src/clustal-omega.c File Reference

#include <assert.h>
#include "clustal-omega.h"
#include "clustal-omega-config.h"
#include "hhalign/general.h"
#include "hhalign/hhfunc.h"
#include "clustal/log.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"

Include dependency graph for clustal-omega.c:

This graph shows which files directly or indirectly include this file:

Defines
#define	INDIRECT_HMM   0
#define	USEHMMER   1
#define	USEHHMAKE   (!USEHMMER)
#define	SHUFFLE_INPUT_SEQ_ORDER   0
#define	SORT_INPUT_SEQS   0
#define	PRINT_TAIL   5
Functions
void	PrintLongVersion (char *pcStr, int iSize)
	Print Long version information to pre-allocated char.
void	FreeAlnOpts (opts_t *prAlnOpts)
	free aln opts members
void	SetDefaultAlnOpts (opts_t *prOpts)
	Sets members of given user opts struct to default values.
void	AlnOptsLogicCheck (opts_t *prOpts)
	Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error.
void	PrintAlnOpts (FILE *prFile, opts_t *prOpts)
	FIXME doc.
int	HmmerVersion ()
	Returns major version of HMMER. Whichever hmmbuild version is found first in your PATH will be used.
int	AlnToHHMFile (mseq_t *prMSeq, char *pcHMMOut)
	Create a HHM file from aligned sequences.
int	AlnToHMMFile (mseq_t *prMSeq, const char *pcHMMOut)
	Create a HMM file from aligned sequences.
int	AlnToHMM (hmm_light *prHMM, mseq_t *prMSeq)
	Convert a multiple sequence structure into a HMM.
void	InitClustalOmega (int iNumThreadsRequested)
	FIXME.
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.
int	AlignmentOrder (int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, bool bUseMbed)
	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.
void	SetAutoOptions (opts_t *prOpts, int iNumSeq)
	Set some options automatically based on number of sequences. Might overwrite some user-set options.
int	Align (mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts)
	The main alignment function which wraps everything else.
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.
Variables
int	iNumberOfThreads

---

Define Documentation

#define INDIRECT_HMM   0

#define PRINT_TAIL   5

#define SHUFFLE_INPUT_SEQ_ORDER   0

#define SORT_INPUT_SEQS   0

#define USEHHMAKE   (!USEHMMER)

#define USEHMMER   1

---

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,
		char *	pcGuidetreeInfile,
		char *	pcGuidetreeOutfile,
		bool	bUseMbed
	)

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

int AlnToHHMFile	(	mseq_t *	prMSeq,
		char *	pcHMMOut
	)

Create a HHM file from aligned sequences.

Warning:

Should be eliminated in the future as building routine should not create intermediate files

Parameters:

[in]	prMSeq	Aligned mseq_t
[in]	pcHMMOut	HMM output file name

Returns:

Non-zero on error

int AlnToHMM	(	hmm_light *	prHMM,
		mseq_t *	prMSeq
	)

Convert a multiple sequence structure into a HMM.

Parameters:

[out]	prHMM	Pointer to preallocted HMM which will be set here
[in]	prMSeq	Pointer to an alignment

Returns:

0 on error, non-0 otherwise

See also:

AlnToHMMFile()

Warning:

the following probably won't work on windows: missing /tmp/. Should be ok on Cygwin though

int AlnToHMMFile	(	mseq_t *	prMSeq,
		const char *	pcHMMOut
	)

Create a HMM file from aligned sequences.

Warning:

Should be replaced in the future by some internal HMM building routine that does not call external programs

Parameters:

[in]	prMSeq	Aligned mseq_t
[in]	pcHMMOut	HMM output file name

Returns:

Non-zero on error

void FreeAlnOpts

(

opts_t *

prAlnOpts

)

free aln opts members

int HmmerVersion

(

)

Returns major version of HMMER. Whichever hmmbuild version is found first in your PATH will be used.

Returns:

-1 on error, major hmmer version otherwise

void InitClustalOmega

(

int

iNumThreadsRequested

)

FIXME.

void PrintAlnOpts	(	FILE *	prFile,
		opts_t *	prOpts
	)

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

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 SetAutoOptions	(	opts_t *	prOpts,
		int	iNumSeq
	)

Set some options automatically based on number of sequences. Might overwrite some user-set options.

Parameters:

[out]	prOpts	Pointer to alignment options structure
[in]	iNumSeq	Number of sequences to align

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