package jalview.util;

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

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.testng.annotations.Test;

public class MapListTest
{

  @Test(groups ={ "Functional" })
  public void testSomething()
  {
    MapList ml = new MapList(new int[]
    { 1, 5, 10, 15, 25, 20 }, new int[]
    { 51, 1 }, 1, 3);
    MapList ml1 = new MapList(new int[]
    { 1, 3, 17, 4 }, new int[]
    { 51, 1 }, 1, 3);
    MapList ml2 = new MapList(new int[]
    { 1, 60 }, new int[]
    { 1, 20 }, 3, 1);
    // test internal consistency
    int to[] = new int[51];
    testMap(ml, 1, 60);
    MapList mldna = new MapList(new int[]
    { 2, 2, 6, 8, 12, 16 }, new int[]
    { 1, 3 }, 3, 1);
    int[] frm = mldna.locateInFrom(1, 1);
    testLocateFrom(mldna, 1, 1, new int[]
    { 2, 2, 6, 7 });
    testMap(mldna, 1, 3);
    /*
     * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
     * toofrom=ml.shiftFrom(too[0]);
     * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
     * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
     */
  }

  private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
  {
    int[] frm = mldna.locateInFrom(i, j);
    assertEquals("Failed test locate from " + i + " to " + j,
            Arrays.toString(frm), Arrays.toString(ks));
  }

  /**
   * test routine. not incremental.
   * 
   * @param ml
   * @param fromS
   * @param fromE
   */
  private void testMap(MapList ml, int fromS, int fromE)
  {
    // todo convert to JUnit style tests
    for (int from = 1; from <= 25; from++)
    {
      int[] too = ml.shiftFrom(from);
      System.out.print("ShiftFrom(" + from + ")==");
      if (too == null)
      {
        System.out.print("NaN\n");
      }
      else
      {
        System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
        System.out.print("\t+--+\t");
        int[] toofrom = ml.shiftTo(too[0]);
        if (toofrom != null)
        {
          if (toofrom[0] != from)
          {
            System.err.println("Mapping not reflexive:" + from + " "
                    + too[0] + "->" + toofrom[0]);
          }
          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
                  + " % " + toofrom[1] + " (" + toofrom[2] + ")");
        }
        else
        {
          System.out.println("ShiftTo(" + too[0] + ")=="
                  + "NaN! - not Bijective Mapping!");
        }
      }
    }
    int mmap[][] = ml.makeFromMap();
    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
            + mmap[0][2] + " " + mmap[0][3] + " ");
    for (int i = 1; i <= mmap[1].length; i++)
    {
      if (mmap[1][i - 1] == -1)
      {
        System.out.print(i + "=XXX");
  
      }
      else
      {
        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
      }
      if (i % 20 == 0)
      {
        System.out.print("\n");
      }
      else
      {
        System.out.print(",");
      }
    }
    // test range function
    System.out.print("\nTest locateInFrom\n");
    {
      int f = mmap[0][2], t = mmap[0][3];
      while (f <= t)
      {
        System.out.println("Range " + f + " to " + t);
        int rng[] = ml.locateInFrom(f, t);
        if (rng != null)
        {
          for (int i = 0; i < rng.length; i++)
          {
            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
          }
        }
        else
        {
          System.out.println("No range!");
        }
        System.out.print("\nReversed\n");
        rng = ml.locateInFrom(t, f);
        if (rng != null)
        {
          for (int i = 0; i < rng.length; i++)
          {
            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
          }
        }
        else
        {
          System.out.println("No range!");
        }
        System.out.print("\n");
        f++;
        t--;
      }
    }
    System.out.print("\n");
    mmap = ml.makeToMap();
    System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
            + mmap[0][2] + " " + mmap[0][3] + " ");
    for (int i = 1; i <= mmap[1].length; i++)
    {
      if (mmap[1][i - 1] == -1)
      {
        System.out.print(i + "=XXX");
  
