X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=aa2c315d10a10ae384d93654d2408f691c270d6e;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=f9c2c4b70e4b4e168c166cde07897d75af72115b;hpb=6c52cc0b81ae3abdc3c5f6f88a23364a0246351a;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index f9c2c4b..aa2c315 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,22 +1,42 @@
+/*
+ * 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.analysis.AlignmentUtils;
 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;
 
@@ -26,9 +46,16 @@ 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(),
@@ -108,13 +135,13 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -128,14 +155,13 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
-          throws Exception
+  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+          String fastasq) throws Exception
   {
     FileParse fp = proxy.getSequenceReader(Arrays
-            .asList(new String[]
-    { sq }));
+            .asList(new String[] { sq }));
     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
-    FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
+    FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
     Assert.assertEquals(sqs.length, trueSqs.length,
             "Different number of sequences retrieved for query " + sq);
@@ -155,63 +181,8 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-  
-    }
-  }
-
-  @Test(suiteName = "live")
-  public void testLiveCheckEnsembl()
-  {
-    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!"));
+    }
   }
 
   @Test(groups = "Functional")
@@ -247,4 +218,75 @@ public class EnsemblSeqProxyTest
     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
   }
-}
\ No newline at end of file
+
+  /**
+   * Test the method that appends a single allele's reverse complement to a
+   * string buffer
+   */
+  @Test(groups = "Functional")
+  public void testReverseComplementAllele()
+  {
+    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());
+
+    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());
+  }
+
+  /**
+   * 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");
+
+    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());
+  }
+
+  @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);
+  }
+}