libMems/ClustalInterface.cpp File Reference

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

Include dependency graph for ClustalInterface.cpp:

Go to the source code of this file.

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

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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.

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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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