-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
*
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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[][]
- {
-
- new String[]
- {
+ .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[]
- {
+ 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);" } });
};
/**
* @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 + "' :";
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);
+ Vector<SequenceNode> oseqs, nseqs;
+ oseqs = new NJTree(new SequenceI[0], 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 = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves(
- nf_regen.getTree(), new Vector());
- assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
+ nseqs = new NJTree(new SequenceI[0], 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();
}
- 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);
if (warns.length() > 0)
{
- fail(stage + warns);
+ Assert.fail(stage + warns);
}
} catch (Exception x)
{
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
git://source.jalview.org / jalview.git / blobdiff