Chromosome.cpp

00001 #include <cassert>
00002 #include "Chromosome.h"
00003 
00004 Chromosome::Chromosome(GenomeSequence* gs, uint chromosomeIndex)
00005 {
00006     assert(gs);
00007     assert(chromosomeIndex < (uint)gs->getChromosomeCount());
00008 
00009     this->gs = gs;
00010     this->chromosomeIndex = chromosomeIndex;
00011     this->offset = gs->getChromosomeStart((int)chromosomeIndex);
00012     this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
00013 }
00014 
00015 Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName)
00016 {
00017     assert(gs);
00018     this->gs = gs;
00019 
00020     this->chromosomeIndex = gs->getChromosome(chromosomeName);
00021     assert(chromosomeIndex != INVALID_CHROMOSOME_INDEX);
00022 
00023     this->offset = gs->getChromosomeStart((int)chromosomeIndex);
00024     this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
00025 }
00026 
00027 Chromosome::Chromosome(const char* genomseSequenceFileName, uint chromosomeIndex, bool isColorSpace) 
00028 {
00029     std::string s(genomseSequenceFileName);
00030     if (this->gs) delete gs;
00031     gs = new GenomeSequence;
00032     assert(gs);
00033     gs->setReferenceName(s);
00034     assert(!gs->open(isColorSpace));
00035     this->chromosomeIndex = chromosomeIndex;
00036     this->offset = gs->getChromosomeStart((int)chromosomeIndex);
00037     this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
00038 }
00039 
00040 Chromosome::Chromosome(const std::string& genomseSequenceFileName, uint chromosomeIndex, bool isColorSpace) 
00041 {
00042     if (this->gs) delete gs;
00043     gs = new GenomeSequence;
00044     assert(gs);
00045     gs->setReferenceName(genomseSequenceFileName);
00046     assert(!gs->open(isColorSpace));
00047     this->chromosomeIndex = chromosomeIndex;
00048     this->offset = gs->getChromosomeStart((int)chromosomeIndex);
00049     this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
00050 }