X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=963ca7c807f7296e1baca5fc685b4e094da64f7f;hb=ce2ac269a3e9b6e52f1e1c4df24f8d5a59ad6933;hp=76ce32ff82c5b9d726f578d36746f4642f3645e6;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 76ce32f..963ca7c 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. * @@ -32,14 +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 @@ -54,29 +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)); } /** @@ -99,6 +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" }) @@ -140,9 +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()); @@ -161,9 +183,9 @@ public class DBRefUtilsTest // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for // PDB ref in Stockholm - 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("PDB", ref.getSource()); assertEquals("1.2", ref.getVersion()); // DBRef id is pdbId + chain code @@ -196,8 +218,9 @@ public class DBRefUtilsTest 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); + 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)); @@ -229,8 +252,9 @@ public class DBRefUtilsTest new int[] { 1, 1 }, 2, 2)); ref3.setMap(map3); - List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, ref2, ref3 }, target); + 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)); @@ -254,7 +278,8 @@ public class DBRefUtilsTest 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 }; + 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)); @@ -282,8 +307,9 @@ public class DBRefUtilsTest 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); + 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));