--- /dev/null
+package jalview.io.gff;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class InterProScanHelperTest
+{
+
+ /**
+ * Test processing one InterProScan GFF line
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testProcessProteinMatch() throws IOException
+ {
+ InterProScanHelper testee = new InterProScanHelper();
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ String[] gff = "Submitted\tPfam\tprotein_match\t5\t30\t0\t+\t.\tName=PF12838;Target=Submitted 5 30;signature_desc=4Fe-4S dicluster domain;ID=match$17_5_30"
+ .split("\\t");
+ SequenceI seq = new Sequence("Prot1", "PQRASTGKEEDVMIWCHQN");
+ seq.createDatasetSequence();
+ AlignmentI align = new Alignment(new SequenceI[] {});
+ Map<String, List<String>> set = Gff3Helper.parseNameValuePairs(gff[8]);
+
+ /*
+ * this should create a mapping from Prot1/5-30 to virtual sequence
+ * match$17_5_30 (added to newseqs) positions 1-26
+ */
+ testee.processProteinMatch(set, seq, gff, align, newseqs, false);
+ assertEquals(1, newseqs.size());
+ assertTrue(newseqs.get(0) instanceof SequenceDummy);
+ assertEquals("match$17_5_30", newseqs.get(0).getName());
+ assertEquals(1, align.getCodonFrames().size());
+ AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
+
+ /*
+ * 'dnaseqs' (map from) is here [Prot1]
+ * 'aaseqs' (map to) is here [match$17_5_30]
+ */
+ // TODO use more suitable naming in AlignedCodonFrame
+ assertEquals(1, mapping.getAaSeqs().length);
+ assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);
+ assertEquals(1, mapping.getdnaSeqs().length);
+ assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
+ assertEquals(1, mapping.getdnaToProt().length);
+ assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
+ assertArrayEquals(new int[] { 5, 30 }, mapping.getdnaToProt()[0]
+ .getFromRanges().get(0));
+ assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
+ assertArrayEquals(new int[] { 1, 26 }, mapping.getdnaToProt()[0]
+ .getToRanges().get(0));
+ }
+
+}