/*
 * 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.io.gff;

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

import java.util.Arrays;
import java.util.List;
import java.util.Map;

import org.testng.annotations.Test;

public class GffHelperBaseTest
{

  /**
   * Test the method that parses lines like <br>
   * ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
   */
  @Test(groups = { "Functional" })
  public void testParseNameValuePairs()
  {
    assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
            .isEmpty());
    assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
            .isEmpty());
    assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
            ",").isEmpty());

    Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
            "hello world", ";", ' ', ", ");
    assertEquals(1, map.size());
    assertEquals(1, map.get("hello").size());
    assertEquals("world", map.get("hello").get(0));

    map = GffHelperBase
            .parseNameValuePairs(
                    "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny; Type=",
                    ";", '=', ",");

    // Type is ignored as no value was supplied
    assertEquals(2, map.size());

    assertEquals(1, map.get("Method").size());
    assertEquals("manual curation", map.get("Method").get(0)); // trimmed

    assertEquals(3, map.get("Notes").size());
    assertEquals("F2 S", map.get("Notes").get(0));
    assertEquals("Metal", map.get("Notes").get(1));
    assertEquals("Shiny", map.get("Notes").get(2));
  }

  /**
   * Test for the method that tries to trim mappings to equivalent lengths
   */
  @Test(groups = "Functional")
  public void testTrimMapping()
  {
    int[] from = { 1, 12 };
    int[] to = { 20, 31 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged

    // from too long:
    from = new int[] { 1, 13 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[1, 12]", Arrays.toString(from)); // trimmed
    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged

    // to too long:
    to = new int[] { 20, 33 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
    assertEquals("[20, 31]", Arrays.toString(to)); // trimmed

    // from reversed:
    from = new int[] { 12, 1 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged

    // to reversed:
    to = new int[] { 31, 20 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
    assertEquals("[31, 20]", Arrays.toString(to)); // unchanged

    // from reversed and too long:
    from = new int[] { 14, 1 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[14, 3]", Arrays.toString(from)); // end trimmed
    assertEquals("[31, 20]", Arrays.toString(to)); // unchanged

    // to reversed and too long:
    to = new int[] { 31, 10 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
    assertEquals("[14, 3]", Arrays.toString(from)); // unchanged
    assertEquals("[31, 20]", Arrays.toString(to)); // end trimmed

    // cdna to peptide (matching)
    from = new int[] { 1, 18 };
    to = new int[] { 4, 9 };
    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
    assertEquals("[1, 18]", Arrays.toString(from)); // unchanged
    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged

    // overlong cdna to peptide
    from = new int[] { 1, 20 };
    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
    assertEquals("[1, 18]", Arrays.toString(from)); // end trimmed
    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged

    // overlong cdna (reversed) to peptide
    from = new int[] { 20, 1 };
    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
    assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged

    // overlong cdna (reversed) to peptide (reversed)
    from = new int[] { 20, 1 };
    to = new int[] { 9, 4 };
    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
    assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
    assertEquals("[9, 4]", Arrays.toString(to)); // unchanged

    // peptide to cdna (matching)
    from = new int[] { 4, 9 };
    to = new int[] { 1, 18 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
    assertEquals("[1, 18]", Arrays.toString(to)); // unchanged

    // peptide to overlong cdna
    to = new int[] { 1, 20 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
    assertEquals("[1, 18]", Arrays.toString(to)); // end trimmed

    // peptide to overlong cdna (reversed)
    to = new int[] { 20, 1 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
    assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed

    // peptide (reversed) to overlong cdna (reversed)
    from = new int[] { 9, 4 };
    to = new int[] { 20, 1 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[9, 4]", Arrays.toString(from)); // unchanged
    assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed

    // overlong peptide to word-length cdna
    from = new int[] { 4, 10 };
    to = new int[] { 1, 18 };
    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[4, 9]", Arrays.toString(from)); // end trimmed
    assertEquals("[1, 18]", Arrays.toString(to)); // unchanged

    // overlong peptide to non-word-length cdna
    from = new int[] { 4, 10 };
    to = new int[] { 1, 19 };
    assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
    assertEquals("[4, 10]", Arrays.toString(from)); // unchanged
    assertEquals("[1, 19]", Arrays.toString(to)); // unchanged

  }
}