Clustal Omega  1.0.3
Data Structures | Defines | Functions | Variables
src/clustal-omega.h File Reference
#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

Defines

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

Functions

void PrintLongVersion (char *pcStr, int iSize)
 Print Long version information to pre-allocated char.
void SetDefaultAlnOpts (opts_t *opts)
 Sets members of given user opts struct to default values.
void FreeAlnOpts (opts_t *aln_opts)
 free aln opts members
void AlnOptsLogicCheck (opts_t *opts)
 Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error.
void PrintAlnOpts (FILE *prFile, opts_t *opts)
 FIXME doc.
void InitClustalOmega (int iNumThreadsToUse)
 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.
int Align (mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts, hhalign_para rHhalignPara)
 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 CLUSTERING_UNKNOWN   0
#define CLUSTERING_UPGMA   1
#define USE_WEIGHTS   0

Function Documentation

int Align ( mseq_t prMSeq,
mseq_t prMSeqProfile,
opts_t prOpts,
hhalign_para  rHhalignPara 
)

The main alignment function which wraps everything else.

Parameters:
[out]prMSeq*the* multiple sequences structure
[in]prMSeqProfileoptional profile to align against
[in]prOptsalignment options to use
[in]rHhalignParaFIXME
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_porder in which nodes/profiles are to be merged/aligned
[out]pdSeqWeights_pSequence weights
[out]pdSeqWeights_pSequence weights
[in]prMSeqThe sequences from which the alignment order is to be calculated
[in]iPairDistTypeMethod of pairwise distance comparison
[in]pcDistmatInfileIf not NULL distances will be read from this file instead of being calculated
[in]pcDistmatOutfileIf not NULL computed pairwise distances will be written to this file
[in]iClusteringTypeClustering method to be used to cluster the pairwise distances
[in]pcGuidetreeInfileIf not NULL guidetree will be read from this file. Skips pairwise distance and guidetree computation
[in]pcGuidetreeOutfileIf not NULL computed guidetree will be written to this file
[in]bUseMbedIf 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]prMSeqProfile1First profile/aligned set of sequences. Merged alignment will be found in here.
[in]prMSeqProfile2First profile/aligned set of sequences
[in]rHhalignParaFIXME
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]prOptsAlready 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]pcStrchar pointer to write to preallocated to hold iSize chars.
[in]iSizesize 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_porder in which nodes/profiles are to be merged/aligned
[in]iNumSeqNumber of sequences
See also:
TraverseTree()
void SetDefaultAlnOpts ( opts_t prOpts)

Sets members of given user opts struct to default values.

Parameters:
[out]prOptsUser opt struct to initialise

Variable Documentation