/*
 * 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 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<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 });
      if (!al.isNucleotide())
      {
        assertTrue(
                "No secondary structure assigned for protein sequence.",
                sq.getAnnotation() != null
                        && sq.getAnnotation().length >= 1
                        && sq.getAnnotation()[0].hasIcons);
      }
    }
  }

}