unit tests for chromosome sequence

otter606 · otter606 · commit 9ca74355a51c · 2021-11-17T21:34:36.000Z
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ChromosomeSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ChromosomeSequenceTest.java
@@ -0,0 +1,163 @@
+package org.biojava.nbio.core.sequence;
+
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.EnumSource;
+import org.junit.jupiter.params.provider.ValueSource;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class ChromosomeSequenceTest {
+
+    private final String chromosome_seq = "ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC";
+
+    @Nested
+    class AfterValidConstruction {
+        ChromosomeSequence seq = null;
+
+        @BeforeEach
+        void before() throws CompoundNotFoundException {
+            seq = new ChromosomeSequence(chromosome_seq);
+        }
+
+        @Test
+        void beginAndEndAreLengthOfSequence() {
+            assertEquals(1, seq.getBioBegin());
+            assertEquals(208, seq.getBioEnd());
+            assertEquals(208, seq.getLength());
+        }
+
+        @Test
+        void noGenesAreDefined() {
+            assertEquals(0, seq.getGeneSequences().size());
+        }
+
+        @Test
+        void chromosomeNumberIsZero() {
+            assertEquals(0, seq.getChromosomeNumber());
+        }
+
+        @Test
+        void sequenceTypeIsUnknown() {
+            assertEquals(DNASequence.DNAType.UNKNOWN, seq.getDNAType());
+        }
+    }
+
+    @Nested
+    class AfterConstructionWithEmptyString {
+        ChromosomeSequence seq = null;
+
+        @BeforeEach
+        void before() throws CompoundNotFoundException {
+            seq = new ChromosomeSequence("");
+        }
+
+        @Test
+        void lengthIsZero() {
+            assertEquals(0, seq.getLength());
+        }
+
+        @Test
+        void endIsBeforeBeginning() {
+            assertEquals(0, seq.getBioEnd());
+            assertEquals(1, seq.getBioBegin());
+        }
+
+    }
+
+    @Test
+    void nullSequenceNotAllowed() throws CompoundNotFoundException {
+        assertThrows(NullPointerException.class, () -> new ChromosomeSequence((String) null));
+    }
+
+    @ParameterizedTest
+    @ValueSource(ints = {Integer.MAX_VALUE, Integer.MIN_VALUE, 100, 0, -1, -100})
+    void anyIntegerIsValidChromosomeNumber(int value) throws CompoundNotFoundException {
+        ChromosomeSequence seq = new ChromosomeSequence(chromosome_seq);
+        seq.setChromosomeNumber(value);
+        assertEquals(value, seq.getChromosomeNumber());
+    }
+
+    @ParameterizedTest
+    @EnumSource(DNASequence.DNAType.class)
+    void anyDNATypeIsValid(DNASequence.DNAType dnaType) throws CompoundNotFoundException {
+        ChromosomeSequence seq = new ChromosomeSequence(chromosome_seq);
+        seq.setDNAType(dnaType);
+        assertEquals(dnaType, seq.getDNAType());
+    }
+
+    @Nested
+    class AddingAndRemovingGeneSequences {
+        ChromosomeSequence seq = null;
+        @BeforeEach
+        void before() throws CompoundNotFoundException {
+            seq = new ChromosomeSequence(chromosome_seq);
+        }
+        @Test
+        void canAddSameGeneTwice(){
+            seq.addGene(new AccessionID("ABCDE1"), 1, 20, Strand.POSITIVE);
+            assertEquals(1, seq.getGeneSequences().size());
+            seq.addGene(new AccessionID("ABCDE1"), 1, 20, Strand.POSITIVE);
+            assertEquals(1, seq.getGeneSequences().size());
+        }
+
+        @Test
+        void isOKToRemoveNonExistentSequence(){
+            seq.removeGeneSequence("XXX");
+        }
+
+        @Test
+        void addAndRemove(){
+            final String accessionId = "ABCDE1";
+            GeneSequence geneSequence = seq.addGene(new AccessionID(accessionId), 1, 20, Strand.POSITIVE);
+            assertEquals(geneSequence.getAccession(), seq.getGene(accessionId).getAccession());
+            assertEquals(1, seq.getGeneSequences().size());
+            seq.removeGeneSequence(accessionId);
+            assertEquals(0, seq.getGeneSequences().size());
+
+        }
+
+        @Test
+        void geneSequenceHasCorrectLength(){
+            final String accessionId = "ABCDE1";
+            GeneSequence geneSequence = seq.addGene(new AccessionID(accessionId), 1, 20, Strand.POSITIVE);
+            assertEquals(20, geneSequence.getLength());
+        }
+
+        @Test
+        void geneSequenceCanHaveBeginAndEndOutsideOfChromosomeSeq(){
+            final String accessionId = "ABCDE1";
+            GeneSequence geneSequence = seq.addGene(new AccessionID(accessionId), Integer.MAX_VALUE-10, Integer.MAX_VALUE, Strand.POSITIVE);
+            assertEquals(11, geneSequence.getLength());
+
+        }
+    }
+
+    @Test
+    void addAndRemoveGeneSequence() throws CompoundNotFoundException {
+        ChromosomeSequence seq = new ChromosomeSequence(chromosome_seq);
+        seq.addGene(new AccessionID("ABCDE1"), 1, 20, Strand.POSITIVE);
+        assertEquals(1, seq.getGeneSequences().size());
+
+
+        // still present
+        assertEquals(1, seq.getGeneSequences().size());
+        // can be added again with sam
+        seq.addGene(new AccessionID("ABCDE1"), 1, 20, Strand.POSITIVE);
+        assertEquals(1, seq.getGeneSequences().size());
+
+    }
+
+
+
+    @Test
+    void addGene() {
+    }
+
+    @Test
+    void getGene() {
+    }
+}
