vg
tools for working with variation graphs
Public Member Functions | List of all members
vg::BaseAligner Class Referenceabstract

#include <aligner.hpp>

Inheritance diagram for vg::BaseAligner:
vg::GSSWAligner vg::Aligner vg::QualAdjAligner

Public Member Functions

virtual void align (Alignment &alignment, const HandleGraph &g, bool traceback_aln, bool print_score_matrices) const =0
 
virtual void align (Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool traceback_aln, bool print_score_matrices) const =0
 Same as previous, but takes advantage of a pre-computed topological order. More...
 

Detailed Description

The abstract interface that any Aligner should implement.

Member Function Documentation

◆ align() [1/2]

virtual void vg::BaseAligner::align ( Alignment alignment,
const HandleGraph g,
bool  traceback_aln,
bool  print_score_matrices 
) const
pure virtual

Store optimal local alignment against a graph in the Alignment object. Gives the full length bonus separately on each end of the alignment.

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align() [2/2]

virtual void vg::BaseAligner::align ( Alignment alignment,
const HandleGraph g,
const vector< handle_t > &  topological_order,
bool  traceback_aln,
bool  print_score_matrices 
) const
pure virtual

Same as previous, but takes advantage of a pre-computed topological order.

Implemented in vg::QualAdjAligner, and vg::Aligner.


The documentation for this class was generated from the following file: