/*
 * 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 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 testFileParser() throws Exception
  {
    for (String pdbStr : testFile)
    {
      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())
      {
        SequenceI sq = asq;
        while (sq.getDatasetSequence()!=null && sq.getAnnotation()==null)
        {
          sq = asq.getDatasetSequence();
        }
        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);
      }
    }
  }
}