X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=963ca7c807f7296e1baca5fc685b4e094da64f7f;hb=ce2ac269a3e9b6e52f1e1c4df24f8d5a59ad6933;hp=6c39b9bf14dcff990dd16a2ef3debef68f831727;hpb=438af5436afff7bc1ce5ab380ec5813a7beb11b9;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 6c39b9b..963ca7c 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -32,12 +32,24 @@ 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 +64,36 @@ 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)); } /** @@ -97,6 +116,11 @@ public class DBRefUtilsTest 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(groups = { "Functional" }) @@ -138,9 +162,9 @@ public class DBRefUtilsTest { SequenceI seq = new Sequence("Seq1", "ABCD"); DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890"); - DBRefEntry[] refs = seq.getDBRefs(); - 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()); @@ -156,9 +180,12 @@ public class DBRefUtilsTest SequenceI seq = new Sequence("Seq1", "ABCD"); DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2", "1WRI A; 7-80;"); - DBRefEntry[] refs = seq.getDBRefs(); - 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 @@ -191,12 +218,13 @@ public class DBRefUtilsTest 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]); + 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)); } /** @@ -224,11 +252,12 @@ public class DBRefUtilsTest 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)); } /** @@ -238,7 +267,7 @@ public class DBRefUtilsTest @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 @@ -248,14 +277,14 @@ public class DBRefUtilsTest 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]); + + 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)); } /** @@ -266,7 +295,7 @@ public class DBRefUtilsTest 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 @@ -277,13 +306,14 @@ public class DBRefUtilsTest 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]); + + 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)); } }