X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FNewickFileTests.java;h=beedb1116bd484004e5b588186b74d4bc11cce34;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=a783b1e3a4836d789a074e493c1b40ddd92a88d9;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java index a783b1e..beedb11 100644 --- a/test/jalview/io/NewickFileTests.java +++ b/test/jalview/io/NewickFileTests.java @@ -22,10 +22,11 @@ package jalview.io; import static org.testng.ConversionUtils.wrapDataProvider; -import jalview.analysis.NJTree; import jalview.analysis.SequenceIdMatcher; +import jalview.analysis.TreeModel; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.gui.JvOptionPane; import java.util.Arrays; import java.util.Collection; @@ -46,6 +47,13 @@ import org.testng.annotations.Test; public class NewickFileTests { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Factory public static Object[] factoryData() { @@ -55,22 +63,17 @@ public class NewickFileTests @Parameters public static Collection data() { - return Arrays - .asList(new Object[][] - { - - 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[] - { - "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[] - { - "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);" } }); + return Arrays.asList(new Object[][] { + + 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[] + { "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[] + { "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);" } }); }; String name, testTree; @@ -84,12 +87,12 @@ public class NewickFileTests /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTreeIO() throws Exception { String stage = "Init", treename = " '" + name + "' :"; @@ -97,19 +100,20 @@ public class NewickFileTests { stage = "Parsing testTree " + treename; System.out.println(treename + "\n" + testTree); - NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE); + NewickFile nf = new NewickFile(testTree, DataSourceType.PASTE); nf.parse(); - AssertJUnit.assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'", + AssertJUnit.assertTrue( + stage + "Invalid Tree '" + nf.getWarningMessage() + "'", nf.isValid()); SequenceNode tree = nf.getTree(); AssertJUnit.assertTrue(stage + "Null Tree", tree != null); stage = "Creating newick file from testTree " + treename; String gentree = new NewickFile(tree).print(nf.HasBootstrap(), nf.HasDistances()); - AssertJUnit.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); + NewickFile nf_regen = new NewickFile(gentree, DataSourceType.PASTE); nf_regen.parse(); AssertJUnit.assertTrue( stage + "Newick file is invalid ('" @@ -119,28 +123,31 @@ public class NewickFileTests 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()); - AssertJUnit.assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0); + Vector oseqs, nseqs; + oseqs = new TreeModel(new SequenceI[0], null, nf) + .findLeaves(nf.getTree()); + 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(); + olsqs[i] = (SequenceI) oseqs.get(i).element(); } - nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves( - nf_regen.getTree(), new Vector()); - AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0); + nseqs = new TreeModel(new SequenceI[0], null, nf_regen) + .findLeaves(nf_regen.getTree()); + 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(); + nsqs[i] = (SequenceI) nseqs.get(i).element(); } - AssertJUnit.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); + SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), + nmatcher = new SequenceIdMatcher(nsqs); SequenceI[] osmatches = omatcher.findIdMatch(nsqs); SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs); @@ -172,7 +179,7 @@ public class NewickFileTests /** * @throws java.lang.Exception */ - @AfterClass + @AfterClass(alwaysRun = true) public static void tearDownAfterClass() throws Exception { }