JAL-1705 tests added, minor bugfix and refactoring

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 3ca74b0..c525e95 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,5 +1,7 @@
 package jalview.ext.ensembl;
 
+import static org.testng.AssertJUnit.assertEquals;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -182,21 +184,21 @@ public class EnsemblSeqProxyTest
       }
 
       @Override
-      public boolean useGetRequest()
+      protected boolean useGetRequest()
       {
         // TODO Auto-generated method stub
         return false;
       }
 
       @Override
-      public String getRequestMimeType()
+      protected String getRequestMimeType(boolean b)
       {
         // TODO Auto-generated method stub
         return null;
       }
 
       @Override
-      public String getResponseMimeType()
+      protected String getResponseMimeType()
       {
         // TODO Auto-generated method stub
         return null;
@@ -208,4 +210,74 @@ public class EnsemblSeqProxyTest
             + (isAvailable ? "UP!"
                     : "DOWN or unreachable ******************* BAD!"));
   }
+
+  /**
+   * Tests for the method that computes all peptide variants given codon
+   * variants
+   */
+  @Test(groups = "Functional")
+  public void testComputePeptideVariants()
+  {
+    String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
+
+    /*
+     * AGT codes for S - this is not included in the variants returned
+     */
+    List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[]", variants.toString());
+
+    // S is reported if it differs from the current value (A):
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
+    assertEquals("[S]", variants.toString());
+
+    /*
+     * synonymous variant is not reported
+     */
+    codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
+    // AGC and AGT both code for S
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
+    assertEquals("[]", variants.toString());
+
+    /*
+     * equivalent variants are only reported once
+     */
+    codonVariants = new String[][] { { "C" }, { "T" },
+        { "A", "C", "G", "T" } };
+    // CTA CTC CTG CTT all code for L
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[L]", variants.toString());
+
+    /*
+     * vary codons 1 and 2; variant products are sorted and non-redundant
+     */
+    codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
+    // aga ata cga cta code for R, I, R, L
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[I, L, R]", variants.toString());
+
+    /*
+     * vary codons 2 and 3
+     */
+    codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
+    // aga agc ata atc code for R, S, I, I
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[I, R]", variants.toString());
+
+    /*
+     * vary codons 1 and 3
+     */
+    codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
+    // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[K, N, Y, STOP]", variants.toString());
+
+    /*
+     * vary codons 1, 2 and 3
+     */
+    codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
+        { "t", "g" } };
+    // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
+    variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
+    assertEquals("[C, R, T, W]", variants.toString());
+  }
 }
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