7 #ifndef _HALALIGNMENT_H
8 #define _HALALIGNMENT_H
27 virtual void createNew(
const std::string& alignmentPath) = 0;
32 virtual void open(
const std::string& alignmentPath,
37 virtual void open(
const std::string& alignmentPath)
const = 0;
40 virtual void close() = 0;
43 virtual void close()
const = 0;
54 const std::string& parentName,
55 double branchLength) = 0;
63 double branchLength = 0) = 0;
87 virtual std::string
getParentName(
const std::string& name)
const = 0;
93 const std::string& childName)
const = 0;
99 const std::string& childName,
104 virtual std::vector<std::string>
109 virtual std::vector<std::string>
129 friend class counted_ptr<Alignment>;
130 friend class counted_ptr<const Alignment>;
virtual std::vector< std::string > getLeafNamesBelow(const std::string &name) const =0
virtual ~Alignment()=0
Definition: halAlignment.h:135
virtual std::string getRootName() const =0
Definition: halGenome.h:24
virtual Genome * addLeafGenome(const std::string &name, const std::string &parentName, double branchLength)=0
virtual void removeGenome(const std::string &name)=0
virtual void open(const std::string &alignmentPath, bool readOnly)=0
virtual void createNew(const std::string &alignmentPath)=0
virtual MetaData * getMetaData()=0
virtual Genome * addRootGenome(const std::string &name, double branchLength=0)=0
virtual double getBranchLength(const std::string &parentName, const std::string &childName) const =0
virtual std::string getNewickTree() const =0
virtual void updateBranchLength(const std::string &parentName, const std::string &childName, double length)=0
virtual hal_size_t getNumGenomes() const =0
virtual void closeGenome(const Genome *genome) const =0
virtual const Genome * openGenome(const std::string &name) const =0
virtual std::vector< std::string > getChildNames(const std::string &name) const =0
virtual std::string getVersion() const =0
Definition: halAlignment.h:21
virtual std::string getParentName(const std::string &name) const =0
virtual void setOptionsFromParser(CLParserConstPtr parser) const =0