/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ 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.analysis;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.fail;

import jalview.analysis.SecStrConsensus.SimpleBP;

import java.util.Vector;

import org.testng.annotations.Test;

public class RnaTest
{
  @Test(groups = { "Functional" })
  public void testGetSimpleBPs() throws WUSSParseException
  {
    String rna = "([{})]"; // JAL-1081 example
    Vector<SimpleBP> bps = Rna.GetSimpleBPs(rna);
    assertEquals(3, bps.size());

    /*
     * the base pairs are added in the order in which the matching base is found
     */
    assertEquals(2, bps.get(0).bp5); // {
    assertEquals(3, bps.get(0).bp3); // }
    assertEquals(0, bps.get(1).bp5); // (
    assertEquals(4, bps.get(1).bp3); // )
    assertEquals(1, bps.get(2).bp5); // [
    assertEquals(5, bps.get(2).bp3); // ]
  }

  @Test(groups = { "Functional" })
  public void testGetSimpleBPs_unmatchedOpener()
  {
    String rna = "(([{})]";
    try
    {
      Rna.GetSimpleBPs(rna);
      fail("expected exception");
    } catch (WUSSParseException e)
    {
      // expected
    }
  }

  @Test(groups = { "Functional" })
  public void testGetSimpleBPs_unmatchedCloser()
  {
    String rna = "([{})]]";
    try
    {
      Rna.GetSimpleBPs(rna);
      fail("expected exception");
    } catch (WUSSParseException e)
    {
      // expected
    }
  }
}