clustal-omega.h File Reference

#include <stdbool.h>
#include "clustal-omega-config.h"
#include "hhalign/general.h"
#include "hhalign/hhfunc.h"
#include "clustal/util.h"
#include "clustal/symmatrix.h"
#include "clustal/tree.h"
#include "clustal/seq.h"
#include "clustal/mbed.h"
#include "clustal/weights.h"
#include "clustal/pair_dist.h"
#include "clustal/hhalign_wrapper.h"

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Data Structures
struct	opts_t

Macros
#define	CLUSTERING_UNKNOWN   0
#define	CLUSTERING_UPGMA   1
#define	USE_WEIGHTS   0

Enumerations
enum	{ INPUT_ORDER = 0, TREE_ORDER }

Functions
void	PrintLongVersion (char *pcStr, int iSize)
	Print Long version information to pre-allocated char. More...
void	SetDefaultAlnOpts (opts_t *opts)
	Sets members of given user opts struct to default values. More...
void	FreeAlnOpts (opts_t *aln_opts)
	free aln opts members More...
void	AlnOptsLogicCheck (opts_t *opts)
	Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error. More...
void	PrintAlnOpts (FILE *prFile, opts_t *opts)
	FIXME doc. More...
void	InitClustalOmega (int iNumThreadsToUse)
	FIXME. More...
void	SequentialAlignmentOrder (int **piOrderLR_p, int iNumSeq)
	Defines an alignment order, which adds sequences sequentially, i.e. one at a time starting with seq 1 & 2. More...
int	AlignmentOrder (int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMBed, bool bPercID)
	Defines the alignment order by calculating a guide tree. In a first-step pairwise distances will be calculated (or read from a file). In a second step those distances will be clustered and a guide-tree created. Steps 1 and 2 will be skipped if a guide-tree file was given, in which case the guide-tree will be just read from the file. More...
int	Align (mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts)
	The main alignment function which wraps everything else. More...
int	AlignProfiles (mseq_t *prMSeqProfile1, mseq_t *prMSeqProfile2, hhalign_para rHhalignPara)
	Align two profiles, ie two sets of prealigned sequences. Already aligned columns won't be changed. More...
int	ReadPseudoCountParams (hhalign_para *rHhalignPara_p, char *pcPseudoFile)
	read pseudo-count 'fudge' parameters from file More...

Variables
int	iNumberOfThreads

Macro Definition Documentation

#define CLUSTERING_UNKNOWN   0

#define CLUSTERING_UPGMA   1

#define USE_WEIGHTS   0

Enumeration Type Documentation

anonymous enum

Enumerator
INPUT_ORDER
TREE_ORDER

Function Documentation

int Align	(	mseq_t *	prMSeq,
		mseq_t *	prMSeqProfile,
		opts_t *	prOpts
	)

The main alignment function which wraps everything else.

Parameters

[out]	prMSeq	the multiple sequences structure
[in]	prMSeqProfile	optional profile to align against
[in]	prOpts	alignment options to use

Returns

0 on success, -1 on failure

Warning

old structure used to be initialised like this: hmm_light rHMM = {0};

int AlignmentOrder	(	int **	piOrderLR_p,
		double **	pdSeqWeights_p,
		mseq_t *	prMSeq,
		int	iPairDistType,
		char *	pcDistmatInfile,
		char *	pcDistmatOutfile,
		int	iClusteringType,
		int	iClustersizes,
		char *	pcGuidetreeInfile,
		char *	pcGuidetreeOutfile,
		char *	pcClusterFile,
		bool	bUseMbed,
		bool	bPercID
	)

Defines the alignment order by calculating a guide tree. In a first-step pairwise distances will be calculated (or read from a file). In a second step those distances will be clustered and a guide-tree created. Steps 1 and 2 will be skipped if a guide-tree file was given, in which case the guide-tree will be just read from the file.

Parameters

[out]	piOrderLR_p	order in which nodes/profiles are to be merged/aligned
[out]	pdSeqWeights_p	Sequence weights
[out]	pdSeqWeights_p	Sequence weights
[in]	prMSeq	The sequences from which the alignment order is to be calculated
[in]	iPairDistType	Method of pairwise distance comparison
[in]	pcDistmatInfile	If not NULL distances will be read from this file instead of being calculated
[in]	pcDistmatOutfile	If not NULL computed pairwise distances will be written to this file
[in]	iClusteringType	Clustering method to be used to cluster the pairwise distances
[in]	pcGuidetreeInfile	If not NULL guidetree will be read from this file. Skips pairwise distance and guidetree computation
[in]	pcGuidetreeOutfile	If not NULL computed guidetree will be written to this file
[in]	bUseMbed	If TRUE, fast mBed guidetree computation will be employed

Returns

Non-zero on error

int AlignProfiles	(	mseq_t *	prMSeqProfile1,
		mseq_t *	prMSeqProfile2,
		hhalign_para	rHhalignPara
	)

Align two profiles, ie two sets of prealigned sequences. Already aligned columns won't be changed.

Parameters

[out]	prMSeqProfile1	First profile/aligned set of sequences. Merged alignment will be found in here.
[in]	prMSeqProfile2	First profile/aligned set of sequences
[in]	rHhalignPara	FIXME

Returns

0 on success, -1 on failure

void AlnOptsLogicCheck

(

opts_t *

prOpts

)

Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error.

Parameters

[in]

prOpts

Already parsed user options

void FreeAlnOpts

(

opts_t *

aln_opts

)

free aln opts members

void InitClustalOmega

(

int

iNumThreadsToUse

)

FIXME.

void PrintAlnOpts	(	FILE *	prFile,
		opts_t *	opts
	)

FIXME doc.

void PrintLongVersion	(	char *	pcStr,
		int	iSize
	)

Print Long version information to pre-allocated char.

Note

short version information is equivalent to PACKAGE_VERSION

Parameters

[out]	pcStr	char pointer to write to preallocated to hold iSize chars.
[in]	iSize	size of pcStr

int ReadPseudoCountParams	(	hhalign_para *	rHhalignPara_p,
		char *	pcPseudoFile
	)

read pseudo-count 'fudge' parameters from file

Parameters

[out]	rHhalignPara_p	structure that holds several hhalign parameters
[in]	pcPseudoFile	name of file with pseudo-count information. format must be collection of pairs of lines where one line specifies name of parameter (gapb,gapd,gape,gapf,gapg,gaph,gapi,pca,pcb,pcc,gapbV,gapdV,gapeV,gapfV,gapgV,gaphV,gapiV,pcaV,pcbV,pccV) followed by second line with the (double) value of this parameter.

order of parameters is not fixed, not all parameters have to be set

void SequentialAlignmentOrder	(	int **	piOrderLR_p,
		int	iNumSeq
	)

Defines an alignment order, which adds sequences sequentially, i.e. one at a time starting with seq 1 & 2.

Parameters

[out]	piOrderLR_p	order in which nodes/profiles are to be merged/aligned
[in]	iNumSeq	Number of sequences

See Also

TraverseTree()

void SetDefaultAlnOpts

(

opts_t *

prOpts

)

Sets members of given user opts struct to default values.

Parameters

[out]

prOpts

User opt struct to initialise

Variable Documentation

int iNumberOfThreads