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mems::MuscleInterface Class Reference

#include <MuscleInterface.h>

Inheritance diagram for mems::MuscleInterface:

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Collaboration diagram for mems::MuscleInterface:

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List of all members.

Public Member Functions

boolean Align (GappedAlignment &cr, AbstractMatch *r_begin, AbstractMatch *r_end, std::vector< genome::gnSequence * > &seq_table)
boolean Align (GappedAlignment &cr, Match *r_begin, Match *r_end, std::vector< genome::gnSequence * > &seq_table)
 Attempts to perform a multiple alignment using Muscle between r_begin and r_end.

boolean CallMuscle (std::vector< std::string > &aln_matrix, const std::vector< std::string > &seq_table)
boolean CallMuscleFast (std::vector< std::string > &aln_matrix, const std::vector< std::string > &seq_table)
void CreateTree (const NumericMatrix< double > &distances, const std::string &tree_filename)
std::string GetExtraMuscleArguments ()
 Get the arguments to use when executing muscle.

void ParseMusclePath (const char *argv0)
 Parse the execution path from argv[0] and set the muscle path accordingly.

bool ProfileAlign (const GappedAlignment &ga1, const GappedAlignment &ga2, GappedAlignment &aln, bool anchored=true)
 Given two gapped alignments in ga1 and ga2, align them and store the result in aln.

bool ProfileAlignFast (const GappedAlignment &ga1, const GappedAlignment &ga2, GappedAlignment &aln, bool anchored=true)
bool Refine (GappedAlignment &ga, size_t windowsize=0)
bool RefineFast (GappedAlignment &ga, size_t windowsize=0)
void SetExtraMuscleArguments (const std::string &extra_args)
 Set the arguments to use when executing muscle.

void SetMusclePath (const std::string &path)
 Set the path to the muscle executable Defaults to "muscle".

 ~MuscleInterface ()

Static Public Member Functions

MuscleInterface & getMuscleInterface ()
 Returns a reference to a usable MuscleInterface.


Protected Member Functions

void ClearCommandLine ()
void SetMuscleArguments (const std::string &extra_args)

Protected Attributes

std::string extra_muscle_arguments
std::string muscle_arguments
char ** muscle_cmdline
std::string muscle_path

Private Member Functions

 MuscleInterface ()
 MuscleInterface (const MuscleInterface &ci)
MuscleInterface & operator= (const MuscleInterface &ci)

Constructor & Destructor Documentation

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

Definition at line 55 of file MuscleInterface.h.

References ClearCommandLine().

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

Definition at line 137 of file MuscleInterface.h.

mems::MuscleInterface::MuscleInterface (   )  [private]
 

Definition at line 373 of file MuscleInterface.cpp.

References muscle_arguments, muscle_cmdline, muscle_path, and mems::parseCommand().

Member Function Documentation

boolean mems::MuscleInterface::Align (  GappedAlignment &  cr,
AbstractMatch *  r_begin,
AbstractMatch *  r_end,
std::vector< genome::gnSequence * > &  seq_table
) 
 

Definition at line 518 of file MuscleInterface.cpp.

References CallMuscleFast(), mems::AbstractMatch::End(), mems::AbstractMatch::Length(), mems::AbstractMatch::Multiplicity(), mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), mems::AbstractMatch::Start(), and uint.

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

Attempts to perform a multiple alignment using Muscle between r_begin and r_end.

Implements mems::GappedAligner.

Definition at line 423 of file MuscleInterface.cpp.

References CallMuscleFast(), mems::getInterveningCoordinates(), mems::Match, mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), and uint.

boolean mems::MuscleInterface::CallMuscle (  std::vector< std::string > &  aln_matrix,
const std::vector< std::string > &  seq_table
) 
 

Definition at line 651 of file MuscleInterface.cpp.

References mems::failure_count, muscle_arguments, muscle_cmdline, muscle_path, mems::pipeExec(), and uint.

Referenced by Refine().

boolean mems::MuscleInterface::CallMuscleFast (  std::vector< std::string > &  aln_matrix,
const std::vector< std::string > &  seq_table
) 
 

Definition at line 704 of file MuscleInterface.cpp.

References MUSCLE(), and seqname.

Referenced by Align().

void mems::MuscleInterface::ClearCommandLine (   )  [inline, protected]
 

Definition at line 122 of file MuscleInterface.h.

References muscle_cmdline.

Referenced by SetMuscleArguments(), SetMusclePath(), and ~MuscleInterface().

void mems::MuscleInterface::CreateTree (  const NumericMatrix< double > &  distances,
const std::string &  tree_filename
) 
 

Definition at line 1138 of file MuscleInterface.cpp.

References Matrix< T >::rows().

Referenced by mems::Aligner::align(), and mems::ProgressiveAligner::alignPP().

std::string mems::MuscleInterface::GetExtraMuscleArguments (   )  [inline]
 

Get the arguments to use when executing muscle.

Definition at line 83 of file MuscleInterface.h.

References extra_muscle_arguments.

MuscleInterface & mems::MuscleInterface::getMuscleInterface (   )  [static]
 

Returns a reference to a usable MuscleInterface.

Definition at line 366 of file MuscleInterface.cpp.

