halapi hierarchichalalignmentformatapi

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hal::Alignment Member List

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 | inline protected pure virtual