### Question:
TranscriptSequenceOntologyDecorator { public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval getStopCodonInterval(); GenomeInterval getFivePrimeUTRInterval(); ImmutableList<GenomeInterval> getFivePrimeUTRExonIntervals(); boolean overlapsWithFivePrimeUTRExon(GenomeInterval itv); GenomeInterval getThreePrimeUTRInterval(); ImmutableList<GenomeInterval> getThreePrimeUTRExonIntervals(); boolean overlapsWithThreePrimeUTRExon(GenomeInterval itv); boolean containsExon(GenomeInterval interval); boolean overlapsWithCDSExon(GenomeInterval interval); boolean liesInCDSExon(GenomeInterval interval); boolean liesInCDSExon(GenomePosition pos); boolean overlapsWithCDS(GenomeInterval interval); boolean liesInCDS(GenomePosition pos); boolean overlapsWithIntron(GenomeInterval changeInterval); boolean liesInIntron(GenomePosition pos); boolean overlapsWithCDSIntron(GenomeInterval changeInterval); boolean liesInCDSIntron(GenomePosition pos); boolean overlapsWithTranslationalStartSite(GenomeInterval interval); boolean liesInTranslationalStartSite(GenomePosition pos); boolean overlapsWithTranslationalStopSite(GenomeInterval interval); boolean liesInTranslationalStopSite(GenomePosition pos); boolean overlapsWithSpliceRegion(GenomeInterval interval); boolean liesInSpliceRegion(GenomePosition pos); boolean overlapsWithSpliceDonorSite(GenomeInterval interval); boolean liesInSpliceDonorSite(GenomePosition pos); boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval); boolean liesInSpliceAcceptorSite(GenomePosition pos); GenomeInterval getUpstreamInterval(); boolean overlapsWithUpstreamRegion(GenomeInterval interval); boolean liesInUpstreamRegion(GenomePosition pos); GenomeInterval getDownstreamInterval(); boolean overlapsWithDownstreamRegion(GenomeInterval interval); boolean liesInDownstreamRegion(GenomePosition pos); boolean overlapsWithFivePrimeUTR(GenomeInterval interval); boolean liesInFivePrimeUTR(GenomePosition pos); boolean overlapsWithThreePrimeUTR(GenomeInterval interval); boolean liesInThreePrimeUTR(GenomePosition pos); boolean liesInIntron(GenomeInterval interval); boolean liesInExon(GenomeInterval interval); boolean liesInExon(GenomePosition pos); boolean overlapsWithExon(GenomeInterval interval); static int UPSTREAM_LENGTH; static int DOWNSTREAM_LENGTH; }### Answer:
@Test public void testLiesInIntron() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.liesInIntron(new GenomeInterval(refDict, Strand.FWD, 1, 6640195, 6640600, PositionType.ZERO_BASED))); Assert.assertTrue(decorator.liesInIntron(new GenomeInterval(refDict, Strand.FWD, 1, 6640196, 6640600, PositionType.ZERO_BASED))); Assert.assertFalse(decorator.liesInIntron(new GenomeInterval(refDict, Strand.FWD, 1, 6640196, 6640601, PositionType.ZERO_BASED))); }