-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.ext.jmol;
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 org.junit.Test;
/**
* @author jimp
- *
+ *
*/
public class PDBFileWithJmolTest
{
+ String[] testFile = new String[]
+ { "./examples/1GAQ.txt" }; // ,
+
+ // "./examples/DNMT1_MOUSE.pdb"
+ // };
+
+ @Test
+ public void testAlignmentLoader() throws Exception
+ {
+ for (String f : testFile)
+ {
+ FileLoader fl = new jalview.io.FileLoader(false);
+ AlignFrame af = fl
+ .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+ validateSecStrRows(af.getViewport().getAlignment());
+ }
+ }
@Test
- public void test() throws Exception
+ public void testFileParser() throws Exception
{
- 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)
+ for (String pdbStr : testFile)
{
- AlignmentI al = new Alignment(new SequenceI[] { sq});
- if (!al.isNucleotide())
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
+ 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)
+ {
+ 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);
+ }
}