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

Definition at line 413 of file MuscleInterface.cpp.

void mems::MuscleInterface::ParseMusclePath (  const char *  argv0  ) 
 

Parse the execution path from argv[0] and set the muscle path accordingly.

Definition at line 380 of file MuscleInterface.cpp.

References SetMusclePath().

bool mems::MuscleInterface::ProfileAlign (  const GappedAlignment &  ga1,
const GappedAlignment &  ga2,
GappedAlignment &  aln,
bool  anchored = true
) 
 

Given two gapped alignments in ga1 and ga2, align them and store the result in aln.

ga1 and ga2 must have equal sequence count and contain disjoint sets of sequences, e.g. for any given seqI, if ga1.LeftEnd(seqI) != NO_MATCH, then ga2.LeftEnd(seqI) == NO_MATCH

Definition at line 897 of file MuscleInterface.cpp.

References mems::debug_muscle, mems::failure_count, mems::GetAlignment(), mems::SparseAbstractMatch<>::LeftEnd(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::SparseAbstractMatch<>::Multiplicity(), muscle_arguments, muscle_cmdline, muscle_path, mems::pipeExec(), mems::SparseAbstractMatch<>::SeqCount(), mems::GappedAlignment::SetAlignment(), mems::SparseAbstractMatch<>::SetLeftEnd(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), SetMuscleArguments(), mems::stripGapColumns(), and uint.

bool mems::MuscleInterface::ProfileAlignFast (  const GappedAlignment &  ga1,
const GappedAlignment &  ga2,
GappedAlignment &  aln,
bool  anchored = true
) 
 

Definition at line 1026 of file MuscleInterface.cpp.

References mems::GetAlignment(), mems::SparseAbstractMatch<>::LeftEnd(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::msaFromSeqTable(), mems::SparseAbstractMatch<>::Multiplicity(), mems::SparseAbstractMatch<>::SeqCount(), mems::GappedAlignment::SetAlignment(), mems::SparseAbstractMatch<>::SetLeftEnd(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::stripGapColumns(), and uint.

Referenced by mems::ProgressiveAligner::refineAlignment().

bool mems::MuscleInterface::Refine (  GappedAlignment &  ga,
size_t  windowsize = 0
) 
 

Definition at line 744 of file MuscleInterface.cpp.

References CallMuscle(), mems::GetAlignment(), mems::SparseAbstractMatch<>::LeftEnd(), mems::SparseAbstractMatch<>::SeqCount(), mems::GappedAlignment::SetAlignment(), SetMuscleArguments(), and uint.

bool mems::MuscleInterface::RefineFast (  GappedAlignment &  ga,
size_t  windowsize = 0
) 
 

Definition at line 796 of file MuscleInterface.cpp.

References mems::GetAlignment(), mems::SparseAbstractMatch<>::LeftEnd(), mems::msaFromSeqTable(), RefineW(), mems::SparseAbstractMatch<>::SeqCount(), mems::GappedAlignment::SetAlignment(), and uint.

Referenced by mems::ProgressiveAligner::refineAlignment().

void mems::MuscleInterface::SetExtraMuscleArguments (  const std::string &  extra_args  ) 
 

Set the arguments to use when executing muscle.

Definition at line 401 of file MuscleInterface.cpp.

References extra_muscle_arguments.

void mems::MuscleInterface::SetMuscleArguments (  const std::string &  extra_args  )  [protected]
 

Definition at line 406 of file MuscleInterface.cpp.

References ClearCommandLine(), extra_muscle_arguments, muscle_arguments, muscle_cmdline, muscle_path, and mems::parseCommand().

Referenced by ProfileAlign(), and Refine().

void mems::MuscleInterface::SetMusclePath (  const std::string &  path  ) 
 

Set the path to the muscle executable Defaults to "muscle".

Definition at line 395 of file MuscleInterface.cpp.

References ClearCommandLine(), muscle_arguments, muscle_cmdline, muscle_path, and mems::parseCommand().

Referenced by ParseMusclePath().

Member Data Documentation

std::string mems::MuscleInterface::extra_muscle_arguments [protected]
 

Definition at line 117 of file MuscleInterface.h.

Referenced by GetExtraMuscleArguments(), SetExtraMuscleArguments(), and SetMuscleArguments().

std::string mems::MuscleInterface::muscle_arguments [protected]
 

Definition at line 116 of file MuscleInterface.h.

Referenced by CallMuscle(), MuscleInterface(), ProfileAlign(), SetMuscleArguments(), and SetMusclePath().

char** mems::MuscleInterface::muscle_cmdline [protected]
 

Definition at line 118 of file MuscleInterface.h.

Referenced by CallMuscle(), ClearCommandLine(), MuscleInterface(), ProfileAlign(), SetMuscleArguments(), and SetMusclePath().

std::string mems::MuscleInterface::muscle_path [protected]
 

Definition at line 115 of file MuscleInterface.h.

Referenced by CallMuscle(), MuscleInterface(), ProfileAlign(), SetMuscleArguments(), and SetMusclePath().

The documentation for this class was generated from the following files:
Generated on Fri Mar 14 06:01:42 2008 for libMems by doxygen 1.3.6