/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
import static org.junit.Assert.*;
import java.util.Vector;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import org.junit.Test;
/**
* @author jimp
*
*/
public class PDBFileWithJmolTest
{
@Test
public void test() throws Exception
{
PDBFileWithJmol jtest = new PDBFileWithJmol("./examples/1GAQ.txt",
jalview.io.AppletFormatAdapter.FILE);
Vector 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 });
if (!al.isNucleotide())
{
assertTrue(
"No secondary structure assigned for protein sequence.",
sq.getAnnotation() != null
&& sq.getAnnotation().length >= 1
&& sq.getAnnotation()[0].hasIcons);
}
}
}
}