles attribute is updated with reverse complement
     assertEquals(revcomp, sf.getValue("alleles"));
-    // verify attributes string is updated with reverse complement
-    assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
-  }
-
-  @Test(groups = "Functional")
-  public void testSortFeatures()
-  {
-    SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 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);
-    List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
-        sf2, sf3, sf4 });
-
-    // sort by start position ascending (forward strand)
-    // sf2 and sf3 tie and should not be reordered by sorting
-    SequenceFeatures.sortFeatures(sfs, true);
-    assertSame(sfs.get(0), sf2);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf1);
-    assertSame(sfs.get(3), sf4);
-
-    // sort by end position descending (reverse strand)
-    SequenceFeatures.sortFeatures(sfs, false);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf2);
-    assertSame(sfs.get(3), sf4);
   }
 }