+++ /dev/null
-/*****************************************************************
- * 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 217 2011-03-19 10:27:10Z andreas $ (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- * Superceded by MSA structure further below; but we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);
-extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline);
-
-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);
-#else
-extern void WriteA2M(FILE *fp, MSA *msa);
-#endif
-/* from clustal.c
- */
-extern MSA *ReadClustal(MSAFILE *afp);
-extern void WriteClustal(FILE *fp, MSA *msa);
-
-/* 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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