22#include "squid/squid.h"
32#define SEQTYPE_UNKNOWN kOtherSeq
33#define SEQTYPE_DNA kDNA
34#define SEQTYPE_RNA kRNA
35#define SEQTYPE_PROTEIN kAmino
40#define AMINOACID_ANY 'X'
41#define NUCLEOTIDE_ANY 'N'
124AddSeq(
mseq_t **prMSeqDest_p,
char *pcSeqName,
char *pcSeqRes);
137 int iSeqType,
int iSeqFmt,
bool bIsProfile,
bool bDealignInputSeqs,
138 int iMaxNumSeq,
int iMaxSeqLen,
char *pcHMMBatch);
156WriteAlignment(
mseq_t *mseq,
const char *aln_outfile,
int msafile_format,
int iWrap,
bool bResno);
void DealignMSeq(mseq_t *mseq)
Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE.
Definition seq.c:302
void AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes)
Creates a new sequence entry and appends it to an existing mseq structure.
Definition seq.c:1217
void ShuffleMSeq(mseq_t *prMSeq)
Shuffle mseq order.
Definition seq.c:228
const char * SeqTypeToStr(int seqtype)
convert int-encoded iSeqType to string
Definition seq.c:376
void SortMSeqByLength(mseq_t *prMSeq, const char cOrder)
Sort sequences by length.
Definition seq.c:1057
void SeqSwap(mseq_t *mseq, int i, int j)
Swap two sequences in an mseq_t structure.
Definition seq.c:262
bool SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs)
Checks if sequences in given mseq structure are aligned. By definition this is only true,...
Definition seq.c:1112
void CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc)
copies an mseq structure
Definition seq.c:744
void LogSqInfo(SQINFO *sqinfo)
debug output of sqinfo struct
Definition seq.c:327
int FindSeqName(char *seqname, mseq_t *mseq)
Definition seq.c:791
void AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll)
Stripped down version of squid's alistat.
Definition seq.c:60
int ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch)
reads sequences from file
Definition seq.c:420
void DealignSeq(char *seq)
Removes all gap-characters from a sequence.
Definition seq.c:1025
void JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd)
Appends an mseq structure to an already existing one. filename will be left untouched.
Definition seq.c:1275
void FreeMSeq(mseq_t **mseq)
Frees an mseq_t and it's members and zeros all members.
Definition seq.c:817
int WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno)
Write alignment to file.
Definition seq.c:884
void NewMSeq(mseq_t **mseq)
allocate and initialise new mseq_t
Definition seq.c:714
structure for storing multiple sequences
Definition seq.h:47
int seqtype
Definition seq.h:49
char *** pppcHMMBNames
Definition seq.h:116
int nseqs
Definition seq.h:48
char ** seq
Definition seq.h:57
char * filename
Definition seq.h:50
int ** ppiHMMBindex
Definition seq.h:117
char ** orig_seq
Definition seq.h:63
bool aligned
Definition seq.h:51
SQINFO * sqinfo
Squid's sequence info structure. Index range: 0–nseq-1.
Definition seq.h:113
int * tree_order
Definition seq.h:67