package jalview.util;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNull;

import jalview.datamodel.HMMNode;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Vector;

import org.testng.annotations.Test;

import junit.extensions.PA;

public class HMMProbabilityDistributionAnalyserTest {

  HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();

  @Test
  public void testMoveToFile() throws IOException
  {

    BufferedReader br = new BufferedReader(new FileReader(
            "test/jalview/util/test_Fams_for_probability_analysis"));
    analyser.moveLocationBy(1, br);

    String line = br.readLine();
    assertEquals(line, "# STOCKHOLM 1.0");
    line = br.readLine();
    assertEquals(line, "seq1 ATW");
    line = br.readLine();
    assertEquals(line, "seq2 ATI");

  }

  @Test
  public void testCountValidResidues()
  {
    analyser.sequences = new Vector<>();
    analyser.hmm = new HiddenMarkovModel();
    analyser.hmm.setProperty("LENG", "8");

    List<HMMNode> nodes = new ArrayList<>();
    nodes.add(new HMMNode());
    for (int i = 1; i < 9; i++)
    {
      HMMNode node = new HMMNode();
      node.setResidueNumber(i - 1);
      nodes.add(node);

    }
    PA.setValue(analyser.hmm, "nodes", nodes);

    SequenceI[] sequence = new Sequence[] {
        new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
        new Sequence("seq3", "--.ATccGc") };
    analyser.sequences.add(sequence[0]);
    analyser.sequences.add(sequence[1]);
    analyser.sequences.add(sequence[2]);

    int count = analyser.countValidResidues();
    assertEquals(count, 16);
  }

  @Test(priority = 0)
  public void testReadBinned() throws IOException
  {
    analyser.readBinned("test/jalview/util/");
    Map<String, Double> map = analyser.binned;
    assertEquals(map.get("1.8"), 4.53);
    assertEquals(map.get("3.4"), 2.65);
    assertEquals(map.get("6.4"), 10.8);
    assertEquals(map.get("0"), 5.4);
  }

  @Test
  public void testReadRaw() throws IOException
  {
    analyser.readRaw("test/jalview/util/");
    List<ArrayList<Double>> list = analyser.raw;

    assertEquals(list.get(0).get(0), 1.43);
    assertNull(list.get(0).get(2));
    assertEquals(list.get(1).get(1), 1.2);
    assertEquals(list.get(2).get(0), 5.6);
    assertEquals(list.get(2).get(2), 6.8);

  }

  @Test(priority = 1)
  public void testProcessData() throws IOException
  {
    analyser.keepRaw = true;
    BufferedReader brFam = new BufferedReader(new FileReader(
            "test/jalview/util/test_Fams_for_probability_analysis"));
    BufferedReader brHMM = new BufferedReader(new FileReader(
            "test/jalview/util/test_HMMs_for_probability_analysis"));
    analyser.readStockholm(brFam);
    analyser.readHMM(brHMM);
    analyser.processData(6);
    Map<String, Double> map = analyser.binned;
    List<ArrayList<Double>> list = analyser.raw;
    assertEquals(map.get("1.8"), 4.863, 0.001d);
    assertEquals(map.get("3.4"), 2.65);
    assertEquals(map.get("0"), 5.4);
    assertEquals(map.get("6.4"), 10.8);
    assertEquals(map.get("1.4"), 0.166667, 0.00001d);
    assertEquals(map.get("4.4"), 0.5);

  }
}