/*
- * 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.gui.AlignFrame;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileLoader;
+
+import java.util.Vector;
-import org.junit.Test;
+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",
+ "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+
+ // "./examples/DNMT1_MOUSE.pdb"
+ // };
- @Test
- public void test() throws Exception
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
{
- PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
- Vector<SequenceI> seqs=jtest.getSeqs();
-
- assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
- for (SequenceI sq:seqs)
+ 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)
{
- AlignmentI al = new Alignment(new SequenceI[] { sq});
- if (!al.isNucleotide())
+ FileLoader fl = new jalview.io.FileLoader(false);
+ AlignFrame af = fl
+ .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+ validateSecStrRows(af.getViewport().getAlignment());
+ }
+ }
+
+ @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(), mcseqs = mctest.getSeqs();
+
+ assertTrue(
+ "No sequences extracted from testfile\n"
+ + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+ : "(No warnings raised)"), seqs != null
+ && seqs.size() > 0);
+ for (SequenceI sq : seqs)
+ {
+ 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);
+ }
+ }
+ }
+
+ private void validateSecStrRows(AlignmentI al)
+ {
+ if (!al.isNucleotide())
+ {
+ for (SequenceI asq : al.getSequences())
{
- assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+ SequenceI sq = asq;
+ boolean hasDs = false;
+ while (sq.getDatasetSequence() != null
+ && sq.getAnnotation() == null)
+ {
+ sq = sq.getDatasetSequence();
+ hasDs = true;
+ }
+ checkFirstAAIsAssoc(sq);
+ if (hasDs)
+ {
+ // also verify if alignment sequence has annotation on it
+ // that is correctly mapped
+ checkFirstAAIsAssoc(asq);
+ }
}
}
}
+ private void checkFirstAAIsAssoc(SequenceI sq)
+ {
+ assertTrue("No secondary structure assigned for protein sequence.",
+ sq.getAnnotation() != null && sq.getAnnotation().length >= 1
+ && sq.getAnnotation()[0].hasIcons);
+ assertTrue(
+ "Secondary structure not associated for sequence "
+ + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+ }
}