X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTest.java;h=31c98391ad4160e154c030b597e876af14988c79;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=8f878f0e25228856ccacb84f3adbabca435f69ba;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 8f878f0..31c9839 100644
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -29,8 +29,11 @@ import jalview.datamodel.AlignedCodon;
 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.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
@@ -119,8 +122,8 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
+            JAL_1312_example_align_fasta, DataSourceType.PASTE,
+            FileFormat.Fasta);
     ColumnSelection cs = new ColumnSelection();
     AlignViewportI av = new AlignViewport(alf, cs);
     Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
@@ -140,8 +143,8 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
+            JAL_1312_example_align_fasta, DataSourceType.PASTE,
+            FileFormat.Fasta);
     int vwidth = 15;
     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
     {
@@ -175,7 +178,7 @@ public class DnaTest
   public void testTranslateCdna_simple() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
+            DataSourceType.PASTE, FileFormat.Fasta);
     ColumnSelection cs = new ColumnSelection();
     AlignViewportI av = new AlignViewport(alf, cs);
     Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
@@ -195,8 +198,8 @@ public class DnaTest
   public void testTranslateCdna_hiddenColumns() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
-    ColumnSelection cs = new jalview.datamodel.ColumnSelection();
+            DataSourceType.PASTE, FileFormat.Fasta);
+    ColumnSelection cs = new ColumnSelection();
     cs.hideColumns(6, 14); // hide codons 3/4/5
     cs.hideColumns(24, 35); // hide codons 9-12
     cs.hideColumns(177, 191); // hide codons 60-64
@@ -457,4 +460,85 @@ public class DnaTest
     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());
+  }
 }