From 4db713f772ee30861f368dcea9f306b987ad01d2 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 Dec 2014 10:47:48 +0000
Subject: [PATCH] JAL-845 first simple unit tests added

---
 test/jalview/analysis/DnaTest.java |   70 ++++++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 test/jalview/analysis/DnaTest.java

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
new file mode 100644
index 0000000..b1ce141
--- /dev/null
+++ b/test/jalview/analysis/DnaTest.java
@@ -0,0 +1,70 @@
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+public class DnaTest
+{
+  // AA encoding codons as ordered on the Jalview help page Amino Acid Table
+  private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
+          + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
+          + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
+          + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
+          + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
+          + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
+          + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
+          + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
+          + "TAC" + "TAA" + "TAG" + "TGA";
+
+  /**
+   * Test simple translation to Amino Acids (with STOP codons translated to X).
+   * 
+   * @throws IOException
+   */
+  @Test
+  public void testCdnaTranslate_simple() throws IOException
+  {
+    AlignmentI alf = new FormatAdapter().readFile(fasta,
+            FormatAdapter.PASTE, "FASTA");
+    final String sequenceAsString = alf
+                .getSequenceAt(0).getSequenceAsString();
+    AlignmentI translated = Dna.CdnaTranslate(alf.getSequencesArray(),
+            new String[]
+            { sequenceAsString }, new int[]
+            { 0, alf.getWidth() - 1 }, alf.getGapCharacter(), null,
+            alf.getWidth(), null);
+    String aa = translated.getSequenceAt(0).getSequenceAsString();
+    assertEquals(
+            "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
+            aa);
+  }
+
+  /**
+   * Test translation excluding hidden columns.
+   * 
+   * @throws IOException
+   */
+  @Test
+  public void testCdnaTranslate_hiddenColumns() throws IOException
+  {
+    AlignmentI alf = new FormatAdapter().readFile(fasta,
+            FormatAdapter.PASTE, "FASTA");
+    ColumnSelection cs = new jalview.datamodel.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
+    AlignmentI translated = Dna.CdnaTranslate(alf.getSequencesArray(),
+            cs.getVisibleSequenceStrings(0, alf.getWidth(),
+                    alf.getSequencesArray()), new int[]
+            { 0, alf.getWidth() - 1 }, alf.getGapCharacter(), null,
+            alf.getWidth(), null);
+    String aa = translated.getSequenceAt(0).getSequenceAsString();
+    assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
+  }
+}
-- 
1.7.10.2