Clustal Omega 1.2.4
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#include <stdbool.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"
Go to the source code of this file.
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. | |
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, 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. | |
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. | |
int | ReadPseudoCountParams (hhalign_para *rHhalignPara_p, char *pcPseudoFile) |
read pseudo-count 'fudge' parameters from file | |
Variables | |
int | iNumberOfThreads |
#define CLUSTERING_UNKNOWN 0 |
#define CLUSTERING_UPGMA 1 |
#define USE_WEIGHTS 0 |
The main alignment function which wraps everything else.
[out] | prMSeq | the multiple sequences structure |
[in] | prMSeqProfile | optional profile to align against |
[in] | prOpts | alignment options to use |
read HMMs specific to individual sequences
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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.
[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 |
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Align two profiles, ie two sets of prealigned sequences. Already aligned columns won't be changed.
[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 |
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Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error.
[in] | prOpts | Already parsed user options |
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free aln opts members
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FIXME.
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FIXME doc.
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Print Long version information to pre-allocated char.
[out] | pcStr | char pointer to write to preallocated to hold iSize chars. |
[in] | iSize | size of pcStr |
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read pseudo-count 'fudge' parameters from file
[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
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Defines an alignment order, which adds sequences sequentially, i.e. one at a time starting with seq 1 & 2.
[out] | piOrderLR_p | order in which nodes/profiles are to be merged/aligned |
[in] | iNumSeq | Number of sequences |
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Sets members of given user opts struct to default values.
[out] | prOpts | User opt struct to initialise |
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