X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=d4574c0d3be32c489ac283be57e2dd5cdeba9283;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=e6066658e41b59dc2e3921cd4ac1c289b744de0b;hpb=3ef44bef1f825d26977dedd1608469712a87fe15;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index e606665..d4574c0 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -1,12 +1,29 @@
+/*
+ * 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.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -14,15 +31,29 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 public class DBRefUtilsTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test the method that selects DBRefEntry items whose source is in a supplied
    * list
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSelectRefs()
   {
     assertNull(DBRefUtils.selectRefs(null, null));
@@ -32,41 +63,45 @@ public class DBRefUtilsTest
     DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
     // Source is converted to upper-case by this constructor!
     DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
-    DBRefEntry[] dbrefs = new DBRefEntry[]
-    { ref1, ref2, ref3 };
-    String[] sources = new String[]
-    { "EMBL", "UNIPROT" };
-
-    DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(3, selected.length);
-    assertSame(ref1, selected[0]);
-    assertSame(ref2, selected[1]);
-    assertSame(ref3, selected[2]);
-
-    sources = new String[]
-    { "EMBL" };
+    List<DBRefEntry> dbrefs = Arrays
+            .asList(new DBRefEntry[]
+            { ref1, ref2, ref3 });
+    String[] sources = new String[] { "EMBL", "UNIPROT" };
+
+    List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
+    assertEquals(3, selected.size());
+    assertSame(ref1, selected.get(0));
+    assertSame(ref2, selected.get(1));
+    assertSame(ref3, selected.get(2));
+
+    sources = new String[] { "EMBL" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(1, selected.length);
-    assertSame(ref1, selected[0]);
+    assertEquals(1, selected.size());
+    assertSame(ref1, selected.get(0));
 
-    sources = new String[]
-    { "UNIPROT" };
+    sources = new String[] { "UNIPROT" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
-    assertEquals(2, selected.length);
-    assertSame(ref2, selected[0]);
-    assertSame(ref3, selected[1]);
+    assertEquals(2, selected.size());
+    assertSame(ref2, selected.get(0));
+    assertSame(ref3, selected.get(1));
 
-    sources = new String[]
-    { "Uniprot", "EMBLCDS" };
+    sources = new String[] { "EMBLCDS" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertNull(selected);
+
+    sources = new String[] { "embl", "uniprot" };
+    selected = DBRefUtils.selectRefs(dbrefs, sources);
+    assertEquals(3, selected.size());
+    assertSame(ref1, selected.get(0));
+    assertSame(ref2, selected.get(1));
+    assertSame(ref3, selected.get(2));
   }
 
   /**
    * Test the method that converts (currently three) database names to a
    * canonical name (not case-sensitive)
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetCanonicalName()
   {
     assertNull(DBRefUtils.getCanonicalName(null));
@@ -75,92 +110,76 @@ public class DBRefUtilsTest
     assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
     assertEquals("UNIPROT",
             DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
-    assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
+    assertEquals("UNIPROT",
+            DBRefUtils.getCanonicalName("uniprotkb/trembl"));
     assertEquals("UNIPROT",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
-    assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
+    assertEquals("UNIPROT",
+            DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
     assertEquals("UNIPROTKB/SWISS-CHEESE",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
-  }
+    assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
+
+    // these are not 'known' to Jalview
+    assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+    assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
 
-  @Test
-  public void testIsDasCoordinateSystem()
-  {
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
-            "PDB", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("PDB", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
-            new DBRefEntry("PDB", "v1", "a1")));
-    // "pdb" is converted to upper-case in DBRefEntry constructor
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("pdb", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
-            "pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
-            "Uniprot", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
-            "UNIPROT", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
-            new DBRefEntry(
-            "pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
-            "EMBL", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
-            "embl", "v1", "a1")));
   }
 
   /**
    * Test 'parsing' a DBRef - non PDB case
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testParseToDbRef()
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
-    DBRefEntry[] refs = seq.getDBRef();
-    assertEquals(1, refs.length);
-    assertSame(ref, refs[0]);
+    List<DBRefEntry> refs = seq.getDBRefs();
+    assertEquals(1, refs.size());
+    assertSame(ref, refs.get(0));
     assertEquals("EMBL", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
-    assertNull(seq.getPDBId());
+    assertTrue(seq.getAllPDBEntries().isEmpty());
+    SequenceI seq2 = new Sequence("Seq2", "ABCD");
+    // Check that whitespace doesn't confuse parseToDbRef
+    DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
+            " a7890");
+    assertEquals(ref, ref2);
   }
 
   /**
    * Test 'parsing' a DBRef - Stockholm PDB format
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testParseToDbRef_PDB()
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
-    DBRefEntry[] refs = seq.getDBRef();
-    assertEquals(1, refs.length);
-    assertSame(ref, refs[0]);
+    // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+    // PDB ref in Stockholm
+
+    List<DBRefEntry> refs = seq.getDBRefs();
+    assertEquals(1, refs.size());
+    assertSame(ref, refs.get(0));
     assertEquals("PDB", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     // DBRef id is pdbId + chain code
     assertEquals("1WRIA", ref.getAccessionId());
-    assertEquals(1, seq.getPDBId().size());
-    PDBEntry pdbRef = seq.getPDBId().get(0);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
     assertEquals("1WRI", pdbRef.getId());
     assertNull(pdbRef.getFile());
-    assertEquals("A", pdbRef.getProperty().get("CHAIN"));
-    assertNull(pdbRef.getType());
+    assertEquals("A", pdbRef.getChainCode());
+    assertEquals("PDB", pdbRef.getType());
   }
 
   /**
    * Test the method that searches for matches references - case when we are
    * matching a reference with no mappings
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSearchRefs_noMapping()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
@@ -173,50 +192,114 @@ public class DBRefUtilsTest
     DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
     // ref5 matches although it has a mapping - ignored
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
-    ref5.setMap(new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1)));
-
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
-    { ref1, ref2, ref3, ref4, ref5 }, target);
-    assertEquals(3, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
-    assertSame(ref5, matches[2]);
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
+
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 }), target,
+                    DBRefUtils.SEARCH_MODE_FULL);
+    assertEquals(3, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
   }
 
   /**
    * Test the method that searches for matches references - case when we are
    * matching a reference with a mapping
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSearchRefs_withMapping()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
-    final Mapping map1 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1));
+    final Mapping map1 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1));
     target.setMap(map1);
 
     // these all match target iff mappings match
     DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
     DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
-    final Mapping map2 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 1, 1));
+    final Mapping map2 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1));
     ref2.setMap(map2);
 
     // different map: no match
     DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
-    final Mapping map3 = new Mapping(new MapList(new int[]
-    { 1, 1 }, new int[]
-    { 1, 1 }, 2, 2));
+    final Mapping map3 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[]
-    { ref1, ref2, ref3 }, target);
-    assertEquals(2, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
+    assertEquals(2, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+  }
+
+  /**
+   * Test the method that searches for matching references based on accession id
+   * only
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_accessionid()
+  {
+
+    DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
+
+    List<DBRefEntry> dbrefs = Arrays
+            .asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 });
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
+    assertEquals(3, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
+  }
+
+  /**
+   * Test the method that searches for matches references - case when we are
+   * matching a reference with null (any) accession id
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_wildcardAccessionid()
+  {
+    DBRefEntry target = new DBRefEntry("EMBL", "2", null);
+
+    DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
+    // constructor changes embl to EMBL
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
+
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 }), target,
+                    DBRefUtils.SEARCH_MODE_FULL);
+    assertEquals(4, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref3, matches.get(2));
+    assertSame(ref5, matches.get(3));
   }
 }