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hierarchichalalignmentformatapi
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hal Namespace Reference

Classes

class  Alignment
 
class  BottomSegment
 
class  BottomSegmentIterator
 
class  CLParser
 
class  ColumnIterator
 
class  DNAIterator
 
class  GappedBottomSegmentIterator
 
class  GappedSegmentIterator
 
class  GappedTopSegmentIterator
 
class  Genome
 
class  MappedSegment
 
class  MetaData
 
class  PositionCache
 
class  Rearrangement
 
class  Segment
 
class  SegmentedSequence
 
class  SegmentIterator
 
class  Sequence
 
class  SequenceIterator
 
class  SlicedSegment
 
class  TopSegment
 
class  TopSegmentIterator
 

Functions

AlignmentPtr hdf5AlignmentInstance ()
 
AlignmentConstPtr hdf5AlignmentInstanceReadOnly ()
 
AlignmentPtr hdf5AlignmentInstance (const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps, bool inMemory=false)
 
AlignmentConstPtr hdf5AlignmentInstanceReadOnly (const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps, bool inMemory=false)
 
AlignmentPtr openHalAlignment (const std::string &path, CLParserConstPtr options)
 
AlignmentConstPtr openHalAlignmentReadOnly (const std::string &path, CLParserConstPtr options)
 
bool operator== (BottomSegmentIteratorConstPtr p1, BottomSegmentIteratorConstPtr p2)
 
bool operator!= (BottomSegmentIteratorConstPtr p1, BottomSegmentIteratorConstPtr p2)
 
template<>
std::string CLParser::convertFromString< std::string > (const std::string &token) const
 
CLParserPtr hdf5CLParserInstance (bool createOptions=false)
 
std::ostream & operator<< (std::ostream &os, const ColumnIterator &cit)
 
bool compatibleWithVersion (const std::string &version)
 
std::vector< std::string > chopString (const std::string &inString, const std::string &separator)
 
char reverseComplement (char c)
 
void reverseComplement (std::string &s)
 
bool isNucleotide (char c)
 
bool isTransition (char c1, char c2)
 
bool isSubstitution (char c1, char c2)
 
bool isTransversion (char c1, char c2)
 
bool isMissingData (char c)
 
bool isMasked (char c)
 
bool isFourfoldDegenerate (char c1, char c2)
 
hal_size_t hammingDistance (const std::string &s1, const std::string &s2)
 
const GenomegetLowestCommonAncestor (const std::set< const Genome * > &inputSet)
 
void getGenomesInSpanningTree (const std::set< const Genome * > &inputSet, std::set< const Genome * > &outputSet)
 
void getGenomesInSubTree (const Genome *root, std::set< const Genome * > &outputSet)
 
std::ostream & operator<< (std::ostream &os, const DNAIterator *dna)
 
bool operator== (GappedBottomSegmentIteratorConstPtr p1, GappedBottomSegmentIteratorConstPtr p2)
 
bool operator!= (GappedBottomSegmentIteratorConstPtr p1, GappedBottomSegmentIteratorConstPtr p2)
 
bool operator== (GappedTopSegmentIteratorConstPtr p1, GappedTopSegmentIteratorConstPtr p2)
 
bool operator!= (GappedTopSegmentIteratorConstPtr p1, GappedTopSegmentIteratorConstPtr p2)
 
std::ostream & operator<< (std::ostream &os, const Segment &s)
 
bool operator< (SegmentIteratorConstPtr segmentIt, hal_index_t genomePos)
 
bool operator> (SegmentIteratorConstPtr segmentIt, hal_index_t genomePos)
 
bool operator== (SequenceIteratorConstPtr p1, SequenceIteratorConstPtr p2)
 
bool operator!= (SequenceIteratorConstPtr p1, SequenceIteratorConstPtr p2)
 
bool operator< (SlicedSegmentConstPtr segmentIt, hal_index_t genomePos)
 
bool operator> (SlicedSegmentConstPtr segmentIt, hal_index_t genomePos)
 
bool operator== (TopSegmentIteratorConstPtr p1, TopSegmentIteratorConstPtr p2)
 
bool operator!= (TopSegmentIteratorConstPtr p1, TopSegmentIteratorConstPtr p2)
 
void validateBottomSegment (const BottomSegment *bottomSegment)
 
void validateTopSegment (const TopSegment *topSegment)
 
void validateSequence (const Sequence *sequence)
 
void validateGenome (const Genome *genome)
 
void validateDuplications (const Genome *genome)
 
void validateAlignment (AlignmentConstPtr alignment)
 

