This is the complete list of members for hal::Alignment, including all inherited members.
addLeafGenome(const std::string &name, const std::string &parentName, double branchLength)=0 | hal::Alignment | pure virtual |
addRootGenome(const std::string &name, double branchLength=0)=0 | hal::Alignment | pure virtual |
close()=0 | hal::Alignment | pure virtual |
close() const =0 | hal::Alignment | pure virtual |
closeGenome(const Genome *genome) const =0 | hal::Alignment | pure 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)=0 | hal::Alignment | pure virtual |
getBranchLength(const std::string &parentName, const std::string &childName) const =0 | hal::Alignment | pure virtual |
getChildNames(const std::string &name) const =0 | hal::Alignment | pure virtual |
getLeafNamesBelow(const std::string &name) const =0 | hal::Alignment | pure virtual |
getMetaData()=0 | hal::Alignment | pure virtual |
getMetaData() const =0 | hal::Alignment | pure virtual |
getNewickTree() const =0 | hal::Alignment | pure virtual |
getNumGenomes() const =0 | hal::Alignment | pure virtual |
getParentName(const std::string &name) const =0 | hal::Alignment | pure virtual |
getRootName() const =0 | hal::Alignment | pure virtual |
getVersion() const =0 | hal::Alignment | pure virtual |
open(const std::string &alignmentPath, bool readOnly)=0 | hal::Alignment | pure virtual |
open(const std::string &alignmentPath) const =0 | hal::Alignment | pure virtual |
openGenome(const std::string &name) const =0 | hal::Alignment | pure virtual |
openGenome(const std::string &name)=0 | hal::Alignment | pure virtual |
removeGenome(const std::string &name)=0 | hal::Alignment | pure virtual |
setOptionsFromParser(CLParserConstPtr parser) const =0 | hal::Alignment | pure virtual |
updateBranchLength(const std::string &parentName, const std::string &childName, double length)=0 | hal::Alignment | pure virtual |
~Alignment()=0 | hal::Alignment | inlineprotectedpure virtual |