mems::ClustalInterface Class Reference

#include <ClustalInterface.h>

Inheritance diagram for mems::ClustalInterface:

[legend]Collaboration diagram for mems::ClustalInterface:

[legend]List of all members.

Public Member Functions
boolean	Align (GappedAlignment &cr, Match *r_begin, Match *r_end, std::vector< genome::gnSequence * > &seq_table)
	Attempts to perform a multiple alignment using ClustalW between r_begin and r_end.
boolean	guideTreeLoaded () const
	returns true if a guide tree has been loaded already
void	SetDistanceMatrix (NumericMatrix< double > &distance_matrix, std::string &tree_filename, boolean reread_tree)
void	SetDistanceMatrix (NumericMatrix< double > &distance_matrix, std::string &tree_filename)
	Set the distance matrix to use when computing alignments, writes the guide tree to the location specified in tree_filename.
void	setGuideTree (std::string &tree_filename, NumericMatrix< double > &dist_mat, uint seq_count)
	Try using the guide tree in the file given by tree_filename.
void	SetMinFlankSize (gnSeqI min_flank)
	Set the minimum flank size used to anchor alignments on the sequences.
	~ClustalInterface ()
Static Public Member Functions
ClustalInterface &	getClustalInterface ()
	Returns a reference to a usable ClustalInterface.
Protected Member Functions
boolean	CallClustal (std::vector< std::string > &seq_table)
Protected Attributes
bool	allocated_aln
int	clustal_score_cutoff
NumericMatrix< double >	distance_matrix
gnSeqI	min_flank_size
Private Member Functions
	ClustalInterface ()
	ClustalInterface (const ClustalInterface &ci)
ClustalInterface &	operator= (const ClustalInterface &ci)

---

Constructor & Destructor Documentation

mems::ClustalInterface::~ClustalInterface (   )  [inline]

Definition at line 53 of file ClustalInterface.h.

mems::ClustalInterface::ClustalInterface (  const ClustalInterface &  ci  )  [inline, private]

Definition at line 95 of file ClustalInterface.h.

mems::ClustalInterface::ClustalInterface (   )  [private]

Definition at line 86 of file ClustalInterface.cpp. References allocated_aln, clustal_score_cutoff, endgappenalties, min_flank_size, no_weights, output_order, and use_endgaps.

---

Member Function Documentation

boolean mems::ClustalInterface::Align (  GappedAlignment &  cr, Match *  r_begin, Match *  r_end, std::vector< genome::gnSequence * > &  seq_table )  [virtual]

Attempts to perform a multiple alignment using ClustalW between r_begin and r_end. Implements mems::GappedAligner. Definition at line 249 of file ClustalInterface.cpp. References amino_acid_codes, CallClustal(), mems::getInterveningCoordinates(), mems::Match, max_aa, seq_array, seqlen_array, mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), and uint.

boolean mems::ClustalInterface::CallClustal (  std::vector< std::string > &  seq_table  )  [protected]

Definition at line 418 of file ClustalInterface.cpp. References allocated_aln, Matrix< double >::cols(), distance_matrix, dna_gap_extend, dna_gap_open, dna_pw_ge_penalty, dna_pw_go_penalty, dnaflag, gap_extend, gap_open, max_aln_length, max_names, names, nseqs, output_clustal, pw_ge_penalty, pw_go_penalty, seq_array, seqlen_array, titles, tmat, and uint. Referenced by Align().

ClustalInterface & mems::ClustalInterface::getClustalInterface (   )  [static]

Returns a reference to a usable ClustalInterface. Definition at line 79 of file ClustalInterface.cpp.

boolean mems::ClustalInterface::guideTreeLoaded (   )  const [inline]

returns true if a guide tree has been loaded already Definition at line 85 of file ClustalInterface.h. References Matrix< double >::cols(), and distance_matrix.

ClustalInterface & mems::ClustalInterface::operator= (  const ClustalInterface &  ci  )  [private]

Definition at line 114 of file ClustalInterface.cpp. References allocated_aln, clustal_score_cutoff, distance_matrix, and min_flank_size.

void mems::ClustalInterface::SetDistanceMatrix (  NumericMatrix< double > &  distance_matrix, std::string &  tree_filename, boolean  reread_tree )

Definition at line 128 of file ClustalInterface.cpp. References allocated_aln, Matrix< double >::cols(), distance_matrix, max_names, names, nseqs, SetDistanceMatrix(), titles, tmat, and uint.

void mems::ClustalInterface::SetDistanceMatrix (  NumericMatrix< double > &  distance_matrix, std::string &  tree_filename )

Set the distance matrix to use when computing alignments, writes the guide tree to the location specified in tree_filename. Parameters: distance_matrix  An NxN distance matrix for the sequences tree_filename  The output file name for the guide tree Definition at line 124 of file ClustalInterface.cpp. Referenced by SetDistanceMatrix().

void mems::ClustalInterface::setGuideTree (  std::string &  tree_filename, NumericMatrix< double > &  dist_mat, uint  seq_count )

Try using the guide tree in the file given by tree_filename. Throws an exception if the tree file couldn't be loaded Parameters: tree_filename  The path to the guide tree file dist_mat  The distance matrix relating sequences seq_count  The number of genomes in the guide tree file Definition at line 201 of file ClustalInterface.cpp. References allocated_aln, distance_matrix, max_names, names, nseqs, titles, tmat, and uint.

void mems::ClustalInterface::SetMinFlankSize (  gnSeqI  min_flank  )  [inline]

Set the minimum flank size used to anchor alignments on the sequences. Definition at line 73 of file ClustalInterface.h. References min_flank_size.

---

Member Data Documentation

bool mems::ClustalInterface::allocated_aln [protected]

Definition at line 93 of file ClustalInterface.h. Referenced by CallClustal(), ClustalInterface(), operator=(), SetDistanceMatrix(), and setGuideTree().

int mems::ClustalInterface::clustal_score_cutoff [protected]

Definition at line 92 of file ClustalInterface.h. Referenced by ClustalInterface(), and operator=().

NumericMatrix< double > mems::ClustalInterface::distance_matrix [protected]

Definition at line 90 of file ClustalInterface.h. Referenced by CallClustal(), guideTreeLoaded(), operator=(), SetDistanceMatrix(), and setGuideTree().

gnSeqI mems::ClustalInterface::min_flank_size [protected]

Definition at line 91 of file ClustalInterface.h. Referenced by ClustalInterface(), operator=(), and SetMinFlankSize().

---

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

• libMems/ClustalInterface.h
• libMems/ClustalInterface.cpp

---