X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=6c39b9bf14dcff990dd16a2ef3debef68f831727;hb=b21429180fdda3586d67b5d0f43c89d35b504be7;hp=af5fd1e683c169a6c20483ad6f28409763ccbfb3;hpb=06e3a52df5af8243cdb67c023c8ddd834711ad36;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index af5fd1e..6c39b9b 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import static org.testng.AssertJUnit.assertEquals; @@ -22,7 +42,7 @@ public class DBRefUtilsTest * Test the method that selects DBRefEntry items whose source is in a supplied * list */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testSelectRefs() { assertNull(DBRefUtils.selectRefs(null, null)); @@ -32,10 +52,8 @@ 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[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 }; + String[] sources = new String[] { "EMBL", "UNIPROT" }; DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources); assertEquals(3, selected.length); @@ -43,21 +61,18 @@ public class DBRefUtilsTest assertSame(ref2, selected[1]); assertSame(ref3, selected[2]); - sources = new String[] - { "EMBL" }; + sources = new String[] { "EMBL" }; selected = DBRefUtils.selectRefs(dbrefs, sources); assertEquals(1, selected.length); assertSame(ref1, selected[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]); - sources = new String[] - { "Uniprot", "EMBLCDS" }; + sources = new String[] { "Uniprot", "EMBLCDS" }; selected = DBRefUtils.selectRefs(dbrefs, sources); assertNull(selected); } @@ -66,7 +81,7 @@ public class DBRefUtilsTest * Test the method that converts (currently three) database names to a * canonical name (not case-sensitive) */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testGetCanonicalName() { assertNull(DBRefUtils.getCanonicalName(null)); @@ -81,9 +96,10 @@ public class DBRefUtilsTest assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL")); assertEquals("UNIPROTKB/SWISS-CHEESE", DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE")); + assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl")); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testIsDasCoordinateSystem() { assertFalse(DBRefUtils.isDasCoordinateSystem(null, null)); @@ -106,8 +122,7 @@ public class DBRefUtilsTest assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry( "UNIPROT", "v1", "a1"))); assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB", - new DBRefEntry( - "pdb", "v1", "a1"))); + new DBRefEntry("pdb", "v1", "a1"))); assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry( "EMBL", "v1", "a1"))); @@ -118,30 +133,30 @@ public class DBRefUtilsTest /** * Test 'parsing' a DBRef - non PDB case */ - @Test(groups ={ "Functional" }) + @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(); + DBRefEntry[] refs = seq.getDBRefs(); assertEquals(1, refs.length); assertSame(ref, refs[0]); assertEquals("EMBL", ref.getSource()); assertEquals("1.2", ref.getVersion()); assertEquals("a7890", ref.getAccessionId()); - assertNull(seq.getAllPDBEntries()); + assertTrue(seq.getAllPDBEntries().isEmpty()); } /** * Test 'parsing' a DBRef - Stockholm PDB format */ - @Test(groups ={ "Functional" }) + @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(); + DBRefEntry[] refs = seq.getDBRefs(); assertEquals(1, refs.length); assertSame(ref, refs[0]); assertEquals("PDB", ref.getSource()); @@ -160,7 +175,7 @@ public class DBRefUtilsTest * Test the method that searches for matches references - case when we are * matching a reference with no mappings */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testSearchRefs_noMapping() { DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234"); @@ -173,12 +188,11 @@ 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))); + 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); + DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1, + ref2, ref3, ref4, ref5 }, target); assertEquals(3, matches.length); assertSame(ref1, matches[0]); assertSame(ref2, matches[1]); @@ -189,34 +203,87 @@ public class DBRefUtilsTest * Test the method that searches for matches references - case when we are * matching a reference with a mapping */ - @Test(groups ={ "Functional" }) + @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); + DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1, + ref2, ref3 }, target); assertEquals(2, matches.length); assertSame(ref1, matches[0]); assertSame(ref2, matches[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))); + + DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, + ref2, ref3, ref4, ref5 }; + DBRefEntry[] matches = DBRefUtils.searchRefs(dbrefs, "A1234"); + assertEquals(3, matches.length); + assertSame(ref1, matches[0]); + assertSame(ref2, matches[1]); + assertSame(ref5, matches[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))); + + DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1, + ref2, ref3, ref4, ref5 }, target); + assertEquals(4, matches.length); + assertSame(ref1, matches[0]); + assertSame(ref2, matches[1]); + assertSame(ref3, matches[2]); + assertSame(ref5, matches[3]); + } }