/** * Need a parent gene sequence and the bioBegin and bioEnd. An Exon sequence doesn't actually imply what the * protein coding sequence will be. This is a little difficult to model and have it make sense. * A gene has a collection of Exon and Intron sequences where the Exon sequences will join up. A gene * sequences has a collection of different possible isoform proteins based on the transcription rules. * A TranscriptionSequence will contain CDSSequence where the CDSSequence will be contained in the ExonSequence. * Thus a ExonSequence is the union of overlapping CDSSequences. * @param parentGeneSequence * @param bioBegin * @param bioEnd */ public ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) { this.setParentSequence(parentGeneSequence); setBioBegin(bioBegin); setBioEnd(bioEnd); }
/** * Need a parent gene sequence and the bioBegin and bioEnd. An Exon sequence doesn't actually imply what the * protein coding sequence will be. This is a little difficult to model and have it make sense. * A gene has a collection of Exon and Intron sequences where the Exon sequences will join up. A gene * sequences has a collection of different possible isoform proteins based on the transcription rules. * A TranscriptionSequence will contain CDSSequence where the CDSSequence will be contained in the ExonSequence. * Thus a ExonSequence is the union of overlapping CDSSequences. * @param parentGeneSequence * @param bioBegin * @param bioEnd */ public ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) { this.setParentSequence(parentGeneSequence); setBioBegin(bioBegin); setBioEnd(bioEnd); }