--- /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+ * Superceded by MSA structure further below; but we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*/
git://source.jalview.org / jabaws.git / blobdiff