src/clustal/seq.h File Reference

#include "squid/squid.h"
#include "util.h"

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Data Structures

struct mseq_t

structure for storing multiple sequences More...

Defines

#define SEQTYPE_UNKNOWN kOtherSeq

#define SEQTYPE_DNA kDNA

#define SEQTYPE_RNA kRNA

#define SEQTYPE_PROTEIN kAmino

#define AMINOACID_ANY 'X'

#define NUCLEOTIDE_ANY 'N'

Functions

void AliStat (mseq_t *prMSeq, bool bSampling, bool bReportAll)

Stripped down version of squid's alistat.

void AddSeq (mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes)

Creates a new sequence entry and appends it to an existing mseq structure.

void SeqSwap (mseq_t *mseq, int i, int j)

Swap two sequences in an mseq_t structure.

void DealignMSeq (mseq_t *mseq)

Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE.

const char * SeqTypeToStr (int seqtype)

convert int-encoded iSeqType to string

int ReadSequences (mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType, int iSeqFmt, int iMaxNumSeq, int iMaxSeqLen)

reads sequences from file

void NewMSeq (mseq_t **mseq)

allocate and initialise new mseq_t

void FreeMSeq (mseq_t **mseq)

Frees an mseq_t and it's members and zeros all members.

void CopyMSeq (mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc)

copies an mseq structure

void LogSqInfo (SQINFO *sqinfo)

debug output of sqinfo struct

int FindSeqName (char *seqname, mseq_t *mseq)

int WriteAlignment (mseq_t *mseq, const char *aln_outfile, int msafile_format)

Write alignment to file.

void DealignSeq (char *seq)

Removes all gap-characters from a sequence.

void ShuffleMSeq (mseq_t *prMSeq)

Shuffle mseq order.

void SortMSeqByLength (mseq_t *prMSeq, const char cOrder)

Sort sequences by length.

void JoinMSeqs (mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd)

Appends an mseq structure to an already existing one. filename will be left untouched.

bool SeqsAreAligned (mseq_t *prMSeq)

Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found.

Define Documentation

#define AMINOACID_ANY 'X'

#define NUCLEOTIDE_ANY 'N'

#define SEQTYPE_DNA kDNA

#define SEQTYPE_PROTEIN kAmino

#define SEQTYPE_RNA kRNA

#define SEQTYPE_UNKNOWN kOtherSeq

int-encoded sequence types. these are in sync with squid's seqtypes and only used for convenience here

Function Documentation

void AddSeq ( mseq_t ** prMSeqDest_p,

char * pcSeqName,

char * pcSeqRes

)

Creates a new sequence entry and appends it to an existing mseq structure.

Parameters:: [out] prMSeqDest_p Already existing and initialised mseq structure

[in] pcSeqName sequence name of the sequence to add

[in] pcSeqRes the actual sequence (residues) to add

Note:: Don't forget to update the align and type flag if necessary!

FIXME allow adding of more features

void AliStat ( mseq_t * prMSeq,

bool bSampling,

bool bReportAll

)

Stripped down version of squid's alistat.

Parameters:: [in] prMSeq The alignment to analyse

[in] bSampling For many sequences: samples from pool

[in] bReportAll Report identities for all sequence pairs

Don't have to worry about sequence case because our version of PairwiseIdentity is case insensitive

mseq to squid msa

FIXME code overlap with WriteAlignment. Make it a function and take code there (contains more comments) as template

void CopyMSeq ( mseq_t ** prMSeqDest_p,

mseq_t * prMSeqSrc

)

copies an mseq structure

Parameters:: [out] prMSeqDest_p Copy of mseq structure

[in] prMSeqSrc Source mseq structure to copy

Note:: caller has to free copy by calling FreeMSeq()

void DealignMSeq ( mseq_t * mseq )

Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE.

Parameters:: [out] mseq The mseq structure to dealign

void DealignSeq ( char * seq )

Removes all gap-characters from a sequence.

Parameters:: [out] seq Sequence to dealign

Note:: seq will not be reallocated

int FindSeqName ( char * seqname,

mseq_t * mseq

)

Parameters:: [in] seqname The sequence name to search for

[in] mseq The multiple sequence structure to search in

Returns:: -1 on failure, sequence index of matching name otherwise

Warning:: If sequence name happens to be used twice, only the first one will be reported back

void FreeMSeq ( mseq_t ** mseq )

Frees an mseq_t and it's members and zeros all members.

Parameters:: [in] mseq mseq_to to free

Note:: use in conjunction with NewMSeq()

See also:: new_mseq

void JoinMSeqs ( mseq_t ** prMSeqDest_p,

mseq_t * prMSeqToAdd

)

Appends an mseq structure to an already existing one. filename will be left untouched.

Parameters:: [in] prMSeqDest_p MSeq structure to which to append to

[out] prMSeqToAdd MSeq structure which is to append

void LogSqInfo ( SQINFO * sqinfo )

debug output of sqinfo struct

Parameters:: [in] sqinfo Squid's SQINFO struct for a certain seqeuence

Note:: useful for debugging only

void NewMSeq ( mseq_t ** prMSeq )

allocate and initialise new mseq_t

Parameters:: [out] prMSeq newly allocated and initialised mseq_t

Note:: caller has to free by calling FreeMSeq()

See also:: FreeMSeq

int ReadSequences ( mseq_t * prMSeq,

char * seqfile,

int iSeqType,

int iSeqFmt,

int iMaxNumSeq,

int iMaxSeqLen

)

reads sequences from file

Parameters:: [out] prMSeq Multiple sequence struct. Must be preallocated. FIXME: would make more sense to allocate it here.

[in] seqfile Sequence file name. If '-' sequence will be read from stdin.

[in] iSeqType int-encoded sequence type. Set to SEQTYPE_UNKNOWN for autodetect (guessed from first sequence)

[in] iMaxNumSeq Return an error, if more than iMaxNumSeq have been read

[in] iMaxSeqLen Return an error, if a seq longer than iMaxSeqLen has been read

Returns:: 0 on success, -1 on error

Note:

Depends heavily on squid
Sequence file format will be guessed
If supported by squid, gzipped files can be read as well.

bool SeqsAreAligned ( mseq_t * prMSeq )

Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found.

Parameters:: [in] prMSeq Sequences to check

Returns:: TRUE if sequences are aligned, FALSE if not

void SeqSwap ( mseq_t * prMSeq,

int i,

int j

)

Swap two sequences in an mseq_t structure.

Parameters:: [out] prMSeq Multiple sequence struct

[in] i Index of first sequence

[in] j Index of seconds sequence

const char* SeqTypeToStr ( int iSeqType )

convert int-encoded iSeqType to string

Parameters:: [in] iSeqType int-encoded sequence type

Returns:: character pointer describing the sequence type

void ShuffleMSeq ( mseq_t * mseq )

Shuffle mseq order.

Parameters:: [out] mseq mseq structure to shuffle

void SortMSeqByLength ( mseq_t * prMSeq,

const char cOrder

)

Sort sequences by length.

Parameters:: [out] prMSeq mseq to sort by length

[out] cOrder Sorting order. 'd' for descending, 'a' for ascending.

int WriteAlignment ( mseq_t * mseq,

const char * pcAlnOutfile,

int outfmt

)

Write alignment to file.

Parameters:: [in] mseq The mseq_t struct containing the aligned sequences

[in] pcAlnOutfile The name of the output file

[in] outfmt The alignment output format (defined in squid.h)

Returns:: Non-zero on error

Note:: We create a temporary squid MSA struct in here because we never use it within clustal. We might be better of using the old clustal output routines instead.

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