package jalview.io.gff;

import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import org.testng.annotations.Test;

public class GffHelperFactoryTest
{

  @Test(groups = "Functional")
  public void testGetHelper()
  {
    assertNull(GffHelperFactory.getHelper(null));

    String tabRegex = "\\t";

    /*
     * column 3 = 'similarity' indicates exonerate GFF alignment data
     */
    String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
    // no attributes (column 9 data):
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);

    // attributes set but unhandled featureGroup - get generic handler
    gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
            Gff3Helper.class);

    // handled featureGroup (exonerate model) values
    gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    // not case-sensitive:
    gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);

    /*
     * InterProScan has 'protein_match' in column 3
     */
    gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);

    /*
     * nothing specific - return the generic GFF3 class if Name=Value is present in col9
     */
    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
    GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
    assertSame(helper.getClass(), Gff3Helper.class);

    // return the generic GFF2 class if "Name Value" is present in col9
    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
    helper = GffHelperFactory.getHelper(gff.split(tabRegex));
    assertSame(helper.getClass(), Gff2Helper.class);
  }
}