      }
      else
      {
        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
      }
      if (i % 20 == 0)
      {
        System.out.print("\n");
      }
      else
      {
        System.out.print(",");
      }
    }
    System.out.print("\n");
    // test range function
    System.out.print("\nTest locateInTo\n");
    {
      int f = mmap[0][2], t = mmap[0][3];
      while (f <= t)
      {
        System.out.println("Range " + f + " to " + t);
        int rng[] = ml.locateInTo(f, t);
        if (rng != null)
        {
          for (int i = 0; i < rng.length; i++)
          {
            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
          }
        }
        else
        {
          System.out.println("No range!");
        }
        System.out.print("\nReversed\n");
        rng = ml.locateInTo(t, f);
        if (rng != null)
        {
          for (int i = 0; i < rng.length; i++)
          {
            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
          }
        }
        else
        {
          System.out.println("No range!");
        }
        f++;
        t--;
        System.out.print("\n");
      }
    }
  }

  /**
   * Tests for method that locates ranges in the 'from' map for given range in
   * the 'to' map.
   */
  @Test(groups ={ "Functional" })
  public void testLocateInFrom_noIntrons()
  {
    /*
     * Simple mapping with no introns
     */
    int[] codons = new int[]
    { 1, 12 };
    int[] protein = new int[]
    { 1, 4 };
    MapList ml = new MapList(codons, protein, 3, 1);
    assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
    assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
    assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
    assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
    assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
    assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
    assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
    assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
    assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
    assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
    assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));

    assertNull(ml.locateInFrom(0, 0));
    assertNull(ml.locateInFrom(1, 5));
    assertNull(ml.locateInFrom(-1, 1));
  }

  /**
   * Tests for method that locates ranges in the 'from' map for given range in
   * the 'to' map.
   */
  @Test(groups ={ "Functional" })
  public void testLocateInFrom_withIntrons()
  {
    /*
     * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
     * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
     */
    int[] codons =
    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
    int[] protein =
    { 1, 4 };
    MapList ml = new MapList(codons, protein, 3, 1);
    assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
    assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
    assertEquals("[10, 10, 12, 12, 14, 14]",
            Arrays.toString(ml.locateInFrom(3, 3)));
    assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
  }

  /**
   * Tests for method that locates ranges in the 'to' map for given range in the
   * 'from' map.
   */
  @Test(groups ={ "Functional" })
  public void testLocateInTo_noIntrons()
  {
    /*
     * Simple mapping with no introns
     */
    int[] codons = new int[]
    { 1, 12 };
    int[] protein = new int[]
    { 1, 4 };
    MapList ml = new MapList(codons, protein, 3, 1);
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
    assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
    assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
    assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
    assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
    assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
    assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
    assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));

    /*
     * A part codon is treated as if a whole one.
     */
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
    assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
    assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
    assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));

    assertNull(ml.locateInTo(0, 0));
    assertNull(ml.locateInTo(1, 13));
    assertNull(ml.locateInTo(-1, 1));
  }

  /**
   * Tests for method that locates ranges in the 'to' map for given range in the
   * 'from' map.
   */
  @Test(groups ={ "Functional" })
  public void testLocateInTo_withIntrons()
  {
    /*
     * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
     * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
     */
    int[] codons =
    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
    /*
     * Mapped proteins at positions 1, 3, 4, 6 in the sequence
     */
    int[] protein =
    { 1, 1, 3, 4, 6, 6 };
    MapList ml = new MapList(codons, protein, 3, 1);

    /*
     * Can't map from an unmapped position
     */
    assertNull(ml.locateInTo(1, 2));
    assertNull(ml.locateInTo(2, 4));
    assertNull(ml.locateInTo(4, 4));

    /*
     * Valid range or subrange of codon1 maps to protein1.
     */
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));

    // codon position 6 starts the next protein:
    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));

    // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
    assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));

