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 1 168 int iPairDistType,
char *pcDistmatInfile,
char *pcDistmatOutfile,
169 int iClusteringType,
int iClustersizes,
170 char *pcGuidetreeInfile,
char *pcGuidetreeOutfile,
char *pcClusterFile,
171 bool bUseMBed,
bool bPercID);
180 mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
Definition: clustal-omega.h:67
int ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile)
read pseudo-count 'fudge' parameters from file
Definition: clustal-omega.c:1466
bool bUseMbed
Definition: clustal-omega.h:103
bool bPileup
Definition: clustal-omega.h:107
int iMaxGuidetreeIterations
Definition: clustal-omega.h:134
bool bIterationsAuto
Definition: clustal-omega.h:130
char * pcDistmatOutfile
Definition: clustal-omega.h:86
int iClusteringType
Definition: clustal-omega.h:91
int Align(mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts)
The main alignment function which wraps everything else.
Definition: clustal-omega.c:959
void FreeAlnOpts(opts_t *aln_opts)
free aln opts members
Definition: clustal-omega.c:163
char * pcClustfile
Definition: clustal-omega.h:95
void PrintLongVersion(char *pcStr, int iSize)
Print Long version information to pre-allocated char.
Definition: clustal-omega.c:149
hhalign_para rHhalignPara
Definition: clustal-omega.h:136
bool bPercID
Definition: clustal-omega.h:115
int iNumIterations
Definition: clustal-omega.h:128
void SetDefaultAlnOpts(opts_t *opts)
Sets members of given user opts struct to default values.
Definition: clustal-omega.c:189
int iHMMInputFiles
Definition: clustal-omega.h:123
void PrintAlnOpts(FILE *prFile, opts_t *opts)
FIXME doc.
Definition: clustal-omega.c:280
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:656
bool bUseKimura
Definition: clustal-omega.h:113
int iNumberOfThreads
Definition: clustal-omega.c:131
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:1418
bool bUseMbedForIteration
Definition: clustal-omega.h:105
void InitClustalOmega(int iNumThreadsToUse)
FIXME.
Definition: clustal-omega.c:621
char * pcDistmatInfile
Definition: clustal-omega.h:84
char ** ppcHMMInput
Definition: clustal-omega.h:120
int iTransitivity
Definition: clustal-omega.h:97
structure for storing multiple sequences
Definition: seq.h:47
Definition: clustal-omega.h:76
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:754
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:231
bool bAutoOptions
Definition: clustal-omega.h:79
int iClustersizes
Definition: clustal-omega.h:93
Definition: clustal-omega.h:67
char * pcGuidetreeOutfile
Definition: clustal-omega.h:109
char * pcPosteriorfile
Definition: clustal-omega.h:99
char * pcGuidetreeInfile
Definition: clustal-omega.h:111
int iMaxHMMIterations
Definition: clustal-omega.h:132
int iPairDistType
Definition: clustal-omega.h:101