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/*****************************************************************
* SQUID - a library of functions for biological sequence analysis
* Copyright (C) 1992-2002 Washington University School of Medicine
*
* This source code is freely distributed under the terms of the
* GNU General Public License. See the files COPYRIGHT and LICENSE
* for details.
*****************************************************************/
#ifndef SQUID_MSA_INCLUDED
#define SQUID_MSA_INCLUDED
/* msa.h
* SRE, Mon May 17 10:24:30 1999
*
* Header file for SQUID's multiple sequence alignment
* manipulation code.
*
* RCS $Id: msa.h 277 2013-05-16 15:42:49Z fabian $ (Original squid RCS Id: msa.h,v 1.12 2002/10/12 04:40:35 eddy Exp)
*/
#include <stdio.h> /* FILE support */
#include "gki.h" /* hash table support */
#include "ssi.h" /* sequence file index support */
#include "squid.h" /* need SQINFO */
/****************************************************
* Obsolete alignment information, AINFO
* Superceded by MSA structure further below; but we
* need AINFO for the near future for backwards
* compatibility.
****************************************************/
/* Structure: aliinfo_s
*
* Purpose: Optional information returned from an alignment file.
*
* flags: always used. Flags for which info is valid/alloced.
*
* alen: mandatory. Alignments are always flushed right
* with gaps so that all aseqs are the same length, alen.
* Available for all alignment formats.
*
* nseq: mandatory. Aligned seqs are indexed 0..nseq-1.
*
* wgt: 0..nseq-1 vector of sequence weights. Mandatory.
* If not explicitly set, weights are initialized to 1.0.
*
* cs: 0..alen-1, just like the alignment. Contains single-letter
* secondary structure codes for consensus structure; "<>^+"
* for RNA, "EHL." for protein. May be NULL if unavailable
* from seqfile. Only available for SELEX format files.
*
* rf: 0..alen-1, just like the alignment. rf is an arbitrary string
* of characters, used for annotating columns. Blanks are
* interpreted as non-canonical columns and anything else is
* considered canonical. Only available from SELEX files.
*
* sqinfo: mandatory. Array of 0..nseq-1
* per-sequence information structures, carrying
* name, id, accession, coords.
*
*/
struct aliinfo_s {
int flags; /* flags for what info is valid */
int alen; /* length of alignment (columns) */
int nseq; /* number of seqs in alignment */
float *wgt; /* sequence weights [0..nseq-1] */
char *cs; /* consensus secondary structure string */
char *rf; /* reference coordinate system */
struct seqinfo_s *sqinfo; /* name, id, coord info for each sequence */
/* Pfam/HMMER pick-ups */
char *name; /* name of alignment */
char *desc; /* description of alignment */
char *acc; /* accession of alignment */
char *au; /* "author" information */
float tc1, tc2; /* trusted score cutoffs (per-seq, per-domain) */
float nc1, nc2; /* noise score cutoffs (per-seq, per-domain) */
float ga1, ga2; /* gathering cutoffs */
};
typedef struct aliinfo_s AINFO;
#define AINFO_TC (1 << 0)
#define AINFO_NC (1 << 1)
#define AINFO_GA (1 << 2)
/*****************************************************************
* MSA
* SRE, Sun Jun 27 15:03:35 1999 [TW 723 over Greenland]
*
* Defines the new data structure and API for multiple
* sequence alignment i/o.
*****************************************************************/
/* The following constants define the Pfam/Rfam cutoff set we'll propagate
* from msa's into HMMER and Infernal models.
*/
#define MSA_CUTOFF_TC1 0
#define MSA_CUTOFF_TC2 1
#define MSA_CUTOFF_GA1 2
#define MSA_CUTOFF_GA2 3
#define MSA_CUTOFF_NC1 4
#define MSA_CUTOFF_NC2 5
#define MSA_MAXCUTOFFS 6
/* Structure: MSA
* SRE, Tue May 18 11:33:08 1999
*
* Our object for a multiple sequence alignment.
*/
typedef struct msa_struct {
/* Mandatory information associated with the alignment.
*/
char **aseq; /* the alignment itself, [0..nseq-1][0..alen-1] */
char **sqname; /* names of sequences, [0..nseq-1][0..alen-1] */
float *wgt; /* sequence weights [0..nseq-1] */
int alen; /* length of alignment (columns) */
int nseq; /* number of seqs in alignment */
/* Optional information that we understand, and might have.
