tidy up RNASeqTest

otter606 · otter606 · commit 570fdaca28c0 · 2022-01-03T16:31:17.000Z
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/RNASequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/RNASequenceTest.java
@@ -1,7 +1,74 @@
 package org.biojava.nbio.core.sequence;
 
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+import org.biojava.nbio.core.sequence.template.Compound;
+import org.biojava.nbio.core.sequence.template.SequenceView;
+import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import static java.util.stream.Collectors.joining;
 import static org.junit.jupiter.api.Assertions.*;
 
 class RNASequenceTest {
 
+    // AUG start, then 3 AA, then stop codon
+    final String rnaSeq    = "AUGGUCGAACUCUGA";
+    final String rnaSeqCompl = "UACCAGCUUGAGACU";
+    final String rnaSeqReversed = "AGUCUCAAGCUGGUA";
+    final String rnaSeqReversedComplement = "UCAGAGUUCGACCAU";
+    RNASequence rna;
+    @BeforeEach
+    void before() throws CompoundNotFoundException {
+        rna = new RNASequence(rnaSeq);
+    }
+
+    @Test
+    void translateToProteinSequence()  {
+        ProteinSequence protein =  rna.getProteinSequence(TranscriptionEngine.getDefault());
+        assertEquals(4, protein.getLength());
+        assertEquals("MVEL", protein.getSequenceAsString());
+    }
+
+    @Test
+    void complement()  {
+        SequenceView<NucleotideCompound> complement = rna.getComplement();
+        assertEquals(rnaSeqCompl, complement.getSequenceAsString());
+        assertEquals(rnaSeq, complement.getViewedSequence().getSequenceAsString());
+        assertEquals(rna.getLength(), complement.getLength());
+    }
+
+    @Test
+    void reverse()  {
+        SequenceView<NucleotideCompound> reversed = rna.getInverse();
+        assertEquals(rnaSeqReversed, reversed.getSequenceAsString());
+        assertEquals(rnaSeq, reversed.getViewedSequence().getSequenceAsString());
+        assertEquals(rna.getLength(), reversed.getLength());
+    }
+
+    @Test
+    void reverseComplement()  {
+        SequenceView<NucleotideCompound> reverseComplement = rna.getReverseComplement();
+        assertEquals(rnaSeqReversedComplement, reverseComplement.getSequenceAsString());
+        assertEquals(rna.getLength(), reverseComplement.getLength());
+        StringBuilder sb = new StringBuilder();
+        for (int i = 1; i <= rna.getLength(); i++) {
+            sb.append(reverseComplement.getCompoundAt(i).toString());
+        }
+        assertEquals(rnaSeqReversedComplement, sb.toString());
+
+        sb = new StringBuilder();
+        for (Compound c: reverseComplement) {
+            sb.append(c.toString());
+        }
+        assertEquals(rnaSeqReversedComplement, sb.toString());
+        assertEquals(rnaSeqReversedComplement, reverseComplement.getAsList().stream().map(Compound::toString).collect(joining("")));
+    }
+
+    @Test
+    void rejectThymineInSequence()  {
+        String dna = rnaSeq.replaceAll("U", "T");
+        assertThrows(CompoundNotFoundException.class, ()->new RNASequence(dna));
+    }
+
 }
