Allele extends Locus { public static Builder builder() { return new Builder(); } Allele(final String name, final String contig, final int start, final int end, final SymbolList sequence, final Lesion lesion); String getName(); void setName(final String name); static Builder builder(); @Override boolean equals(final Object right); @Override int hashCode(); Allele doubleCrossover(final Allele right); Allele merge(final Allele right, final long minimumOverlap); Allele leftHardClip(final String pattern); Allele rightHardClip(final String pattern); final SymbolList sequence; final Lesion lesion; }
@Test public void testBuilder() { assertNotNull(builder()); }
@Test public void testBuilderSubstitution() throws IllegalSymbolException, AlleleException { temp = builder() .withContig("chr6") .withStart(1) .withEnd(2) .withSequence(DNATools.createDNA("A")) .withLesion(Allele.Lesion.SUBSTITUTION) .build(); assertEquals(temp.getContig(), "chr6"); assertEquals(temp.getStart(), 1); assertEquals(temp.getEnd(), 2); assertEquals(temp.sequence.seqString(), "a"); assertEquals(temp.lesion, Allele.Lesion.SUBSTITUTION); temp = builder() .withContig("chr6") .withStart(1) .withEnd(2) .withLesion(Allele.Lesion.SUBSTITUTION) .build(); assertEquals(temp.sequence.seqString(), "-"); }