31#include "clustal-omega-config.h"
38#include "hhalign/general.h"
39#include "hhalign/hhfunc.h"
55#define CLUSTERING_UNKNOWN 0
56#define CLUSTERING_UPGMA 1
170 int iPairDistType,
char *pcDistmatInfile,
char *pcDistmatOutfile,
171 int iClusteringType,
int iClustersizes,
172 char *pcGuidetreeInfile,
char *pcGuidetreeOutfile,
char *pcClusterFile,
173 bool bUseMBed,
bool bPercID);
182 mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
void SetDefaultAlnOpts(opts_t *opts)
Sets members of given user opts struct to default values.
Definition clustal-omega.c:189
void AlnOptsLogicCheck(opts_t *opts)
Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error.
Definition clustal-omega.c:232
int Align(mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts)
The main alignment function which wraps everything else.
Definition clustal-omega.c:960
int ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile)
read pseudo-count 'fudge' parameters from file
Definition clustal-omega.c:1532
void FreeAlnOpts(opts_t *aln_opts)
free aln opts members
Definition clustal-omega.c:163
void PrintAlnOpts(FILE *prFile, opts_t *opts)
FIXME doc.
Definition clustal-omega.c:281
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...
Definition clustal-omega.c:657
void PrintLongVersion(char *pcStr, int iSize)
Print Long version information to pre-allocated char.
Definition clustal-omega.c:149
int iNumberOfThreads
Definition clustal-omega.c:131
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 c...
Definition clustal-omega.c:755
@ INPUT_ORDER
Definition clustal-omega.h:67
@ TREE_ORDER
Definition clustal-omega.h:67
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.
Definition clustal-omega.c:1484
void InitClustalOmega(int iNumThreadsToUse)
FIXME.
Definition clustal-omega.c:622
structure for storing multiple sequences
Definition seq.h:47
Definition clustal-omega.h:76
int iPairDistType
Definition clustal-omega.h:101
int iTransitivity
Definition clustal-omega.h:97
bool bUseMbed
Definition clustal-omega.h:103
char * pcDistmatOutfile
Definition clustal-omega.h:86
int iClustersizes
Definition clustal-omega.h:93
int iMaxHMMIterations
Definition clustal-omega.h:134
bool bIterationsAuto
Definition clustal-omega.h:132
int iClusteringType
Definition clustal-omega.h:91
bool bUseMbedForIteration
Definition clustal-omega.h:105
bool bPileup
Definition clustal-omega.h:107
int iHMMInputFiles
Definition clustal-omega.h:123
hhalign_para rHhalignPara
Definition clustal-omega.h:138
char * pcGuidetreeOutfile
Definition clustal-omega.h:109
char * pcDistmatInfile
Definition clustal-omega.h:84
char * pcClustfile
Definition clustal-omega.h:95
bool bUseKimura
Definition clustal-omega.h:113
int iMaxGuidetreeIterations
Definition clustal-omega.h:136
bool bPercID
Definition clustal-omega.h:115
char ** ppcHMMInput
Definition clustal-omega.h:120
char * pcPosteriorfile
Definition clustal-omega.h:99
char * pcHMMBatch
Definition clustal-omega.h:125
char * pcGuidetreeInfile
Definition clustal-omega.h:111
bool bAutoOptions
Definition clustal-omega.h:79
int iNumIterations
Definition clustal-omega.h:130