X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=72f5a348cd89c495742b7d606d79e1e78d1fef22;hb=da31d3e5aebfcdbb1ae7084bbc75bbc3539ee2e6;hp=c525e95317d3f5df95df921b25b45e275b1ebaa7;hpb=56b5f4d5ca50971a34c9284bbb4b0507f7ba8a71;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index c525e95..72f5a34 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,27 +1,60 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+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.net.MalformedURLException;
-import java.net.URL;
 import java.util.Arrays;
 import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-
 public class EnsemblSeqProxyTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private static final Object[][] allSeqs = new Object[][] {
       {
           new EnsemblProtein(),
@@ -93,7 +126,11 @@ 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"
@@ -101,20 +138,16 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
-  @DataProvider(name = "queries")
-  public Object[][] createQueryData(Method m)
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
   {
-    return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @Test(dataProvider = "queries")
-  public void testIsValidReference(String query) throws Exception
+  @AfterClass(alwaysRun = true)
+  public void tearDown()
   {
-    EnsemblSequenceFetcher esq = new EnsemblProtein();
-    Assert.assertTrue(esq.isValidReference(query),
-            "Expected reference string " + query
-                    + " to be valid for regex "
-                    + esq.getAccessionValidator().toString());
+    SequenceOntologyFactory.setInstance(null);
   }
 
   @DataProvider(name = "ens_seqs")
@@ -125,23 +158,21 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
-          throws Exception
+  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, AppletFormatAdapter.PASTE);
-    SequenceI[] trueSqs = trueRes.getSeqsAsArray();
-    Assert.assertEquals(sqs.length, trueSqs.length,
+    FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
+    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,
@@ -152,132 +183,83 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-  
     }
   }
 
-  @Test(suiteName = "live")
-  public void testLiveCheckEnsembl()
+  @Test(groups = "Functional")
+  public void getGenomicRangesFromFeatures()
   {
-    EnsemblRestClient sf = new EnsemblRestClient()
-    {
-
-      @Override
-      public String getDbName()
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      public AlignmentI getSequenceRecords(String queries) throws Exception
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      protected URL getUrl(List<String> ids) throws MalformedURLException
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
 
-      @Override
-      protected boolean useGetRequest()
-      {
-        // TODO Auto-generated method stub
-        return false;
-      }
-
-      @Override
-      protected String getRequestMimeType(boolean b)
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-      @Override
-      protected String getResponseMimeType()
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-
-    };
-    boolean isAvailable = sf.isEnsemblAvailable();
-    System.out.println("Ensembl is "
-            + (isAvailable ? "UP!"
-                    : "DOWN or unreachable ******************* BAD!"));
   }
 
   /**
-   * Tests for the method that computes all peptide variants given codon
-   * variants
+   * Test the method that appends a single allele's reverse complement to a
+   * string buffer
    */
   @Test(groups = "Functional")
-  public void testComputePeptideVariants()
+  public void testReverseComplementAllele()
   {
-    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());
+    StringBuilder sb = new StringBuilder();
+    EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
+    EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
+    EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
+    EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
+    EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
+    assertEquals("C,c,G,A,T", sb.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());
+    sb = new StringBuilder();
+    EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
+    EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
+    EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
+    assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.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());
+  /**
+   * Test the method that computes the reverse complement of the alleles in a
+   * sequence_variant feature
+   */
+  @Test(groups = "Functional")
+  public void testReverseComplementAlleles()
+  {
+    String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
+    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");
 
-    /*
-     * 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());
+    EnsemblSeqProxy.reverseComplementAlleles(sf);
+    String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
+    // verify description is updated with reverse complement
+    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());
+  }
 
-    /*
-     * 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());
+  @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 });
 
-    /*
-     * 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());
+    // 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);
 
-    /*
-     * 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());
+    // 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);
   }
-}
\ No newline at end of file
+}