halapi
hierarchichalalignmentformatapi
|
_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 |