halapi
hierarchichalalignmentformatapi
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]
MetaGroupNamehal::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()=0hal::Alignment [inline, protected, pure virtual]
~HDF5Alignment() (defined in hal::HDF5Alignment)hal::HDF5Alignment
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