X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;fp=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=f75223512736dac65ef6243a842e8df15b86a698;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
deleted file mode 100644
index f752235..0000000
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ /dev/null
@@ -1,206 +0,0 @@
-/*
- * 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.ws.seqfetcher;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.analysis.CrossRef;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.dbsources.Uniprot;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-/**
- * @author jimp
- * 
- */
-public class DbRefFetcherTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  /**
-   * @throws java.lang.Exception
-   */
-  @BeforeClass(alwaysRun = true)
-  public static void setUpBeforeClass() throws Exception
-  {
-    jalview.bin.Cache.initLogger();
-  }
-
-  /**
-   * @throws java.lang.Exception
-   */
-  @AfterClass(alwaysRun = true)
-  public static void tearDownAfterClass() throws Exception
-  {
-  }
-
-  /**
-   * Tests that standard protein database sources include Uniprot (as the first)
-   * and also PDB. (Additional sources are dependent on availability of DAS
-   * services.)
-   */
-  @Test(groups = { "Functional" })
-  public void testStandardProtDbs()
-  {
-    List<String> defdb = new ArrayList<>();
-    defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
-    defdb.add(DBRefSource.PDB);
-    List<DbSourceProxy> srces = new ArrayList<>();
-    SequenceFetcher sfetcher = SequenceFetcher.getInstance();
-    boolean pdbFound = false;
-
-    for (String ddb : defdb)
-    {
-      List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-
-      if (srcesfordb != null)
-      {
-        // TODO is this right? get duplicate entries
-        srces.addAll(srcesfordb);
-      }
-    }
-
-    int i = 0;
-    int uniprotPos = -1;
-    for (DbSourceProxy s : srces)
-    {
-      if (s instanceof Uniprot && uniprotPos == -1)
-      {
-        uniprotPos = i;
-      }
-      if (s instanceof Pdb)
-      {
-        pdbFound = true;
-      }
-      i++;
-    }
-
-    assertTrue("Failed to find Uniprot source as first source amongst "
-            + srces.size() + " sources (source was at position "
-            + uniprotPos + ")", uniprotPos == 0);
-    assertTrue("Failed to find PDB source amongst " + srces.size()
-            + " sources", pdbFound);
-  }
-
-  /**
-   * Tests retrieval of one entry from EMBL. Test is dependent on availability
-   * of network and the EMBL service.
-   * 
-   * @throws Exception
-   */
-  @Test(groups = { "External" })
-  public void testEmblUniprotProductRecovery() throws Exception
-  {
-    String retrievalId = "V00488";
-    DbSourceProxy embl = SequenceFetcher.getInstance().getSourceProxy(
-            DBRefSource.EMBL).get(0);
-    assertNotNull("Couldn't find the EMBL retrieval client", embl);
-    verifyProteinNucleotideXref(retrievalId, embl);
-  }
-
-  /**
-   * Tests retrieval of one entry from EMBLCDS. Test is dependent on
-   * availability of network and the EMBLCDS service.
-   * 
-   * @throws Exception
-   */
-  @Test(groups = { "External" })
-  public void testEmblCDSUniprotProductRecovery() throws Exception
-  {
-    String retrievalId = "AAH29712";
-    DbSourceProxy embl = SequenceFetcher.getInstance()
-            .getSourceProxy(
-            DBRefSource.EMBLCDS).get(0);
-    assertNotNull("Couldn't find the EMBL retrieval client", embl);
-    verifyProteinNucleotideXref(retrievalId, embl);
-  }
-
-  /**
-   * Helper method to perform database retrieval and verification of results.
-   * 
-   * @param retrievalId
-   * @param embl
-   * @throws Exception
-   */
-  private void verifyProteinNucleotideXref(String retrievalId,
-          DbSourceProxy embl) throws Exception
-  {
-    AlignmentI alsq = embl.getSequenceRecords(retrievalId);
-    assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
-    assertEquals("Didn't retrieve right number of records", 1,
-            alsq.getHeight());
-    SequenceI seq = alsq.getSequenceAt(0);
-    assertEquals("Wrong sequence name", embl.getDbSource() + "|"
-            + retrievalId, seq.getName());
-    List<SequenceFeature> sfs = seq.getSequenceFeatures();
-    assertFalse("Sequence features missing", sfs.isEmpty());
-    assertTrue(
-            "Feature not CDS",
-            FeatureProperties.isCodingFeature(embl.getDbSource(),
- sfs.get(0).getType()));
-    assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
-    List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
-            new String[] { DBRefSource.UNIPROT });
-    assertNotNull(dr);
-    assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
-    assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
-            .getMap().getMappedWidth(), 1);
-    assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
-            .getMap().getWidth(), 3);
-    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
-            .findXrefSequences(dr.get(0).getSource(), true);
-    assertNotNull(
-            "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
-            sprods);
-    assertEquals("Didn't xref right number of records", 1,
-            sprods.getHeight());
-    SequenceI proteinSeq = sprods.getSequenceAt(0);
-    assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
-            .getSequenceAsString());
-    assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
-            proteinSeq.getName());
-  }
-}