halapi hierarchichalalignmentformatapi

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hal::HDF5Alignment Member List
This is the complete list of members for hal::HDF5Alignment, including all inherited members.

_aprops (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_cprops (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_dcprops (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_dirty (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_file (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_flags (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_metaData (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
_nodeMap (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[mutable, protected]`
_openGenomes (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[mutable, protected]`
_tree (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
addGenomeToTree(const std::string &name, const std::pair< std::string, double > &parentName, const std::vector< std::pair< std::string, double > > &childNames) (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
addLeafGenome(const std::string &name, const std::string &parentName, double branchLength) | hal::HDF5Alignment | `[virtual]`
addRootGenome(const std::string &name, double branchLength) | hal::HDF5Alignment | `[virtual]`
close() | hal::HDF5Alignment | `[virtual]`
counted_ptr< Alignment > (defined in hal::Alignment) | hal::Alignment | `[friend]`
counted_ptr< const Alignment > (defined in hal::Alignment) | hal::Alignment | `[friend]`
createNew(const std::string &alignmentPath) | hal::HDF5Alignment | `[virtual]`
GenomesGroupName (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected, static]`
getBranchLength(const std::string &parentName, const std::string &childName) const | hal::HDF5Alignment | `[virtual]`
getChildNames(const std::string &name) const | hal::HDF5Alignment | `[virtual]`
getLeafNamesBelow(const std::string &name) const | hal::HDF5Alignment | `[virtual]`
getMetaData() | hal::HDF5Alignment | `[virtual]`
getMetaData() const | hal::HDF5Alignment | `[virtual]`
getNewickTree() const | hal::HDF5Alignment | `[virtual]`
getNumGenomes() const | hal::HDF5Alignment | `[virtual]`
getParentName(const std::string &name) const | hal::HDF5Alignment | `[virtual]`
getRootName() const | hal::HDF5Alignment | `[virtual]`
HDF5Alignment() (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
HDF5Alignment(const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps) (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
hdf5AlignmentInstance() | hal::HDF5Alignment | `[friend]`
hdf5AlignmentInstance(const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps) | hal::HDF5Alignment | `[friend]`
hdf5AlignmentInstanceReadOnly() | hal::HDF5Alignment | `[friend]`
hdf5AlignmentInstanceReadOnly(const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps) | hal::HDF5Alignment | `[friend]`
loadTree() (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
MetaGroupName | hal::HDF5Alignment | `[protected, static]`
open(const std::string &alignmentPath, bool readOnly) | hal::HDF5Alignment | `[virtual]`
openConstGenome(const std::string &name) const (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[virtual]`
openGenome(const std::string &name) (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[virtual]`
removeGenome(const std::string &name) | hal::HDF5Alignment | `[virtual]`
TreeGroupName (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected, static]`
writeTree() (defined in hal::HDF5Alignment) | hal::HDF5Alignment | `[protected]`
~Alignment()=0 | hal::Alignment | `[inline, protected, pure virtual]`
~HDF5Alignment() (defined in hal::HDF5Alignment) | hal::HDF5Alignment |

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