libMems/ClustalInterface.cpp File Reference

#include "libMems/ClustalInterface.h"
#include <sstream>
#include "libGenome/gnFilter.h"
#include <fstream>
#include "libClustalW/clustalw.h"

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Namespaces

namespace  mems

Defines

#define MISALIGNMENT_WORKAROUND
 When performing progressive alignment, clustalW misaligns the first sequence for some reason.


Variables

char * amino_acid_codes
FILE * clustal_outfile
float dna_gap_extend
float dna_gap_open
float dna_pw_ge_penalty
float dna_pw_go_penalty
Boolean dnaflag
Boolean endgappenalties
Boolean explicit_dnaflag
float gap_extend
float gap_open
sint gap_pos1
FILE * gcg_outfile
Boolean interactive
sint max_aa
sint max_aln_length
sint max_names
char ** names
FILE * nbrf_outfile
FILE * nexus_outfile
Boolean no_weights
sint nseqs
Boolean output_clustal
Boolean output_gcg
Boolean output_gde
Boolean output_nbrf
Boolean output_nexus
sint output_order
Boolean output_phylip
FILE * phylip_outfile
float pw_ge_penalty
float pw_go_penalty
char ** seq_array
sint * seqlen_array
char * seqname
char ** titles
double ** tmat
Boolean use_endgaps
Boolean usemenu


Define Documentation

#define MISALIGNMENT_WORKAROUND
 

When performing progressive alignment, clustalW misaligns the first sequence for some reason.

define MISALIGNMENT_WORKAROUND to enable a workaround for this bug. The workaround adds an additional copy of the first sequence to each alignment then removes the misaligned copy of the first sequence.

Definition at line 74 of file ClustalInterface.cpp.


Variable Documentation

char* amino_acid_codes
 

Definition at line 48 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::Align().

FILE* clustal_outfile
 

Definition at line 46 of file ClustalInterface.cpp.

float dna_gap_extend
 

Definition at line 35 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

float dna_gap_open
 

Definition at line 35 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

float dna_pw_ge_penalty
 

Definition at line 41 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

float dna_pw_go_penalty
 

Definition at line 41 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

Boolean dnaflag
 

Definition at line 23 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

Boolean endgappenalties
 

Definition at line 57 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::ClustalInterface().

Boolean explicit_dnaflag
 

Definition at line 23 of file ClustalInterface.cpp.

float gap_extend
 

Definition at line 34 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), and mems::PairwiseScoringScheme::PairwiseScoringScheme().

float gap_open
 

Definition at line 34 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), and mems::PairwiseScoringScheme::PairwiseScoringScheme().

sint gap_pos1
 

Definition at line 53 of file ClustalInterface.cpp.

FILE * gcg_outfile
 

Definition at line 46 of file ClustalInterface.cpp.

Boolean interactive
 

Definition at line 24 of file ClustalInterface.cpp.

sint max_aa
 

Definition at line 49 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::Align().

sint max_aln_length
 

Definition at line 31 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

sint max_names
 

Definition at line 22 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), mems::ClustalInterface::SetDistanceMatrix(), and mems::ClustalInterface::setGuideTree().

char** names
 

Definition at line 28 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), mems::gnAlignedSequences::outputNexus(), mems::ClustalInterface::SetDistanceMatrix(), and mems::ClustalInterface::setGuideTree().

FILE * nbrf_outfile
 

Definition at line 46 of file ClustalInterface.cpp.

FILE * nexus_outfile
 

Definition at line 46 of file ClustalInterface.cpp.

Boolean no_weights
 

Definition at line 60 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::ClustalInterface().

sint nseqs
 

Definition at line 26 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), mems::ClustalInterface::SetDistanceMatrix(), and mems::ClustalInterface::setGuideTree().

Boolean output_clustal
 

Definition at line 45 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

Boolean output_gcg
 

Definition at line 45 of file ClustalInterface.cpp.

Boolean output_gde
 

Definition at line 45 of file ClustalInterface.cpp.

Boolean output_nbrf
 

Definition at line 45 of file ClustalInterface.cpp.

Boolean output_nexus
 

Definition at line 45 of file ClustalInterface.cpp.

sint output_order
 

Definition at line 59 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::ClustalInterface().

Boolean output_phylip
 

Definition at line 45 of file ClustalInterface.cpp.

FILE * phylip_outfile
 

Definition at line 46 of file ClustalInterface.cpp.

float pw_ge_penalty
 

Definition at line 40 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

float pw_go_penalty
 

Definition at line 40 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal().

char** seq_array
 

Definition at line 29 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::Align(), and mems::ClustalInterface::CallClustal().

sint* seqlen_array
 

Definition at line 27 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::Align(), and mems::ClustalInterface::CallClustal().

char* seqname
 

Definition at line 25 of file ClustalInterface.cpp.

Referenced by mems::MuscleInterface::CallMuscleFast().

char ** titles
 

Definition at line 28 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), mems::ClustalInterface::SetDistanceMatrix(), and mems::ClustalInterface::setGuideTree().

double** tmat
 

Definition at line 54 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::CallClustal(), mems::ClustalInterface::SetDistanceMatrix(), and mems::ClustalInterface::setGuideTree().

Boolean use_endgaps
 

Definition at line 56 of file ClustalInterface.cpp.

Referenced by mems::ClustalInterface::ClustalInterface().

Boolean usemenu
 

Definition at line 23 of file ClustalInterface.cpp.


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