test case for biojava#344

andreasprlic · andreasprlic · commit 184b22072e0b · 2015-12-04T16:21:50.000-08:00
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java b/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java
@@ -0,0 +1,57 @@
+package org.biojava.nbio.core;
+
+import junit.framework.TestCase;
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.DNASequence;
+import org.biojava.nbio.core.sequence.RNASequence;
+import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
+import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
+import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+import org.biojava.nbio.core.sequence.io.RNASequenceCreator;
+import org.biojava.nbio.core.sequence.template.Compound;
+import org.biojava.nbio.core.sequence.template.CompoundSet;
+import org.biojava.nbio.core.sequence.template.Sequence;
+import org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator;
+import org.junit.Test;
+
+/**
+ * A Test case for https://github.com/biojava/biojava/issues/344
+ *
+ * Created by andreas on 12/4/15.
+ */
+
+public class TestAmbiguityCompoundSet extends TestCase{
+
+    @Test
+    public void testCompountSet(){
+        try {
+
+            CompoundSet<NucleotideCompound> dnaSet = AmbiguityDNACompoundSet.getDNACompoundSet();
+            CompoundSet<NucleotideCompound> rnaSet = AmbiguityRNACompoundSet.getRNACompoundSet();
+
+            DNASequence dna=new DNASequence("AGTCS", dnaSet);
+
+            assertEquals("AGTCS",dna.toString());
+
+            RNASequence rna = dna.getRNASequence();
+
+            rna = new RNASequence(dna.getSequenceAsString().replaceAll("T", "U"), AmbiguityRNACompoundSet.getRNACompoundSet()); //fails with missing compound S
+
+            assertEquals("AGUCS",rna.toString());
+
+            /** now, do the translation also using the underlying API (should not be needed for a user)
+             *
+             */
+            DNAToRNATranslator translator = new DNAToRNATranslator(new RNASequenceCreator(rnaSet
+                    ),dnaSet,rnaSet,false);
+
+            Sequence<NucleotideCompound> translated = translator.createSequence(dna);
+
+            assertEquals("AGUCS", translated.toString());
+            
+        } catch (CompoundNotFoundException e) {
+            e.printStackTrace();
+            fail(e.getMessage());
+        }
+    }
+}
