X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=45dfd5ec665a146d05429a96649f33c722ca2d5c;hb=refs%2Fheads%2Ffeatures%2FJAL-1953_Archeopteryx_with_Jalview_2_11_2;hp=933fe0fa3a9c7af2027f0efe8c4a81ed7d789728;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 933fe0f..45dfd5e 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,7 +21,6 @@ package jalview.util; import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; @@ -32,12 +31,24 @@ 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 @@ -52,29 +63,38 @@ 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 }; + List dbrefs = Arrays + .asList(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]); + List 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" }; 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)); } /** @@ -90,43 +110,20 @@ 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")); // since JAL-1953 Pfam is also a canonical database name - @Test(groups = { "Functional" }) - 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"))); } /** @@ -137,13 +134,18 @@ public class DBRefUtilsTest { 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 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.getAllPDBEntries()); + 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); } /** @@ -155,9 +157,12 @@ public class DBRefUtilsTest 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 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 @@ -187,15 +192,18 @@ 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 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)); } /** @@ -206,27 +214,92 @@ public class DBRefUtilsTest 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 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 dbrefs = Arrays + .asList(new DBRefEntry[] + { ref1, ref2, ref3, ref4, ref5 }); + List 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 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)); } }