Chromosome Class Reference

Public Member Functions
	Chromosome (GenomeSequence *gs, unsigned int chrosomeIndex)
	Chromosome (GenomeSequence *gs, const char *chromosomeName)
	Chromosome (const char *genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
	Chromosome (const std::string &genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
genomeIndex_t	Length () const
char	operator[] (genomeIndex_t index) const
const char *	Name () const

Detailed Description

Definition at line 6 of file Chromosome.h.

Constructor & Destructor Documentation

Chromosome() [1/4]

Chromosome::Chromosome ( GenomeSequence * gs, unsigned int chrosomeIndex )

explicit

Definition at line 4 of file Chromosome.cpp.

{
    assert(gs);
    assert(chromosomeIndex < (unsigned int)gs->getChromosomeCount());
 
    this->gs = gs;
    this->chromosomeIndex = chromosomeIndex;
    this->offset = gs->getChromosomeStart((int)chromosomeIndex);
    this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}

Chromosome() [2/4]

Chromosome::Chromosome ( GenomeSequence * gs, const char * chromosomeName )

explicit

Definition at line 15 of file Chromosome.cpp.

{
    assert(gs);
    this->gs = gs;
 
    this->chromosomeIndex = gs->getChromosome(chromosomeName);
    assert(chromosomeIndex != INVALID_CHROMOSOME_INDEX);
 
    this->offset = gs->getChromosomeStart((int)chromosomeIndex);
    this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}

Chromosome() [3/4]

Chromosome::Chromosome ( const char * genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace )

explicit

Definition at line 27 of file Chromosome.cpp.

{
    std::string s(genomseSequenceFileName);
    gs = new GenomeSequence;
    assert(gs);
    gs->setReferenceName(s);
    assert(!gs->open(isColorSpace));
    this->chromosomeIndex = chromosomeIndex;
    this->offset = gs->getChromosomeStart((int)chromosomeIndex);
    this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}

Chromosome() [4/4]

Chromosome::Chromosome ( const std::string & genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace )

explicit

Definition at line 39 of file Chromosome.cpp.

{
    gs = new GenomeSequence;
    assert(gs);
    gs->setReferenceName(genomseSequenceFileName);
    assert(!gs->open(isColorSpace));
    this->chromosomeIndex = chromosomeIndex;
    this->offset = gs->getChromosomeStart((int)chromosomeIndex);
    this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}

Member Function Documentation

Length()

genomeIndex_t Chromosome::Length ( ) const

inline

Definition at line 12 of file Chromosome.h.

    {
        return chromosomeSize;
    }

Name()

const char * Chromosome::Name ( ) const

inline

Definition at line 22 of file Chromosome.h.

                             {
        return gs->getChromosomeName(this->chromosomeIndex);
    }

operator[]()

char Chromosome::operator[] ( genomeIndex_t index ) const

inline

Definition at line 17 of file Chromosome.h.

    {
        index += offset;
        return (*gs)[index];
    }

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The documentation for this class was generated from the following files:

• general/Chromosome.h
• general/Chromosome.cpp