X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FNewickFileTests.java;h=60c29348af9a99c90b2c6036722644a997b5bc0c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bd0bb52dd1e6c77083d5e6ec6ff423c29148a84b;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java index bd0bb52..60c2934 100644 --- a/test/jalview/io/NewickFileTests.java +++ b/test/jalview/io/NewickFileTests.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,51 +20,51 @@ */ package jalview.io; -import static org.junit.Assert.*; - -import java.util.Arrays; -import java.util.Collection; -import java.util.Iterator; -import java.util.Vector; +import static org.testng.ConversionUtils.wrapDataProvider; import jalview.analysis.NJTree; import jalview.analysis.SequenceIdMatcher; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; -import org.jmol.util.ArrayUtil; -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; -import org.junit.runner.RunWith; -import org.junit.runners.Parameterized; +import java.util.Arrays; +import java.util.Collection; +import java.util.Vector; + import org.junit.runners.Parameterized.Parameters; +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Factory; +import org.testng.annotations.Test; /** * @author jimp * */ -@RunWith(Parameterized.class) public class NewickFileTests { + @Factory + public static Object[] factoryData() + { + return wrapDataProvider(NewickFileTests.class, data()); + } + @Parameters public static Collection data() { return Arrays - .asList(new Object[][] - { + .asList(new Object[][] { - new String[] - { + new String[] { "Simple uniref50 newick", "(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" }, - new String[] - { + new String[] { "Tree with quotes", "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" }, - new String[] - { + new String[] { "Tree with double escaped comma in node", "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } }); }; @@ -80,12 +80,12 @@ public class NewickFileTests /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } - @Test + @Test(groups = { "Functional" }) public void testTreeIO() throws Exception { String stage = "Init", treename = " '" + name + "' :"; @@ -95,45 +95,49 @@ public class NewickFileTests System.out.println(treename + "\n" + testTree); NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE); nf.parse(); - assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'", + AssertJUnit.assertTrue( + stage + "Invalid Tree '" + nf.getWarningMessage() + "'", nf.isValid()); SequenceNode tree = nf.getTree(); - assertTrue(stage + "Null Tree", tree != null); + AssertJUnit.assertTrue(stage + "Null Tree", tree != null); stage = "Creating newick file from testTree " + treename; String gentree = new NewickFile(tree).print(nf.HasBootstrap(), nf.HasDistances()); - assertTrue(stage + "Empty string generated", gentree != null - && gentree.trim().length() > 0); + AssertJUnit.assertTrue(stage + "Empty string generated", + gentree != null && gentree.trim().length() > 0); stage = "Parsing regenerated testTree " + treename; NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE); nf_regen.parse(); - assertTrue( + AssertJUnit.assertTrue( stage + "Newick file is invalid ('" + nf_regen.getWarningMessage() + "')", nf_regen.isValid()); SequenceNode tree_regen = nf.getTree(); - assertTrue(stage + "Null Tree", tree_regen != null); + AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null); stage = "Compare original and generated tree" + treename; Vector oseqs, nseqs; oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(), new Vector()); - assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0); + AssertJUnit.assertTrue(stage + "No nodes in original tree.", + oseqs.size() > 0); SequenceI[] olsqs = new SequenceI[oseqs.size()]; for (int i = 0, iSize = oseqs.size(); i < iSize; i++) { olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element(); } - nseqs = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves( + nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves( nf_regen.getTree(), new Vector()); - assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0); + AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", + nseqs.size() > 0); SequenceI[] nsqs = new SequenceI[nseqs.size()]; for (int i = 0, iSize = nseqs.size(); i < iSize; i++) { nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element(); } - assertTrue(stage + " Different number of leaves (original " - + olsqs.length + " and regen " + nsqs.length + ")", + AssertJUnit.assertTrue(stage + + " Different number of leaves (original " + olsqs.length + + " and regen " + nsqs.length + ")", olsqs.length == nsqs.length); SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher( nsqs); @@ -157,7 +161,7 @@ public class NewickFileTests if (warns.length() > 0) { - fail(stage + warns); + Assert.fail(stage + warns); } } catch (Exception x) {