+++ /dev/null
-/*
- * 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.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;
-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(groups = { "Functional" })
- public void testSelectRefs()
- {
- assertNull(DBRefUtils.selectRefs(null, null));
- assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
-
- DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
- 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");
- 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.size());
- assertSame(ref1, selected.get(0));
-
- sources = new String[] { "UNIPROT" };
- selected = DBRefUtils.selectRefs(dbrefs, sources);
- assertEquals(2, selected.size());
- assertSame(ref2, selected.get(0));
- assertSame(ref3, selected.get(1));
-
- 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(groups = { "Functional" })
- public void testGetCanonicalName()
- {
- assertNull(DBRefUtils.getCanonicalName(null));
- assertEquals("", DBRefUtils.getCanonicalName(""));
- assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
- assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
- assertEquals("UNIPROT",
- DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
- assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
- assertEquals("UNIPROT",
- DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
- 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 'parsing' a DBRef - non PDB case
- */
- @Test(groups = { "Functional" })
- public void testParseToDbRef()
- {
- SequenceI seq = new Sequence("Seq1", "ABCD");
- DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
- 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());
- assertTrue(seq.getAllPDBEntries().isEmpty());
- }
-
- /**
- * Test 'parsing' a DBRef - Stockholm PDB format
- */
- @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;");
- // 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.getAllPDBEntries().size());
- PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
- assertEquals("1WRI", pdbRef.getId());
- assertNull(pdbRef.getFile());
- 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(groups = { "Functional" })
- public void testSearchRefs_noMapping()
- {
- DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
-
- DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
- // constructor changes embl to EMBL
- 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", "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)));
-
- 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(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));
- 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));
- 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));
- ref3.setMap(map3);
-
- 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));
- }
-}
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