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JAL-736 JAL-1645 brief documentation about physicochemical property conservation...
[jalview.git]
/
test
/
jalview
/
io
/
NewickFileTests.java
diff --git
a/test/jalview/io/NewickFileTests.java
b/test/jalview/io/NewickFileTests.java
index
42b5641
..
261ffc6
100644
(file)
--- a/
test/jalview/io/NewickFileTests.java
+++ b/
test/jalview/io/NewickFileTests.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*
* This file is part of Jalview.
*
@@
-20,41
+20,45
@@
*/
package jalview.io;
*/
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 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.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
*
*/
/**
* @author jimp
*
*/
-@RunWith(Parameterized.class)
public class NewickFileTests
{
public class NewickFileTests
{
+ @Factory
+ public static Object[] factoryData()
+ {
+ return wrapDataProvider(NewickFileTests.class, data());
+ }
+
@Parameters
public static Collection data()
{
return Arrays
.asList(new Object[][]
{
@Parameters
public static Collection data()
{
return Arrays
.asList(new Object[][]
{
-
+
new String[]
{
"Simple uniref50 newick",
new String[]
{
"Simple uniref50 newick",
@@
-80,12
+84,12
@@
public class NewickFileTests
/**
* @throws java.lang.Exception
*/
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
}
public static void setUpBeforeClass() throws Exception
{
}
- @Test
+ @Test(groups ={ "Functional" })
public void testTreeIO() throws Exception
{
String stage = "Init", treename = " '" + name + "' :";
public void testTreeIO() throws Exception
{
String stage = "Init", treename = " '" + name + "' :";
@@
-95,44
+99,44
@@
public class NewickFileTests
System.out.println(treename + "\n" + testTree);
NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
nf.parse();
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();
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());
stage = "Creating newick file from testTree " + treename;
String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
nf.HasDistances());
- assertTrue(stage + "Empty string generated", gentree != null
+ 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();
&& 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();
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());
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();
}
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());
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();
}
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 "
+ 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(
+ olsqs.length + " and regen " + nsqs.length + ")",
olsqs.length == nsqs.length);
SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
@@
-157,7
+161,7
@@
public class NewickFileTests
if (warns.length() > 0)
{
if (warns.length() > 0)
{
- fail(stage + warns);
+ Assert.fail(stage + warns);
}
} catch (Exception x)
{
}
} catch (Exception x)
{