/** * Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0. The * GeneSequence that is returned will have a reference to parent chromosome sequence * which actually contains the sequence data. Strand is important for positive and negative * direction where negative strand means we need reverse complement. If negative strand then * bioBegin will be greater than bioEnd * * * @param accession * @param begin * @param end * @param strand * @return */ public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) { GeneSequence geneSequence = new GeneSequence(this, bioBegin, bioEnd, strand); geneSequence.setAccession(accession); geneSequenceHashMap.put(accession.toString(), geneSequence); return geneSequence; }
/** * Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0. The * GeneSequence that is returned will have a reference to parent chromosome sequence * which actually contains the sequence data. Strand is important for positive and negative * direction where negative strand means we need reverse complement. If negative strand then * bioBegin will be greater than bioEnd * * * @param accession * @param begin * @param end * @param strand * @return */ public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) { GeneSequence geneSequence = new GeneSequence(this, bioBegin, bioEnd, strand); geneSequence.setAccession(accession); geneSequenceHashMap.put(accession.toString(), geneSequence); return geneSequence; }