package jalview.ws2.actions.annotation;

import static jalview.testutils.Matchers.matchesSequenceString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.hasSize;

import java.util.List;

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

import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;

public class AnnotationJobTest
{
  @Test(groups = { "Functional" })
  public void testCreate_EqualLengthNoGapsSubmitGaps()
  {
    var alignment = new Alignment(new Sequence[] {
       new Sequence("test1", "ACACACACACA"),
       new Sequence("test2", "AVAVAVAVAVA"),
       new Sequence("test3", "AVWVAVWVAVW")
    });
    var annotJob = AnnotationJob.create(alignment, true, false, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACACACACACA"),
            matchesSequenceString("AVAVAVAVAVA"),
            matchesSequenceString("AVWVAVWVAVW")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_EqualLengthNoGapsNoSubmitGaps()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACACACACACA"),
        new Sequence("test2", "AVAVAVAVAVA"),
        new Sequence("test3", "AVWVAVWVAVW")
    });
    var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACACACACACA"),
            matchesSequenceString("AVAVAVAVAVA"),
            matchesSequenceString("AVWVAVWVAVW")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_UnequalLengthNoGapsNoSubmitGaps()
  {
    var alignment = new Alignment(new Sequence[] {
       new Sequence("test1", "ACACACACACA"),
       new Sequence("test2", "AVAVAVAVAVAVA"),
       new Sequence("test3", "AVWVAVWVAVWV")
    });
    var annotJob = AnnotationJob.create(alignment, true, false, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACACACACACA"),
            matchesSequenceString("AVAVAVAVAVAVA"),
            matchesSequenceString("AVWVAVWVAVWV")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_UnequalLengthNoGapsSubmitGaps()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACACACACACA"),
        new Sequence("test2", "AVAVAVAVAVAVA"),
        new Sequence("test3", "AVWVAVWVAVWV")
     });
     var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
     assertThat(annotJob.getInputSequences(), contains(
             matchesSequenceString("ACACACACACA"),
             matchesSequenceString("AVAVAVAVAVAVA"),
             matchesSequenceString("AVWVAVWVAVWV")
     ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_UnequalLengthNoGapsSubmitGapsRequireAligned()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACACACACACA"),
        new Sequence("test2", "AVAVAVAVAVAVA"),
        new Sequence("test3", "AVWVAVWVAVWV")
     });
     var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
     assertThat(annotJob.getInputSequences(), contains(
             matchesSequenceString("ACACACACACA--"),
             matchesSequenceString("AVAVAVAVAVAVA"),
             matchesSequenceString("AVWVAVWVAVWV-")
     ));
  }

  @DataProvider
  public Object[] alignmentWithShortSequences()
  {
    return new Object[] {
        new Alignment(new Sequence[] {
            new Sequence("test1", "AAAAA"),
            new Sequence("test2", "ACAACAAACAAC"),
            new Sequence("test3", "ACA")
        }),
        new Alignment(new Sequence[] {
            new Sequence("test1", "----AAAAA---"),
            new Sequence("test2", "ACAACAAACAAC"),
            new Sequence("test3", "-----ACA----")
        }),
        new Alignment(new Sequence[] {
            new Sequence("test1", "--AAA---AA--"),
            new Sequence("test2", "ACAACAAACAAC"),
            new Sequence("test3", "-------ACA--")
        }),
    };
  }

  @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
  public void testCreate_TooShortSequence_ShortSequenceRemoved(Alignment aln)
  {
    var annotJob = AnnotationJob.create(aln, true, false, false, false, 0);
    assertThat(annotJob.getInputSequences(), hasSize(1));
  }

  @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
  public void testCreate_TooShortSequenceAndSubmitGaps_ShortSeqRemoved(Alignment aln)
  {
    var annotJob = AnnotationJob.create(aln, true, true, false, false, 0);
    assertThat(annotJob.getInputSequences(), hasSize(1));
  }

  @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
  public void testCreate_TooShortSequenceAndRequireAligned_ShortSeqRemoved(Alignment aln)
  {
    var annotJob = AnnotationJob.create(aln, true, true, true, false, 0);
    assertThat(annotJob.getInputSequences(), hasSize(1));
  }

