#include <halAlignment.h>
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class | counted_ptr< Alignment > |
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class | counted_ptr< const Alignment > |
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Interface for a hierarhcical alignment. Responsible for creating and accessing genomes and tree information. Accesssing a HAL file must always start with an Alignment object
hal::Alignment::~Alignment |
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inlineprotectedpure virtual |
virtual Genome* hal::Alignment::addLeafGenome |
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const std::string & |
name, |
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const std::string & |
parentName, |
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double |
branchLength |
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) |
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pure virtual |
Add a new genome to the alignment
- Parameters
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name | name of new genome in alignment (must be unique) |
parent | name of parent genome in tree (must exist) |
branchLength | distance between new genome and parent |
virtual Genome* hal::Alignment::addRootGenome |
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const std::string & |
name, |
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double |
branchLength = 0 |
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) |
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pure virtual |
Add a new genome as root to the alignment. The previous root (if exists) will be a child of the new genome
- Parameters
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name | name of new genome in alignment (must be unique) |
branchLength | distance between new genome and previous root (if exists) |
virtual void hal::Alignment::close |
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pure virtual |
virtual void hal::Alignment::close |
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const |
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pure virtual |
virtual void hal::Alignment::closeGenome |
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const Genome * |
genome | ) |
const |
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pure virtual |
Close an open genome. All pointers to this genome become invalid and openGenome needs to be called again to access it
- Parameters
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virtual void hal::Alignment::createNew |
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const std::string & |
alignmentPath | ) |
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pure virtual |
Create new alignment (overwriting any existing alignments)
- Parameters
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alignmentPath | location on disk |
virtual double hal::Alignment::getBranchLength |
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const std::string & |
parentName, |
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const std::string & |
childName |
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) |
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pure virtual |
Get the branch length between two genomes in the phylogeny
- Parameters
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parentName | name of parent genome |
childName | name of child genome |
virtual std::vector<std::string> hal::Alignment::getChildNames |
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const std::string & |
name | ) |
const |
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pure virtual |
Get names of child genomes in the phylogeny (empty vector for leaves)
- Parameters
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virtual std::vector<std::string> hal::Alignment::getLeafNamesBelow |
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const std::string & |
name | ) |
const |
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pure virtual |
Get the names of all leaves below a given genome
- Parameters
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virtual MetaData* hal::Alignment::getMetaData |
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pure virtual |
virtual const MetaData* hal::Alignment::getMetaData |
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const |
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pure virtual |
Get read-only instance of Alignment's metadata
virtual std::string hal::Alignment::getNewickTree |
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const |
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pure virtual |
Get a newick-formatted phylogeny to the alignment
virtual hal_size_t hal::Alignment::getNumGenomes |
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const |
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pure virtual |
Get the number of genomes (including internal ancestors) in the alignment
virtual std::string hal::Alignment::getParentName |
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const std::string & |
name | ) |
const |
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pure virtual |
Get name of parent genome in the phylogeny (empty string for root)
- Parameters
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virtual std::string hal::Alignment::getRootName |
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const |
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pure virtual |
Get name of root genome (empty string for empty alignment)
virtual std::string hal::Alignment::getVersion |
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const |
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pure virtual |
Get version used to create the file
virtual void hal::Alignment::open |
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const std::string & |
alignmentPath, |
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bool |
readOnly |
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) |
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pure virtual |
Open an existing alignment
- Parameters
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alignmentPath | location on disk |
readOnly | access flag |
virtual void hal::Alignment::open |
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const std::string & |
alignmentPath | ) |
const |
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pure virtual |
Open an existing alignment for reading only
- Parameters
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alignmentPath | location on disk |
virtual const Genome* hal::Alignment::openGenome |
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const std::string & |
name | ) |
const |
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pure virtual |
Open an existing genome for reading and updating
- Parameters
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name | Name of genome to open |
virtual Genome* hal::Alignment::openGenome |
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const std::string & |
name | ) |
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pure virtual |
Open an exsting genome for reading
- Parameters
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name | Name of genome to open |
virtual void hal::Alignment::removeGenome |
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const std::string & |
name | ) |
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pure virtual |
Remove a genome from the alignment
- Parameters
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path | Path of genome to remove |
virtual void hal::Alignment::setOptionsFromParser |
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CLParserConstPtr |
parser | ) |
const |
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pure virtual |
Set options from parser
- Parameters
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clParser | pointer to command-line parser |
virtual void hal::Alignment::updateBranchLength |
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const std::string & |
parentName, |
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const std::string & |
childName, |
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double |
length |
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) |
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pure virtual |
Change the branch length between two genomes in the phylogeny
- Parameters
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parentName | name of parent genome |
childName | name of child genome |
The documentation for this class was generated from the following file: