cobalt.hpp File Reference

Interface for CMultiAligner. More...

#include <util/math/matrix.hpp>
#include <corelib/ncbifile.hpp>
#include <algo/align/nw/nw_pssm_aligner.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/biotree/BioTreeContainer.hpp>
#include <objects/blast/Blast4_archive.hpp>
#include <algo/cobalt/base.hpp>
#include <algo/cobalt/resfreq.hpp>
#include <algo/cobalt/seq.hpp>
#include <algo/cobalt/hit.hpp>
#include <algo/cobalt/hitlist.hpp>
#include <algo/cobalt/dist.hpp>
#include <algo/cobalt/tree.hpp>
#include <algo/cobalt/exception.hpp>
#include <algo/cobalt/kmercounts.hpp>
#include <algo/cobalt/clusterer.hpp>
#include <algo/cobalt/options.hpp>

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Classes
class	CMultiAligner
	Simultaneously align multiple protein sequences. More...
struct	CMultiAligner::SProgress
	Structure for reporting alignment progress. More...
struct	CMultiAligner::SSegmentLoc
struct	CMultiAligner::SGraphNode
class	CMultiAligner::compare_sseg_db_idx
struct	CMultiAligner::SColumn
	Column in an alignment used for combining result from multiple alignment and pair-wise in-cluster alignments. More...

Detailed Description

Interface for CMultiAligner.

Definition in file cobalt.hpp.