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