Variables

const hal_index_t NULL_INDEX
 

Detailed Description

HAL API namespace

Function Documentation

std::vector<std::string> hal::chopString ( const std::string &  inString,
const std::string &  separator 
)

C++ style strtok-type function. Can't remember why I wrote it

hal_size_t hal::hammingDistance ( const std::string &  s1,
const std::string &  s2 
)
inline

Count the mutations between two DNA strings

AlignmentPtr hal::hdf5AlignmentInstance ( )

Get an instance of an HDF5-implemented Alignment with default parameters for everything

AlignmentPtr hal::hdf5AlignmentInstance ( const H5::FileCreatPropList &  fileCreateProps,
const H5::FileAccPropList &  fileAccessProps,
const H5::DSetCreatPropList &  datasetCreateProps,
bool  inMemory = false 
)

Get an instance of an HDF5-implemented Alignment while specifying

Parameters
fileCreatePropsFile creation properties. fairly low-level and should generally be set to H5::FileCreatPropList::DEFAULT
fileAccessPropsFile access properties. Contains cache-related stuff
datasetCreatePropsCompression and chunking parameters among others
inMemoryStore all data in memory (overrides and disables hdf5 cache)
AlignmentConstPtr hal::hdf5AlignmentInstanceReadOnly ( )

Get read-only instance of an HDF5-implemented Alignment with default parameters for everything

AlignmentConstPtr hal::hdf5AlignmentInstanceReadOnly ( const H5::FileCreatPropList &  fileCreateProps,
const H5::FileAccPropList &  fileAccessProps,
const H5::DSetCreatPropList &  datasetCreateProps,
bool  inMemory = false 
)

Get a read-only instance of an HDF5-implemented Alignment while specifying

Parameters
fileCreatePropsFile creation properties. fairly low-level and should generally be set to H5::FileCreatPropList::DEFAULT
fileAccessPropsFile access properties. Contains cache-related stuff
datasetCreatePropsCompression and chunking parameters among others
inMemoryStore all data in memory (overrides and disables hdf5 cache)
CLParserPtr hal::hdf5CLParserInstance ( bool  createOptions = false)

Get an instance of an HDF5-implemented CLParser

Parameters
createOptionsset to true if tool will need to create a new hal file (as opposed to just reading an existing one)
bool hal::isFourfoldDegenerate ( char  c1,
char  c2 
)
inline

test if 3rd codon position is 4-fold degenerate given first 2 positions

bool hal::isNucleotide ( char  c)
inline

Check if a DNA character is a valid base (or n-chracter)

AlignmentPtr hal::openHalAlignment ( const std::string &  path,
CLParserConstPtr  options 
)

Get an alignment instance from a file by automatically detecting which implementation to use. (will currently (and probably forever more) just return an HDF5 instance since that's all that exists)

Parameters
pathPath of file to open
optionsCommand line options information
AlignmentConstPtr hal::openHalAlignmentReadOnly ( const std::string &  path,
CLParserConstPtr  options 
)

Get a read-only alignment instance from a file by automatically detecting which implementation to use. (will currently (and probably forever more) just return an HDF5 instance since that's all that exists)

Parameters
pathPath of file to open
optionsCommand line options information
char hal::reverseComplement ( char  c)
inline

Get the DNA reverse complement of a character. If the input is not a nucleotide, then just return it as is (ie no error checking)

void hal::reverseComplement ( std::string &  s)

Get the reversed complement of a string (in place

void hal::validateAlignment ( AlignmentConstPtr  alignment)

Go through an alignment, and throw an excpetion if anything appears out of whack.

void hal::validateBottomSegment ( const BottomSegment *  bottomSegment)

Go through a bottom segment, and throw an exception if anything appears out of whack.

void hal::validateDuplications ( const Genome *  genome)

Go through a genome, and throw an exception if any duplications appears out of whack.

void hal::validateGenome ( const Genome *  genome)

Go through a genome, and throw an exception if anything appears out of whack.

void hal::validateSequence ( const Sequence *  sequence)

Go through a sequence, and throw an exception if anything appears out of whack.

void hal::validateTopSegment ( const TopSegment *  topSegment)

Go through a top segment, and throw an exception if anything appears out of whack.