X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=69b2ad48a75b9c681b737e30c1078f468999fa3c;hb=f59dd9efbb3dfc313ab0b0507832e21cd0076fe1;hp=71f0212a2cc07d3a7aad3a26e45d3434374c5a85;hpb=0ae70dbd95d7eb6932c1ec1252628f58f0989668;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 71f0212..69b2ad4 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,23 +1,39 @@
+/*
+ * 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.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import static org.testng.AssertJUnit.assertSame;
 
-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;
 
@@ -27,9 +43,16 @@ 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(),
@@ -101,7 +124,11 @@ 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"
@@ -109,13 +136,13 @@ 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);
@@ -129,23 +156,21 @@ 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,
@@ -156,99 +181,15 @@ 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")
   public void getGenomicRangesFromFeatures()
   {
 
   }
 
-  @Test(groups = "Functional")
-  public void testIsTranscriptIdentifier()
-  {
-    EnsemblSeqProxy testee = new EnsemblGene();
-    assertFalse(testee.isTranscriptIdentifier(null));
-    assertFalse(testee.isTranscriptIdentifier(""));
-    assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
-    assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
-    assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
-    assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
-    assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
-    assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
-  }
-
-  @Test(groups = "Functional")
-  public void testIsGeneIdentifier()
-  {
-    EnsemblSeqProxy testee = new EnsemblGene();
-    assertFalse(testee.isGeneIdentifier(null));
-    assertFalse(testee.isGeneIdentifier(""));
-    assertFalse(testee.isGeneIdentifier("ENST00000012345"));
-    assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
-    assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
-    assertFalse(testee.isGeneIdentifier("ensg00000012345"));
-    assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
-    assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
-  }
-
   /**
    * Test the method that appends a single allele's reverse complement to a
    * string buffer
@@ -301,15 +242,22 @@ public class EnsemblSeqProxyTest
     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
-    SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+    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
-    EnsemblSeqProxy.sortFeatures(sfs, true);
-    assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+    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)
-    EnsemblSeqProxy.sortFeatures(sfs, false);
-    assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+    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
+}