/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
 * Copyright (C) 2015 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.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.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"
  // };

  @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    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)
    {
      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())
      {
        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);
  }
}