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)=0hal::Alignmentpure virtual
addRootGenome(const std::string &name, double branchLength=0)=0hal::Alignmentpure virtual
close()=0hal::Alignmentpure virtual
close() const =0hal::Alignmentpure virtual
closeGenome(const Genome *genome) const =0hal::Alignmentpure virtual
counted_ptr< Alignment > (defined in hal::Alignment)hal::Alignmentfriend
counted_ptr< const Alignment > (defined in hal::Alignment)hal::Alignmentfriend
createNew(const std::string &alignmentPath)=0hal::Alignmentpure virtual
getBranchLength(const std::string &parentName, const std::string &childName) const =0hal::Alignmentpure virtual
getChildNames(const std::string &name) const =0hal::Alignmentpure virtual
getLeafNamesBelow(const std::string &name) const =0hal::Alignmentpure virtual
getMetaData()=0hal::Alignmentpure virtual
getMetaData() const =0hal::Alignmentpure virtual
getNewickTree() const =0hal::Alignmentpure virtual
getNumGenomes() const =0hal::Alignmentpure virtual
getParentName(const std::string &name) const =0hal::Alignmentpure virtual
getRootName() const =0hal::Alignmentpure virtual
getVersion() const =0hal::Alignmentpure virtual
open(const std::string &alignmentPath, bool readOnly)=0hal::Alignmentpure virtual
open(const std::string &alignmentPath) const =0hal::Alignmentpure virtual
openGenome(const std::string &name) const =0hal::Alignmentpure virtual
openGenome(const std::string &name)=0hal::Alignmentpure virtual
removeGenome(const std::string &name)=0hal::Alignmentpure virtual
setOptionsFromParser(CLParserConstPtr parser) const =0hal::Alignmentpure virtual
updateBranchLength(const std::string &parentName, const std::string &childName, double length)=0hal::Alignmentpure virtual
~Alignment()=0hal::Alignmentinlineprotectedpure virtual