package jalview.ws.jws1;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

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

public class JPredWSUtilsTest
{
  @Test(groups = { "Functional" })
  public void testSingleSeqPrediction()
  {

  }

  @Test(groups = { "Functional" })
  public void testSingleSeqPredictionHiddenRegion()
  {

  }

  @Test(groups = { "Functional" })
  public void testMsaPrediction()
  {

  }

  @Test(groups = { "Functional" })
  public void testMsaPredictionHiddenRegion()
  {

  }

  @Test(groups = { "Functional" })
  public void testInsertHiddenResidues()
  {
    // orig: asdfPPPPPPPasdfPPPPasdf
    // pred: PPPPPPPPPPP
    // al: -----P-P-P---P---P----P---P-P--PP---P---
    // s1: SSSSSSS-SS---S---SSSSSS---S-S--SSSSSSSSS
    // s2: SSSSSSS-SSSSSSSSSSS----SSS-S-SSS-----SSS
    SequenceI orig = new Sequence("orig", "asdfPPPPPPPasdfPPPPasdf"), pred = new Sequence(
            "pred", "PPPPPPPPPPP"), al = new Sequence("al/5-23",
            "-----P-P-P---P---P----P---P-P--PP---P---"), s1 = new Sequence(
            "s1", "SSSSSSS-SS---S---SSSSSS---S-S--SSSSSSSSS"), s2 = new Sequence(
            "s2", "SSSSSSS-SSSSSSSSSSS----SSS-S-SSS-----SSS");

    AlignmentI alpred = new Alignment(new SequenceI[] { al, s1, s2 });
    JPredWSUtils.insertHiddenResidues(alpred, '.', new int[] { 5, 6, 7, 8,
        9, 10, 11, 16, 17, 18, 19 }, orig);
    Assert.assertEquals(alpred.getSequenceAt(2).getSequenceAsString(),
            "....SSSSSSS-SS---S---SSSSSS---S....-S--SSSSSSSSS....");
    Assert.assertEquals(alpred.getSequenceAt(1).getSequenceAsString(),
            "....SSSSSSS-SSSSSSSSSSS----SSS-....S-SSS-----SSS....");
    Assert.assertEquals(alpred.getSequenceAt(0).getSequenceAsString(),
            "asdf-----P-P-P---P---P----P---Pasdf-P--PP---P---asdf");

    // result:
    //
    // al: asdf-----P-P-P---P---P----P---Pasdf-P--PP---P---asdf
    // s1: ....SSSSSSS-SS---S---SSSSSS---S....-S--SSSSSSSSS....
    // s2: ....SSSSSSS-SSSSSSSSSSS----SSS-....S-SSS-----SSS....
  }
}