develop merge

[jalview.git] / test / jalview / io / gff / InterProScanHelperTest.java

diff --git a/test/jalview/io/gff/InterProScanHelperTest.java b/test/jalview/io/gff/InterProScanHelperTest.java
new file mode 100644 (file)
index 0000000..2ef4c99
--- /dev/null
+++ b/test/jalview/io/gff/InterProScanHelperTest.java
@@ -0,0 +1,71 @@
+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));
+  }
+
+}