/*
- * 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.jmol;
-import static org.junit.Assert.*;
-
-import java.util.Vector;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
-import org.junit.Test;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
/**
* @author jimp
*/
public class PDBFileWithJmolTest
{
- String[] testFile = new String[]
- { "./examples/1GAQ.txt" }; // ,
+ String[] testFile = new String[] { "./examples/1GAQ.txt",
+ "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
// "./examples/DNMT1_MOUSE.pdb"
// };
- @Test
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ }
+
+ @Test(groups = { "Functional" })
public void testAlignmentLoader() throws Exception
{
for (String f : testFile)
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testFileParser() throws Exception
{
for (String pdbStr : testFile)
{
+ PDBfile mctest = new PDBfile(false, false, false, pdbStr,
+ AppletFormatAdapter.FILE);
PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
jalview.io.AppletFormatAdapter.FILE);
- Vector<SequenceI> seqs = jtest.getSeqs();
+ Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
assertTrue(
"No sequences extracted from testfile\n"
&& seqs.size() > 0);
for (SequenceI sq : seqs)
{
- AlignmentI al = new Alignment(new SequenceI[]
- { sq });
+ assertEquals("JMol didn't process " + pdbStr
+ + " to the same sequence as MCView",
+ sq.getSequenceAsString(), mcseqs.remove(0)
+ .getSequenceAsString());
+ AlignmentI al = new Alignment(new SequenceI[] { sq });
validateSecStrRows(al);
}
}