/** * A class that keeps track of the details of a GeneSequence which is difficult to properly model. Two important concepts that is difficult * to make everything flexible but still work. You can have GFF features that only describe Exons or Exons/Introns or CDS regions and one * or more Transcriptions. You can have exon sequences but that does not imply transcription to the actual protein. * * The GeneSequence will keep track of Exons and Introns but to get a Protein sequence you need to start with a * TranscriptSequence and then add CDS sequences. * * This is also a key class in the biojava-3-genome module for reading and writing GFF3 files * * @param parentDNASequence * @param begin * @param end inclusive of end * @param strand force a gene to have strand and transcription sequence will inherit */ public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand) { chromosomeSequence = parentSequence; setParentSequence(parentSequence); setBioBegin(begin); setBioEnd(end); setStrand(strand); this.setCompoundSet(DNACompoundSet.getDNACompoundSet()); }
/** * A class that keeps track of the details of a GeneSequence which is difficult to properly model. Two important concepts that is difficult * to make everything flexible but still work. You can have GFF features that only describe Exons or Exons/Introns or CDS regions and one * or more Transcriptions. You can have exon sequences but that does not imply transcription to the actual protein. * * The GeneSequence will keep track of Exons and Introns but to get a Protein sequence you need to start with a * TranscriptSequence and then add CDS sequences. * * This is also a key class in the biojava-3-genome module for reading and writing GFF3 files * * @param parentDNASequence * @param begin * @param end inclusive of end * @param strand force a gene to have strand and transcription sequence will inherit */ public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand) { chromosomeSequence = parentSequence; setParentSequence(parentSequence); setBioBegin(begin); setBioEnd(end); setStrand(strand); this.setCompoundSet(DNACompoundSet.getDNACompoundSet()); }