*/
int flags; /* flags for what optional info is valid */
int type; /* kOtherSeq, kRNA/hmmNUCLEIC, or kAmino/hmmAMINO */
char *name; /* name of alignment, or NULL */
char *desc; /* description of alignment, or NULL */
char *acc; /* accession of alignment, or NULL */
char *au; /* "author" information, or NULL */
char *ss_cons; /* consensus secondary structure string, or NULL */
char *sa_cons; /* consensus surface accessibility string, or NULL */
char *rf; /* reference coordinate system, or NULL */
char **sqacc; /* accession numbers for individual sequences */
char **sqdesc; /* description lines for individual sequences */
char **ss; /* per-seq secondary structure annotation, or NULL */
char **sa; /* per-seq surface accessibility annotation, or NULL */
float cutoff[MSA_MAXCUTOFFS]; /* NC, TC, GA cutoffs propagated to Pfam/Rfam */
int cutoff_is_set[MSA_MAXCUTOFFS];/* TRUE if a cutoff is set; else FALSE */
/* Optional information that we don't understand.
* That is, we know what type of information it is, but it's
* either (interpreted as) free-text comment, or it's Stockholm
* markup with unfamiliar tags.
*/
char **comment; /* free text comments, or NULL */
int ncomment; /* number of comment lines */
int alloc_ncomment; /* number of comment lines alloc'ed */
char **gf_tag; /* markup tags for unparsed #=GF lines */
char **gf; /* annotations for unparsed #=GF lines */
int ngf; /* number of unparsed #=GF lines */
int alloc_ngf; /* number of gf lines alloc'ed */
char **gs_tag; /* markup tags for unparsed #=GS lines */
char ***gs; /* [0..ngs-1][0..nseq-1][free text] markup */
GKI *gs_idx; /* hash of #=GS tag types */
int ngs; /* number of #=GS tag types */
char **gc_tag; /* markup tags for unparsed #=GC lines */
char **gc; /* [0..ngc-1][0..alen-1] markup */
GKI *gc_idx; /* hash of #=GC tag types */
int ngc; /* number of #=GC tag types */
char **gr_tag; /* markup tags for unparsed #=GR lines */
char ***gr; /* [0..ngr][0..nseq-1][0..alen-1] markup */
GKI *gr_idx; /* hash of #=GR tag types */
int ngr; /* number of #=GR tag types */
/* Stuff we need for our own maintenance of the data structure
*/
GKI *index; /* name ->seqidx hash table */
int nseqalloc; /* number of seqs currently allocated for */
int nseqlump; /* lump size for dynamic expansions of nseq */
int *sqlen; /* individual sequence lengths during parsing */
int *sslen; /* individual ss lengths during parsing */
int *salen; /* individual sa lengths during parsing */
int lastidx; /* last index we saw; use for guessing next */
} MSA;
#define MSA_SET_WGT (1 << 0) /* track whether wgts were set, or left at default 1.0 */
/* Structure: MSAFILE
* SRE, Tue May 18 11:36:54 1999
*
* Defines an alignment file that's open for reading.
*/
typedef struct msafile_struct {
FILE *f; /* open file pointer */
char *fname; /* name of file. used for diagnostic output */
int linenumber; /* what line are we on in the file */
char *buf; /* buffer for line input w/ sre_fgets() */
int buflen; /* current allocated length for buf */
SSIFILE *ssi; /* open SSI index file; or NULL, if none. */
int do_gzip; /* TRUE if f is a pipe from gzip -dc (need pclose(f)) */
int do_stdin; /* TRUE if f is stdin (don't close f, not our problem) */
int format; /* format of alignment file we're reading */
} MSAFILE;
/* Alignment file formats.
* Must coexist with sqio.c/squid.h unaligned file format codes.