  @Test(groups = { "Functional" })
  public void testCreate_EmptyColumnAndSubmitGaps_ColumnExtruded()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACA-ACAA--CACA"),
        new Sequence("test2", "AVA-AVAA-AVAVA"),
        new Sequence("test3", "AVAWAVAA-AVWVA")
    });
    var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACA-ACAA-CACA"),
            matchesSequenceString("AVA-AVAAAVAVA"),
            matchesSequenceString("AVAWAVAAAVWVA")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_EmptyColumnAndRequireAligned_ColumnExtruded()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACA-ACAA--CACA"),
        new Sequence("test2", "AVA-AVAA-AVAVA"),
        new Sequence("test3", "AVAWAVAA-AVWVA")
    });
    var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACA-ACAA-CACA"),
            matchesSequenceString("AVA-AVAAAVAVA"),
            matchesSequenceString("AVAWAVAAAVWVA")
    ));
  }

  @Test(groups = { "Functional"} )
  public void testCreate_ContainsNonStandardAndNoFilterNonStandard_NonStandardRemain()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACACAOACACAC"),
        new Sequence("test2", "ABAVAVAVABAV")
    });
    var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACACAOACACAC"),
            matchesSequenceString("ABAVAVAVABAV")
    ));
  }

  @Test(groups = { "Functional"} )
  public void testCreate_ContainsNonStandardAndFilterNonStandard_NonStandardToGap()
  {
    var alignment = new Alignment(new Sequence[] {
        new Sequence("test1", "ACACAOACACAC"),
        new Sequence("test2", "ABAVAVAVABAV")
    });
    var annotJob = AnnotationJob.create(alignment, true, true, true, true, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("ACACA-ACACAC"),
            matchesSequenceString("A-AVAVAVA-AV")
    ));
  }

  @DataProvider
  public Object[] alignmentWithNonStandardInColumns()
  {
    return new Object[] {
        new Alignment(new Sequence[] {
            new Sequence("test1", "A-AAAOAAAAAAAA"),
            new Sequence("test2", "ABAAA-AAAAAAAA")
        }),
        new Alignment(new Sequence[] {
            new Sequence("test1", "ABAAAOAAAAAAAA"),
            new Sequence("test2", "ABAAABAAAAAAAA")
        }),
        new Alignment(new Sequence[] {
            new Sequence("test1", "A-AAAOAAAAAAAA"),
            new Sequence("test2", "A-AAA-AAAAAAAA")
        })
    };
  }

  @Test(groups = { "Functional" }, dataProvider = "alignmentWithNonStandardInColumns")
  public void testCreate_NonStandardInColumnsAndFilterNonStandard_ColumnsExtruded(Alignment aln)
  {
    var annotJob = AnnotationJob.create(aln, true, true, true, true, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("AAAAAAAAAAAA"),
            matchesSequenceString("AAAAAAAAAAAA")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_SequenceGroup_RegionSubmitted()
  {
    var group = new SequenceGroup(List.of(
       new Sequence("test1", "CCCCAAATAAATAAATCCC"),
       new Sequence("test2", "----AAATAAATAAAT---")
    ));
    group.setStartRes(4);
    group.setEndRes(15);
    var annotJob = AnnotationJob.create(group, true, false, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("AAATAAATAAAT"),
            matchesSequenceString("AAATAAATAAAT")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_RegionIncludingGaps_RegionSubmittedWithoutGaps()
  {
    var group = new SequenceGroup(List.of(
       new Sequence("test1", "CCCC-AAATAAATAAAT--CCC"),
       new Sequence("test2", "-----AAATAAATAAAT-----")
    ));
    group.setStartRes(4);
    group.setEndRes(18);
    var annotJob = AnnotationJob.create(group, true, false, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("AAATAAATAAAT"),
            matchesSequenceString("AAATAAATAAAT")
    ));
  }

  @Test(groups = { "Functional" })
  public void testCreate_RegionIncludingGapsAndSubmitGaps_RegionSubmittedGapsExtruded()
  {
    var group = new SequenceGroup(List.of(
       new Sequence("test1", "CCCC-AAATAAATAAAT--CCC"),
       new Sequence("test2", "-----AAATAAATAAAT-----")
    ));
    group.setStartRes(4);
    group.setEndRes(18);
    var annotJob = AnnotationJob.create(group, true, true, false, false, 0);
    assertThat(annotJob.getInputSequences(), contains(
            matchesSequenceString("AAATAAATAAAT"),
            matchesSequenceString("AAATAAATAAAT")
    ));
  }
}