1 package jalview.io.gff;
3 import static org.testng.AssertJUnit.assertNull;
4 import static org.testng.AssertJUnit.assertSame;
5 import static org.testng.AssertJUnit.assertTrue;
7 import org.testng.annotations.Test;
9 public class GffHelperFactoryTest
12 @Test(groups = "Functional")
13 public void testGetHelper()
15 assertNull(GffHelperFactory.getHelper(null));
17 String tabRegex = "\\t";
20 * column 3 = 'similarity' indicates exonerate GFF alignment data
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);
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(),
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);
35 gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
36 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
38 gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
39 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
41 gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
42 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
44 gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
45 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
47 gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
48 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
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);
55 * InterProScan has 'protein_match' in column 3
57 gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
58 assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
61 * nothing specific - return the generic GFF3 class if Name=Value is present in col9
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);
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);