ost::seq::alg Namespace Reference

Namespaces
namespace	mat
namespace	renumber

Data Structures
struct	AlignmentOpts
	options for local and global sequence alignment algorithms More...
class	InsDel
	get insertions and deletions of an alignment More...
struct	RefMode
class	SubstWeightMatrix
	position-independet substitution weight matrix More...

Typedefs
typedef boost::shared_ptr < SubstWeightMatrix >	SubstWeightMatrixPtr

Functions
std::vector< Real > DLLEXPORT_OST_SEQ_ALG	Conservation (const AlignmentHandle &aln, bool assign=true, const String &prop_name="cons")
AlignmentHandle DLLEXPORT_OST_SEQ_ALG	MergePairwiseAlignments (const AlignmentList &pairwise_alns, const ConstSequenceHandle &ref_seq)
Real DLLEXPORT_OST_SEQ_ALG	SequenceIdentity (const AlignmentHandle &aln, RefMode::Type ref_mode=RefMode::LONGER_SEQUENCE, int seq_a=0, int seq_b=1)
SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG	SubstWeightMatrixFromInfo (const info::InfoGroup &group)
void DLLEXPORT_OST_SEQ_ALG	SubstWeightMatrixToInfo (const SubstWeightMatrixPtr &subst_mat, info::InfoGroup &group)

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Typedef Documentation

typedef boost::shared_ptr<SubstWeightMatrix> SubstWeightMatrixPtr

Definition at line 32 of file subst_weight_matrix.hh.

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Function Documentation

std::vector<Real> DLLEXPORT_OST_SEQ_ALG ost::seq::alg::Conservation	(	const AlignmentHandle &	aln,
		bool	assign = true,
		const String &	prop_name = "cons"
	)

Calculates conservation scores for each column in the alignment.

The conservation score is a value between 0 and 1. The bigger the number the more conserved the aligned residues are.

assign If true, the conservation scores are assigned to attached residues. The name of the property can be changed with the prop_name parameter. Useful when coloring entities based on sequence conservation. prop_name The property name for assigning the conservation to attached residues. Defaults to 'cons'.

AlignmentHandle DLLEXPORT_OST_SEQ_ALG ost::seq::alg::MergePairwiseAlignments	(	const AlignmentList &	pairwise_alns,
		const ConstSequenceHandle &	ref_seq
	)

merge a list of pairwise alignments into one multiple sequence alignment

All sequences in the pairwise sequence alignments are a realigned to the reference sequence. This is useful to merge the results of a BLAST or HMM database search into one multiple sequence alignment.

The method does not produce the optimal multiple sequence alignemnt for all the sequences.

Parameters:

pairwise_alignments	is a list of AlignmentHandles, each containing two sequences
ref_seq	is the reference sequence. The reference sequence must not contain any gaps.

Real DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SequenceIdentity	(	const AlignmentHandle &	aln,
		RefMode::Type	ref_mode = RefMode::LONGER_SEQUENCE,
		int	seq_a = 0,
		int	seq_b = 1
	)

calculate sequence identity for two sequences in an alignment

Parameters:

ref_mode	influences the way the sequence identity is calculated. When set to LONGER_SEQUENCE, the sequence identity is calculated as the number of matches divided by the length of the longer sequence. If set to ALIGNMENT, the sequence identity is calculated as the number of matches divided by the number of aligned residues.
seq_a	is the index of the first sequence
seq_b	is the index of the second sequence
aln	is the sequence alignment

Returns:

sequence identity in the range 0 to 100

SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SubstWeightMatrixFromInfo

(

const info::InfoGroup &

group

)

void DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SubstWeightMatrixToInfo	(	const SubstWeightMatrixPtr &	subst_mat,
		info::InfoGroup &	group
	)