  }

  /**
   * Test equals method.
   */
  @Test(groups ={ "Functional" })
  public void testEquals()
  {
    int[] codons = new int[]
    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
    int[] protein = new int[]
    { 1, 4 };
    MapList ml = new MapList(codons, protein, 3, 1);
    MapList ml1 = new MapList(codons, protein, 3, 1); // same values
    MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
    MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
    codons[2] = 4;
    MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
    protein[1] = 3;
    MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ

    assertTrue(ml.equals(ml));
    assertTrue(ml.equals(ml1));
    assertTrue(ml1.equals(ml));

    assertFalse(ml.equals(null));
    assertFalse(ml.equals("hello"));
    assertFalse(ml.equals(ml2));
    assertFalse(ml.equals(ml3));
    assertFalse(ml.equals(ml6));
    assertFalse(ml.equals(ml7));
    assertFalse(ml6.equals(ml7));

    try
    {
      MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
      assertFalse(ml.equals(ml4));
    } catch (NullPointerException e)
    {
      // actually thrown by constructor before equals can be called
    }
    try
    {
      MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
      assertFalse(ml.equals(ml5));
    } catch (NullPointerException e)
    {
      // actually thrown by constructor before equals can be called
    }
  }

  /**
   * Test for the method that flattens a list of ranges into a single array.
   */
  @Test(groups ={ "Functional" })
  public void testGetRanges()
  {
    List<int[]> ranges = new ArrayList<int[]>();
    ranges.add(new int[]
    { 2, 3 });
    ranges.add(new int[]
    { 5, 6 });
    assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
  }

  /**
   * Check state after construction
   */
  @Test(groups ={ "Functional" })
  public void testConstructor()
  {
    int[] codons =
    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
    int[] protein =
    { 1, 1, 3, 4, 6, 6 };
    MapList ml = new MapList(codons, protein, 3, 1);
    assertEquals(3, ml.getFromRatio());
    assertEquals(2, ml.getFromLowest());
    assertEquals(18, ml.getFromHighest());
    assertEquals(1, ml.getToLowest());
    assertEquals(6, ml.getToHighest());
    assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
            prettyPrint(ml.getFromRanges()));
    assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));

    /*
     * Also copy constructor
     */
    MapList ml2 = new MapList(ml);
    assertEquals(3, ml2.getFromRatio());
    assertEquals(2, ml2.getFromLowest());
    assertEquals(18, ml2.getFromHighest());
    assertEquals(1, ml2.getToLowest());
    assertEquals(6, ml2.getToHighest());
    assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
            prettyPrint(ml2.getFromRanges()));
    assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
  }

  /**
   * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
   * 
   * @param ranges
   * @return
   */
  private String prettyPrint(List<int[]> ranges)
  {
    StringBuilder sb = new StringBuilder(ranges.size() * 5);
    boolean first = true;
    sb.append("{");
    for (int[] range : ranges)
    {
      if (!first)
      {
        sb.append(", ");
      }
      sb.append(Arrays.toString(range));
      first = false;
    }
    sb.append("}");
    return sb.toString();
  }

  /**
   * Test the method that creates an inverse mapping
   */
  @Test(groups ={ "Functional" })
  public void testGetInverse()
  {
    int[] codons =
    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
    int[] protein =
    { 1, 1, 3, 4, 6, 6 };

    MapList ml = new MapList(codons, protein, 3, 1);
    MapList ml2 = ml.getInverse();
    assertEquals(ml.getFromRatio(), ml2.getToRatio());
    assertEquals(ml.getFromRatio(), ml2.getToRatio());
    assertEquals(ml.getToHighest(), ml2.getFromHighest());
    assertEquals(ml.getFromHighest(), ml2.getToHighest());
    assertEquals(prettyPrint(ml.getFromRanges()),
            prettyPrint(ml2.getToRanges()));
    assertEquals(prettyPrint(ml.getToRanges()),
            prettyPrint(ml2.getFromRanges()));
  }

  @Test(groups ={ "Functional" })
  public void testToString()
  {
    MapList ml = new MapList(new int[]
    { 1, 5, 10, 15, 25, 20 }, new int[]
    { 51, 1 }, 1, 3);
    String s = ml.toString();
    assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
            s);
  }
}