/*
 * 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.datamodel;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import org.testng.annotations.Test;

public class SequenceFeatureTest
{
  @Test(groups = { "Functional" })
  public void testCopyConstructor()
  {
    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
            12.5f, "group");
    sf1.setValue("STRAND", "+");
    sf1.setValue("Note", "Testing");
    Integer count = new Integer(7);
    sf1.setValue("Count", count);

    SequenceFeature sf2 = new SequenceFeature(sf1);
    assertEquals("type", sf2.getType());
    assertEquals("desc", sf2.getDescription());
    assertEquals(22, sf2.getBegin());
    assertEquals(33, sf2.getEnd());
    assertEquals("+", sf2.getValue("STRAND"));
    assertEquals("Testing", sf2.getValue("Note"));
    // shallow clone of otherDetails map - contains the same object values!
    assertSame(count, sf2.getValue("Count"));
  }

  /**
   * Tests for retrieving a 'miscellaneous details' property value, with or
   * without a supplied default
   */
  @Test(groups = { "Functional" })
  public void testGetValue()
  {
    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
            12.5f, "group");
    sf1.setValue("STRAND", "+");
    assertEquals("+", sf1.getValue("STRAND"));
    assertNull(sf1.getValue("strand")); // case-sensitive
    assertEquals(".", sf1.getValue("unknown", "."));
    Integer i = new Integer(27);
    assertSame(i, sf1.getValue("Unknown", i));
  }

  /**
   * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
   */
  @Test(groups = { "Functional" })
  public void testGetStrand()
  {
    SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
            "group");
    assertEquals(0, sf.getStrand());
    sf.setValue("STRAND", "+");
    assertEquals(1, sf.getStrand());
    sf.setValue("STRAND", "-");
    assertEquals(-1, sf.getStrand());
    sf.setValue("STRAND", ".");
    assertEquals(0, sf.getStrand());
  }

  /**
   * Tests for equality, and that equal objects have the same hashCode
   */
  @Test(groups = { "Functional" })
  public void testEqualsAndHashCode()
  {
    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
            12.5f, "group");
    sf1.setValue("ID", "id");
    sf1.setValue("Name", "name");
    sf1.setValue("Parent", "parent");
    sf1.setStrand("+");
    sf1.setPhase("1");
    SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
            12.5f, "group");
    sf2.setValue("ID", "id");
    sf2.setValue("Name", "name");
    sf2.setValue("Parent", "parent");
    sf2.setStrand("+");
    sf2.setPhase("1");

    assertFalse(sf1.equals(null));
    assertTrue(sf1.equals(sf2));
    assertTrue(sf2.equals(sf1));
    assertEquals(sf1.hashCode(), sf2.hashCode());

    // changing type breaks equals:
    String restores = sf2.getType();
    sf2.setType("Type");
    assertFalse(sf1.equals(sf2));
    sf2.setType(restores);

    // changing description breaks equals:
    restores = sf2.getDescription();
    sf2.setDescription("Desc");
    assertFalse(sf1.equals(sf2));
    sf2.setDescription(restores);

    // changing score breaks equals:
    float restoref = sf2.getScore();
    sf2.setScore(12.4f);
    assertFalse(sf1.equals(sf2));
    sf2.setScore(restoref);

    // NaN doesn't match a number
    restoref = sf2.getScore();
    sf2.setScore(Float.NaN);
    assertFalse(sf1.equals(sf2));

    // NaN matches NaN
    sf1.setScore(Float.NaN);
    assertTrue(sf1.equals(sf2));
    sf1.setScore(restoref);
    sf2.setScore(restoref);

    // changing start position breaks equals:
    int restorei = sf2.getBegin();
    sf2.setBegin(21);
    assertFalse(sf1.equals(sf2));
    sf2.setBegin(restorei);

    // changing end position breaks equals:
    restorei = sf2.getEnd();
    sf2.setEnd(32);
    assertFalse(sf1.equals(sf2));
    sf2.setEnd(restorei);

    // changing feature group breaks equals:
    restores = sf2.getFeatureGroup();
    sf2.setFeatureGroup("Group");
    assertFalse(sf1.equals(sf2));
    sf2.setFeatureGroup(restores);

    // changing ID breaks equals:
    restores = (String) sf2.getValue("ID");
    sf2.setValue("ID", "id2");
    assertFalse(sf1.equals(sf2));
    sf2.setValue("ID", restores);

    // changing Name breaks equals:
    restores = (String) sf2.getValue("Name");
    sf2.setValue("Name", "Name");
    assertFalse(sf1.equals(sf2));
    sf2.setValue("Name", restores);

    // changing Parent breaks equals:
    restores = (String) sf1.getValue("Parent");
    sf1.setValue("Parent", "Parent");
    assertFalse(sf1.equals(sf2));
    sf1.setValue("Parent", restores);

    // changing strand breaks equals:
    restorei = sf2.getStrand();
    sf2.setStrand("-");
    assertFalse(sf1.equals(sf2));
    sf2.setStrand(restorei == 1 ? "+" : "-");

    // changing phase breaks equals:
    restores = sf1.getPhase();
    sf1.setPhase("2");
    assertFalse(sf1.equals(sf2));
    sf1.setPhase(restores);

    // restore equality as sanity check:
    assertTrue(sf1.equals(sf2));
    assertTrue(sf2.equals(sf1));
    assertEquals(sf1.hashCode(), sf2.hashCode());

    // changing status doesn't change equals:
    sf1.setStatus("new");
    assertTrue(sf1.equals(sf2));
  }

  @Test(groups = { "Functional" })
  public void testIsContactFeature()
  {
    SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
            "group");
    assertFalse(sf.isContactFeature());
    sf.setType("");
    assertFalse(sf.isContactFeature());
    sf.setType(null);
    assertFalse(sf.isContactFeature());
    sf.setType("Disulfide Bond");
    assertTrue(sf.isContactFeature());
    sf.setType("disulfide bond");
    assertTrue(sf.isContactFeature());
    sf.setType("Disulphide Bond");
    assertTrue(sf.isContactFeature());
    sf.setType("disulphide bond");
    assertTrue(sf.isContactFeature());
  }
}