* Rules:
* - 0 is an unknown/unassigned format
* - <100 reserved for unaligned formats
* - >100 reserved for aligned formats
*/
#define MSAFILE_UNKNOWN 0 /* unknown format */
#define MSAFILE_STOCKHOLM 101 /* Pfam/HMMER's Stockholm format */
#define MSAFILE_SELEX 102 /* Obsolete(!): old HMMER/SELEX format */
#define MSAFILE_MSF 103 /* GCG MSF format */
#define MSAFILE_CLUSTAL 104 /* Clustal V/W format */
#define MSAFILE_A2M 105 /* aligned FASTA (A2M is UCSC terminology) */
#define MSAFILE_PHYLIP 106 /* Felsenstein's PHYLIP format */
#define MSAFILE_EPS 107 /* Encapsulated PostScript (output only) */
#ifdef CLUSTALO
#define MSAFILE_VIENNA 108 /* Vienna: concatenated fasta */
#endif
#define IsAlignmentFormat(fmt) ((fmt) > 100)
/* from msa.c
*/
extern MSAFILE *MSAFileOpen(char *filename, int format, char *env);
extern MSA *MSAFileRead(MSAFILE *afp);
extern void MSAFileClose(MSAFILE *afp);
extern void MSAFree(MSA *msa);
#ifdef CLUSTALO
extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline, int iWrap, int bResno);
#else
extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline);
#endif
extern int MSAFileRewind(MSAFILE *afp);
extern int MSAFilePositionByKey(MSAFILE *afp, char *key);
extern int MSAFilePositionByIndex(MSAFILE *afp, int idx);
extern int MSAFileFormat(MSAFILE *afp);
extern MSA *MSAAlloc(int nseq, int alen);
extern void MSAExpand(MSA *msa);
extern char *MSAFileGetLine(MSAFILE *afp);
extern void MSASetSeqAccession(MSA *msa, int seqidx, char *acc);
extern void MSASetSeqDescription(MSA *msa, int seqidx, char *desc);
extern void MSAAddComment(MSA *msa, char *s);
extern void MSAAddGF(MSA *msa, char *tag, char *value);
extern void MSAAddGS(MSA *msa, char *tag, int seqidx, char *value);
extern void MSAAppendGC(MSA *msa, char *tag, char *value);
extern char *MSAGetGC(MSA *msa, char *tag);
extern void MSAAppendGR(MSA *msa, char *tag, int seqidx, char *value);
extern void MSAVerifyParse(MSA *msa);
extern int MSAGetSeqidx(MSA *msa, char *name, int guess);
extern MSA *MSAFromAINFO(char **aseq, AINFO *ainfo);
extern void MSAMingap(MSA *msa);
extern void MSANogap(MSA *msa);
extern void MSAShorterAlignment(MSA *msa, int *useme);
extern void MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new);
extern char *MSAGetSeqAccession(MSA *msa, int idx);
extern char *MSAGetSeqDescription(MSA *msa, int idx);
extern char *MSAGetSeqSS(MSA *msa, int idx);
extern char *MSAGetSeqSA(MSA *msa, int idx);
extern float MSAAverageSequenceLength(MSA *msa);
/* from a2m.c
*/
extern MSA *ReadA2M(MSAFILE *afp);
#ifdef CLUSTALO
//extern void WriteA2M(FILE *fp, MSA *msa, int vienna);
extern void WriteA2M(FILE *fp, MSA *msa, int iWrap);
#else
extern void WriteA2M(FILE *fp, MSA *msa);
#endif
/* from clustal.c
*/
extern MSA *ReadClustal(MSAFILE *afp);
#ifdef CLUSTALO
extern void WriteClustal(FILE *fp, MSA *msa, int iWrap, int bResno);
extern void WriteClustalForR(MSA *msa, int iWrap, int bResno, int *result_c, char ***result_v);
#else
extern void WriteClustal(FILE *fp, MSA *msa);
extern void WriteClustalForR(MSA *msa, int *result_c, char ***result_v);
#endif
/* from eps.c
*/
extern void EPSWriteSmallMSA(FILE *fp, MSA *msa);
/* from msf.c
*/
extern MSA *ReadMSF(MSAFILE *afp);
extern void WriteMSF(FILE *fp, MSA *msa);
/* from phylip.c
*/
extern MSA *ReadPhylip(MSAFILE *afp);
extern void WritePhylip(FILE *fp, MSA *msa);
/* from selex.c
*/
extern MSA *ReadSELEX(MSAFILE *afp);
extern void WriteSELEX(FILE *fp, MSA *msa);
extern void WriteSELEXOneBlock(FILE *fp, MSA *msa);
/* from stockholm.c
*/
extern MSA *ReadStockholm(MSAFILE *afp);
extern void WriteStockholm(FILE *fp, MSA *msa);
extern void WriteStockholmOneBlock(FILE *fp, MSA *msa);
#endif /*SQUID_MSA_INCLUDED*/
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