halapi
hierarchichalalignmentformatapi
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_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] |