test/jalview/io/gff/GffHelperFactoryTest.java

   1 package jalview.io.gff;
   2
   3 import static org.testng.AssertJUnit.assertNull;
   4 import static org.testng.AssertJUnit.assertSame;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import org.testng.annotations.Test;
   8
   9 public class GffHelperFactoryTest
  10 {
  11
  12   @Test(groups = "Functional")
  13   public void testGetHelper()
  14   {
  15     assertNull(GffHelperFactory.getHelper(null));
  16
  17     String tabRegex = "\\t";
  18
  19     /*
  20      * column 3 = 'similarity' indicates exonerate GFF alignment data
  21      */
  22     String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
  23     // no attributes (column 9 data):
  24     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
  25
  26     // attributes set but unhandled featureGroup - get generic handler
  27     gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  28     assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
  29             Gff3Helper.class);
  30
  31     // handled featureGroup (exonerate model) values
  32     gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  33     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  34
  35     gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  36     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  37
  38     gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  39     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  40
  41     gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  42     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  43
  44     gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  45     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  46
  47     gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
  48     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  49
  50     // not case-sensitive:
  51     gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
  52     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
  53
  54     /*
  55      * InterProScan has 'protein_match' in column 3
  56      */
  57     gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
  58     assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
  59
  60     /*
  61      * nothing specific - return the generic GFF3 class if Name=Value is present in col9
  62      */
  63     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
  64     GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
  65     assertSame(helper.getClass(), Gff3Helper.class);
  66
  67     // return the generic GFF2 class if "Name Value" is present in col9
  68     gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
  69     helper = GffHelperFactory.getHelper(gff.split(tabRegex));
  70     assertSame(helper.getClass(), Gff2Helper.class);
  71   }
  72 }