import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import jalview.io.FormatAdapter;
import java.io.IOException;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DnaTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// @formatter:off
// AA encoding codons as ordered on the Jalview help page Amino Acid Table
private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
}
+
+ /**
+ * Test dna complementing
+ */
+ @Test(groups = "Functional")
+ public void testGetComplement()
+ {
+ assertEquals('t', Dna.getComplement('a'));
+ assertEquals('T', Dna.getComplement('A'));
+ assertEquals('a', Dna.getComplement('t'));
+ assertEquals('A', Dna.getComplement('T'));
+ assertEquals('c', Dna.getComplement('g'));
+ assertEquals('C', Dna.getComplement('G'));
+ assertEquals('g', Dna.getComplement('c'));
+ assertEquals('G', Dna.getComplement('C'));
+ // note uU --> aA but not vice versa
+ assertEquals('a', Dna.getComplement('u'));
+ assertEquals('A', Dna.getComplement('U'));
+ // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
+ assertEquals('r', Dna.getComplement('y'));
+ assertEquals('R', Dna.getComplement('Y'));
+ assertEquals('y', Dna.getComplement('r'));
+ assertEquals('Y', Dna.getComplement('R'));
+ assertEquals('k', Dna.getComplement('m'));
+ assertEquals('K', Dna.getComplement('M'));
+ assertEquals('m', Dna.getComplement('k'));
+ assertEquals('M', Dna.getComplement('K'));
+ assertEquals('b', Dna.getComplement('v'));
+ assertEquals('B', Dna.getComplement('V'));
+ assertEquals('v', Dna.getComplement('b'));
+ assertEquals('V', Dna.getComplement('B'));
+ assertEquals('d', Dna.getComplement('h'));
+ assertEquals('D', Dna.getComplement('H'));
+ assertEquals('h', Dna.getComplement('d'));
+ assertEquals('H', Dna.getComplement('D'));
+ assertEquals('Q', Dna.getComplement('Q'));
+ }
+
+ @Test(groups = "Functional")
+ public void testReverseSequence()
+ {
+ String seq = "-Ac-GtU--rYkMbVdHNX-";
+ String seqRev = new StringBuilder(seq).reverse().toString();
+
+ // reverse:
+ SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
+ assertEquals(1, reversed.getStart());
+ assertEquals(15, reversed.getEnd());
+ assertEquals(20, reversed.getLength());
+ assertEquals(seqRev, reversed.getSequenceAsString());
+ assertEquals("Seq1|rev", reversed.getName());
+
+ // reverse complement:
+ SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
+ assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
+ assertEquals("Seq1|revcomp", revcomp.getName());
+ }
+
+ @Test(groups = "Functional")
+ public void testReverseCdna()
+ {
+ String seq = "-Ac-GtU--rYkMbVdHNX-";
+ String seqRev = new StringBuilder(seq).reverse().toString();
+ String seqDs = seq.replaceAll("-", "");
+ String seqDsRev = new StringBuilder(seqDs).reverse().toString();
+
+ SequenceI dna = new Sequence("Seq1", seq);
+ Alignment al = new Alignment(new SequenceI[] { dna });
+ al.createDatasetAlignment();
+ assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceAsString());
+
+ ColumnSelection cs = new ColumnSelection();
+ AlignViewportI av = new AlignViewport(al, cs);
+ Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+ AlignmentI reversed = testee.reverseCdna(false);
+ assertEquals(1, reversed.getHeight());
+ assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
+ assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
+ .getSequenceAsString());
+ }
}