JAL-845 cDNA mapping: select on sequence translation instead of name

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 2711a36..f56dd5d 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 import jalview.analysis.AlignmentUtils.MappingResult;
@@ -568,4 +569,48 @@ public class AlignmentUtilsTests
     assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
   }
 
+  /**
+   * Test the method that tests whether a CDNA sequence translates to a protein
+   * sequence
+   */
+  @Test
+  public void testTranslatesAs()
+  {
+    assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+            "FPKG".toCharArray()));
+    // with start codon
+    assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
+            3, "FPKG".toCharArray()));
+    // with stop codon1
+    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
+            0, "FPKG".toCharArray()));
+    // with stop codon2
+    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
+            0, "FPKG".toCharArray()));
+    // with stop codon3
+    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
+            0, "FPKG".toCharArray()));
+    // with start and stop codon1
+    assertTrue(AlignmentUtils.translatesAs(
+            "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray()));
+    // with start and stop codon2
+    assertTrue(AlignmentUtils.translatesAs(
+            "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray()));
+    // with start and stop codon3
+    assertTrue(AlignmentUtils.translatesAs(
+            "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray()));
+
+    // wrong protein
+    assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+            0,
+            "FPMG".toCharArray()));
+  }
+
+  @Test
+  public void testTranslatesAs_withAmbiguityCodes()
+  {
+    // R means A or G
+    assertTrue(AlignmentUtils.translatesAs("car".toCharArray(), 0,
+            "Q".toCharArray()));
+  }
 }