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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()=0 | hal::Genome | `[inline, protected, pure virtual]`
~HDF5Genome() (defined in hal::HDF5Genome) | hal::HDF5Genome | `[virtual]`
~SegmentedSequence()=0 | hal::SegmentedSequence | `[inline, protected, pure virtual]`

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