--- /dev/null
+package jalview.io.gff;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+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.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class Gff3HelperTest
+{
+
+ /**
+ * Test processing one PASA GFF line giving a match from forward strand to
+ * forward strand
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testProcessCdnaMatch_forwardToForward() throws IOException
+ {
+ GffHelperBase testee = new Gff3Helper();
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ String[] gff = "gi|68711\tblat-pasa\tcDNA_match\t12923\t13060\t98.55\t+\t.\tID=align_68;Target=gi|N37351 1 138 +"
+ .split("\\t");
+ SequenceI seq = new Sequence("gi|68711",
+ "GAATTCGTTCATGTAGGTTGATTTTTATT");
+ seq.createDatasetSequence();
+ AlignmentI align = new Alignment(new SequenceI[] {});
+
+ /*
+ * this should create a mapping from gi|68711/12923-13060
+ * to virtual sequence gi|N37351 (added to newseqs) positions 1-138
+ */
+ testee.processGff(seq, gff, align, newseqs, false);
+ assertEquals(1, newseqs.size());
+ assertTrue(newseqs.get(0) instanceof SequenceDummy);
+ assertEquals("gi|N37351", newseqs.get(0).getName());
+ assertEquals(1, align.getCodonFrames().size());
+ AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
+
+ /*
+ * 'dnaseqs' (map from) is here [gi|68711]
+ * 'aaseqs' (map to) is here [gi|N37351]
+ */
+ // 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[] { 12923, 13060 }, mapping.getdnaToProt()[0]
+ .getFromRanges().get(0));
+ assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
+ assertArrayEquals(new int[] { 1, 138 }, mapping.getdnaToProt()[0]
+ .getToRanges().get(0));
+ }
+
+ /**
+ * Test processing one PASA GFF line giving a match from forward strand to
+ * reverse strand
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testProcessCdnaMatch_forwardToReverse() throws IOException
+ {
+ GffHelperBase testee = new Gff3Helper();
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ String[] gff = "gi|68711\tblat-pasa\tcDNA_match\t12923\t13060\t98.55\t+\t.\tID=align_68;Target=gi|N37351 1 138 -"
+ .split("\\t");
+ SequenceI seq = new Sequence("gi|68711",
+ "GAATTCGTTCATGTAGGTTGATTTTTATT");
+ seq.createDatasetSequence();
+ AlignmentI align = new Alignment(new SequenceI[] {});
+
+ /*
+ * this should create a mapping from gi|68711/12923-13060
+ * to virtual sequence gi|N37351 (added to newseqs) positions 138-1
+ */
+ testee.processGff(seq, gff, align, newseqs, false);
+ assertEquals(1, newseqs.size());
+ assertTrue(newseqs.get(0) instanceof SequenceDummy);
+ assertEquals("gi|N37351", newseqs.get(0).getName());
+ assertEquals(1, align.getCodonFrames().size());
+ AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
+
+ /*
+ * 'dnaseqs' (map from) is here [gi|68711]
+ * 'aaseqs' (map to) is here [gi|N37351]
+ */
+ // 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[] { 12923, 13060 }, mapping.getdnaToProt()[0]
+ .getFromRanges().get(0));
+ assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
+ assertArrayEquals(new int[] { 138, 1 }, mapping.getdnaToProt()[0]
+ .getToRanges().get(0));
+ }
+
+ /**
+ * Test processing one PASA GFF line giving a match from reverse complement
+ * strand to forward strand
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testProcessCdnaMatch_reverseToForward() throws IOException
+ {
+ GffHelperBase testee = new Gff3Helper();
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ String[] gff = "gi|68711\tblat-pasa\tcDNA_match\t12923\t13060\t98.55\t-\t.\tID=align_68;Target=gi|N37351 1 138 +"
+ .split("\\t");
+ SequenceI seq = new Sequence("gi|68711",
+ "GAATTCGTTCATGTAGGTTGATTTTTATT");
+ seq.createDatasetSequence();
+ AlignmentI align = new Alignment(new SequenceI[] {});
+
+ /*
+ * (For now) we don't process reverse complement mappings; to do this
+ * would require (a) creating a virtual sequence placeholder for the
+ * reverse complement (b) resolving the sequence by its id from some
+ * source (GFF ##FASTA or other) (c) creating the reverse complement
+ * sequence (d) updating the mapping to be to the reverse complement
+ */
+ SequenceFeature sf = testee.processGff(seq, gff, align, newseqs, false);
+ assertNull(sf);
+ assertTrue(newseqs.isEmpty());
+ }
+
+ /**
+ * Test processing two PASA GFF lines representing a spliced mapping
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testProcessCdnaMatch_spliced() throws IOException
+ {
+ GffHelperBase testee = new Gff3Helper();
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+ SequenceI seq = new Sequence("gi|68711",
+ "GAATTCGTTCATGTAGGTTGATTTTTATT");
+ seq.createDatasetSequence();
+ AlignmentI align = new Alignment(new SequenceI[] {});
+
+ // mapping from gi|68711 12923-13060 to gi|N37351 1-138
+ String[] gff = "gi|68711\tblat-pasa\tcDNA_match\t12923\t13060\t98.55\t+\t.\tID=align_68;Target=gi|N37351 1 138 +"
+ .split("\\t");
+ testee.processGff(seq, gff, align, newseqs, false);
+ // mapping from gi|68711 13411-13550 to gi|N37351 139-278
+ gff = "gi|68711\tblat-pasa\tcDNA_match\t13411\t13550\t98.55\t+\t.\tID=align_68;Target=gi|N37351 139 278 +"
+ .split("\\t");
+ testee.processGff(seq, gff, align, newseqs, false);
+
+ assertEquals(1, newseqs.size());
+ assertTrue(newseqs.get(0) instanceof SequenceDummy);
+ assertEquals("gi|N37351", newseqs.get(0).getName());
+
+ // only 1 AlignedCodonFrame added to the alignment with both mappings!
+ // (this is important for 'align cdna to genome' to work correctly)
+ assertEquals(1, align.getCodonFrames().size());
+ AlignedCodonFrame mapping = align.getCodonFrames().get(0);
+
+ /*
+ * 'dnaseqs' (map from) is here [gi|68711]
+ * 'aaseqs' (map to) is here [gi|N37351]
+ */
+ // 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(2, mapping.getdnaToProt()[0].getFromRanges().size());
+ // the two spliced dna ranges are combined in one MapList
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0]
+ .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 13411, 13550 }, mapping.getdnaToProt()[0]
+ .getFromRanges().get(1));
+ assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
+ // the two cdna ranges are merged into one contiguous region
+ assertArrayEquals(new int[] { 1, 278 }, mapping.getdnaToProt()[0]
+ .getToRanges().get(0));
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff