/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.paradise;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.FastaFile;
import java.io.Reader;
import java.util.Iterator;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
import MCview.PDBfile;
public class TestAnnotate3D
{
- @Test
+ @Test(groups = { "Functional" }, enabled = false)
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
testRNAMLcontent(ids, null);
}
- @Test
+ @Test(groups = { "Functional" }, enabled = false)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Functional" }, enabled = false)
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
testRNAMLcontent(readers, pdbf);
}
+ @Test(groups = { "Functional" }, enabled = false)
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
sb.append(line + "\n");
}
assertTrue("No data returned by Annotate3D", sb.length() > 0);
- AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ final String lines = sb.toString();
+ AlignmentI al = new FormatAdapter().readFile(lines,
FormatAdapter.PASTE, "RNAML");
if (al == null || al.getHeight() == 0)
{
- System.out.println(sb.toString());
+ System.out.println(lines);
}
assertTrue("No alignment returned.", al != null);
assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
String sq_ = new String(sq.getSequence()).toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- if (new String(_struseq.getSequence()).toLowerCase().equals(
- sq_))
+ final String lowerCase = new String(_struseq.getSequence())
+ .toLowerCase();
+ if (lowerCase.equals(sq_))
{
struseq = _struseq;
break;
}
if (struseq == null)
{
- Assert.fail("Couldn't find this sequence in original input:\n"
- + new FastaFile().print(new SequenceI[]
- { sq })
- + "\n\nOriginal input:\n"
- + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ AssertJUnit
+ .fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile()
+ .print(new SequenceI[] { sq })
+ + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray())
+ + "\n");
}
}
}