halapi
hierarchichalalignmentformatapi
hal::HDF5Genome Member List
This is the complete list of members for hal::HDF5Genome, including all inherited members.
_alignment (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_alignmentPtr (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_bottomArray (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_childCache (defined in hal::HDF5Genome)hal::HDF5Genome [mutable, protected]
_dcprops (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_dnaArray (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_group (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_h5Parent (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_metaData (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_name (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_numChildrenInBottomArray (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_parentCache (defined in hal::HDF5Genome)hal::HDF5Genome [mutable, protected]
_sequenceArray (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
_sequenceNameCache (defined in hal::HDF5Genome)hal::HDF5Genome [mutable, protected]
_sequencePosCache (defined in hal::HDF5Genome)hal::HDF5Genome [mutable, protected]
_topArray (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
bottomArrayName (defined in hal::HDF5Genome)hal::HDF5Genome [protected, static]
create() (defined in hal::HDF5Genome)hal::HDF5Genome
deleteSequenceCache() (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
dnaArrayName (defined in hal::HDF5Genome)hal::HDF5Genome [protected, static]
getBottomSegmentIterator(hal_index_t position)hal::HDF5Genome [virtual]
getBottomSegmentIterator(hal_index_t position) const hal::HDF5Genome [virtual]
getChild(hal_size_t childIdx)hal::HDF5Genome [virtual]
getChild(hal_size_t childIdx) const hal::HDF5Genome [virtual]
getMetaData()hal::HDF5Genome [virtual]
getMetaData() const hal::HDF5Genome [virtual]
getName() const hal::HDF5Genome [virtual]
getNumBottomSegments() const hal::HDF5Genome [virtual]
getNumChildren() const hal::HDF5Genome [virtual]
getNumSequences() const hal::HDF5Genome [virtual]
getNumTopSegments() const hal::HDF5Genome [virtual]
getParent()hal::HDF5Genome [virtual]
getParent() const hal::HDF5Genome [virtual]
getSequence(const std::string &name)hal::HDF5Genome [virtual]
getSequence(const std::string &name) const hal::HDF5Genome [virtual]
getSequenceBySite(hal_size_t position)hal::HDF5Genome [virtual]
getSequenceBySite(hal_size_t position) const hal::HDF5Genome [virtual]
getSequenceIterator(hal_index_t position)hal::HDF5Genome [virtual]
getSequenceIterator(hal_index_t position) const hal::HDF5Genome [virtual]
getSequenceLength() const hal::HDF5Genome [virtual]
getString(std::string &outString) const hal::HDF5Genome [virtual]
getSubString(std::string &outString, hal_size_t start, hal_size_t length) const hal::HDF5Genome [virtual]
getTopSegmentIterator(hal_index_t position)hal::HDF5Genome [virtual]
getTopSegmentIterator(hal_index_t position) const hal::HDF5Genome [virtual]
HDF5BottomSegmentIterator (defined in hal::HDF5Genome)hal::HDF5Genome [friend]
HDF5DNAIterator (defined in hal::HDF5Genome)hal::HDF5Genome [friend]
HDF5Genome(const std::string &name, HDF5Alignment *alignment, H5::CommonFG *h5Parent, const H5::DSetCreatPropList &dcProps) (defined in hal::HDF5Genome)hal::HDF5Genome
HDF5SequenceIterator (defined in hal::HDF5Genome)hal::HDF5Genome [friend]
HDF5TopSegmentIterator (defined in hal::HDF5Genome)hal::HDF5Genome [friend]
metaGroupName (defined in hal::HDF5Genome)hal::HDF5Genome [protected, static]
read() (defined in hal::HDF5Genome)hal::HDF5Genome
readSequences() (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
resetTreeCache() (defined in hal::HDF5Genome)hal::HDF5Genome
sequenceArrayName (defined in hal::HDF5Genome)hal::HDF5Genome [protected, static]
setBottomDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)hal::HDF5Genome [virtual]
setDimensions(const std::vector< hal::Sequence::Info > &sequenceDimensions)hal::HDF5Genome [virtual]
setString(const std::string &inString)hal::HDF5Genome [virtual]
setSubString(const std::string &intString, hal_size_t start, hal_size_t length)hal::HDF5Genome [virtual]
setTopDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)hal::HDF5Genome [virtual]
topArrayName (defined in hal::HDF5Genome)hal::HDF5Genome [protected, static]
write() (defined in hal::HDF5Genome)hal::HDF5Genome
writeSequences(const std::vector< hal::Sequence::Info > &sequenceDimensions) (defined in hal::HDF5Genome)hal::HDF5Genome [protected]
~Genome()=0hal::Genome [inline, protected, pure virtual]
~HDF5Genome() (defined in hal::HDF5Genome)hal::HDF5Genome [virtual]
~SegmentedSequence()=0hal::SegmentedSequence [inline, protected, pure virtual]
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