X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=ca5bca35282b031b1ff98b5f6685ad4c64d725c8;hb=3edf7ac9c103688aa89a9a7f7bc56fca46403ad4;hp=5e0683e106fa5f5c58c8df781c3d1f8bbe3d14a7;hpb=318e3baf6738dea7b20640bc3e46814bd566811c;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 5e0683e..ca5bca3 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -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; @@ -32,14 +31,23 @@ import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; 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 @@ -74,9 +82,16 @@ public class DBRefUtilsTest assertSame(ref2, selected[0]); assertSame(ref3, selected[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.length); + assertSame(ref1, selected[0]); + assertSame(ref2, selected[1]); + assertSame(ref3, selected[2]); } /** @@ -99,39 +114,12 @@ public class DBRefUtilsTest assertEquals("UNIPROTKB/SWISS-CHEESE", DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE")); assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl")); - } - @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"))); + // these are not 'known' to Jalview + assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM")); + assertEquals("pfam", DBRefUtils.getCanonicalName("pfam")); - 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 */ @@ -147,6 +135,11 @@ public class DBRefUtilsTest assertEquals("1.2", ref.getVersion()); assertEquals("a7890", ref.getAccessionId()); 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); } /** @@ -197,8 +190,7 @@ public class DBRefUtilsTest 1 }, 1, 1))); List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, - ref2, ref3, ref4, ref5 }, target); + ref1, ref2, ref3, ref4, ref5 }, target); assertEquals(3, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1)); @@ -231,8 +223,7 @@ public class DBRefUtilsTest ref3.setMap(map3); List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, - ref2, ref3 }, target); + ref1, ref2, ref3 }, target); assertEquals(2, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1)); @@ -245,7 +236,7 @@ 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 @@ -255,9 +246,8 @@ 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[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 }; List matches = DBRefUtils.searchRefs(dbrefs, "A1234"); assertEquals(3, matches.size()); assertSame(ref1, matches.get(0)); @@ -273,7 +263,7 @@ 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 @@ -284,10 +274,9 @@ 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))); - + List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, - ref2, ref3, ref4, ref5 }, target); + ref1, ref2, ref3, ref4, ref5 }, target); assertEquals(4, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1));