package jalview.datamodel;

import java.util.Iterator;
import java.util.SortedMap;
import java.util.TreeMap;

import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;

public class CigarParserTest
{
  @BeforeClass(alwaysRun = true)
  public void setup()
  {



  }

  @DataProvider(name = "reads")
  public Object[][] createReadsData()
  {
    SortedMap<Integer, Integer> noinsertions = new TreeMap<>();

    SortedMap<Integer, Integer> insertions = new TreeMap<>();
    insertions.put(8, 3);
    insertions.put(105, 2);

    SortedMap<Integer, Integer> insertions2 = new TreeMap<>();
    insertions2.put(11, 2);

    SortedMap<Integer, Integer> insertions3 = new TreeMap<>();
    insertions3.put(8, 3);
    insertions3.put(105, 3);

    SortedMap<Integer, Integer> insertions4 = new TreeMap<>();
    insertions4.put(8, 3);
    insertions4.put(105, 2);
    insertions4.put(109, 3);
    insertions4.put(112, 1);

    String read = "CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC";

    return new Object[][] { { "1S84M2I14M", read, 21,
        "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
        insertions }, // first residue is G (accounting for C soft clip) at
                      // position 21 + 3 (insertions at position 8)
        { "1S84M2I14M", read, 21,
            "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGA-GGAGCTCGTTGGTC",
            insertions3 }, // read has 2 insertions accounted for in
                           // insertions3, 3rd insertion is added as gap at
                           // position 105
        { "1S84M2I14M", read, 21,
            "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAG---CTC-GTTGGTC",
            insertions4 }, // 2 insertions in read accounted for at position
                           // 105; 3 insertions at 109 and 1 insertion at 112
        { "44M1D57M",
        read,
        3,
            "--CGAAG---CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
        insertions },
        { "101M",
            read, 4,
            "---CGAA---GCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
            insertions },
        { "6M2D76M19S",
            "CGAAGCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTCCC",
            4,
            "---CGAAGC----TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGA",
            insertions2 },

        { "44M1D57M",
            read,
            3,
            "--CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
            noinsertions },
        { "101M",
            read, 4,
            "---CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
            noinsertions },
        { "5S96M", read, 7,
            "------CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
            noinsertions },
        { "96M5H", read, 7,
            "------CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGT",
            noinsertions }, };
  }

  @Test(dataProvider = "reads", groups = { "Functional" })
  public void testParse(String cigar, String read, int start, String result,
          SortedMap<Integer, Integer> insertions)
  {
    SAMRecord rec = new SAMRecord(null);
    rec.setCigarString(cigar);
    rec.setReadString(read);
    rec.setAlignmentStart(start);

    CigarParser cp = new CigarParser('-');
    String bfresult = cp.parseCigarToSequence(rec, insertions, 1);

    System.out.println(result);
    System.out.println(bfresult);
    Assert.assertEquals(bfresult, result);
  }

  @Test(groups = { "Functional" })
  public void testGetInsertions()
  {
    final SAMRecordSetBuilder builder = new SAMRecordSetBuilder();
    builder.addFrag("read_1", 22, 30000, false, false,
            "101M", "", 0);
    builder.addFrag("read_2", 22, 28835, false, false,
            "50M3I48M", "", 0);
    builder.addFrag("read_3", 22, 28835, false, false, "3M1I75M2I1M", "",
            0);
    builder.addFrag("read_4", 22, 28865, false, false, "48M3I49M", "", 0);
    builder.addFrag("read_5", 22, 28865, false, false, "49M3I47M2D2M", "",
            0);
    builder.addFrag("read_6", 22, 27000, false, false, "2M4I90M5S", "", 0);
    builder.addFrag("read_7", 22, 27000, false, false, "2M1I98M", "", 0);

    builder.addFrag("read_8", 22, 27000, false, false, "3M200N2I5M", "", 0);

    Iterator<SAMRecord> it = builder.iterator();
    CigarParser cp = new CigarParser('-');
    SortedMap<Integer, Integer> insertions = cp.getInsertions(it);
    Assert.assertEquals(insertions.size(), 6);
    Assert.assertTrue(insertions.containsKey(28838));
    Assert.assertEquals((int) insertions.get(28838), 1);
    Assert.assertTrue(insertions.containsKey(28885));
    Assert.assertEquals((int) insertions.get(28885), 3);
    Assert.assertTrue(insertions.containsKey(28913));
    Assert.assertEquals((int) insertions.get(28913), 3);
    Assert.assertTrue(insertions.containsKey(28914));
    Assert.assertEquals((int) insertions.get(28914), 3);
    Assert.assertTrue(insertions.containsKey(27002));
    Assert.assertEquals((int) insertions.get(27002), 4);
    Assert.assertTrue(insertions.containsKey(27203));
    Assert.assertEquals((int) insertions.get(27203), 2);
  }
}