public static void main(String[] args) { try { ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>(); ChromosomeSequence seq1 = new ChromosomeSequence( "ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC"); GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE); gene1.addExon(new AccessionID("t1_1_10"), 1, 10); gene1.addExon(new AccessionID("t1_12_15"), 12, 15); GeneSequence gene2 = seq1.addGene(new AccessionID("gene2"), 1, 20, Strand.NEGATIVE); gene2.addExon(new AccessionID("t2_1_10"), 1, 10); gene2.addExon(new AccessionID("t2_12_15"), 12, 15); sequences.add(gene1); sequences.add(gene2); FastaGeneWriter fastaWriter = new FastaGeneWriter( System.out, sequences, new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(), true); fastaWriter.process(); } catch (Exception e) { e.printStackTrace(); } }