[med-svn] [psortb] 02/04: New upstream version 3.0.4+dfsg
Andreas Tille
tille at debian.org
Wed Apr 5 14:50:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository psortb.
commit ff5aa84d7140cb35662be125f44b56adf3cfef58
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 5 14:21:07 2017 +0200
New upstream version 3.0.4+dfsg
---
algorithm-hmm/src/include/gki.h | 51 ----
algorithm-hmm/src/include/msa.h | 286 --------------------
algorithm-hmm/src/include/rk.h | 40 ---
algorithm-hmm/src/include/sqfuncs.h | 293 ---------------------
algorithm-hmm/src/include/squid.h | 473 ----------------------------------
algorithm-hmm/src/include/squidconf.h | 77 ------
algorithm-hmm/src/include/ssi.h | 193 --------------
algorithm-hmm/src/include/stopwatch.h | 59 -----
8 files changed, 1472 deletions(-)
diff --git a/algorithm-hmm/src/include/gki.h b/algorithm-hmm/src/include/gki.h
deleted file mode 100644
index c056320..0000000
--- a/algorithm-hmm/src/include/gki.h
+++ /dev/null
@@ -1,51 +0,0 @@
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SQUID_GKI_INCLUDED
-#define SQUID_GKI_INCLUDED
-
-/* gki.h
- * SRE, Sat May 1 15:07:22 1999
- *
- * Declarations of structures, functions for generic key index
- * module: emulation of Perl hashes. See gki.c.
- *
- * RCS $Id: gki.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- */
-
-/* gki_elem:
- * key, array index pairs are kept in linked list structures.
- */
-struct gki_elem {
- char *key;
- int idx;
- struct gki_elem *nxt;
-};
-
-/* gki:
- * a dynamically resized hash structure;
- * contains a hash table and associated data
- */
-typedef struct {
- struct gki_elem **table;
-
- int primelevel;
- int nhash;
- int nkeys;
-} GKI;
-
-GKI *GKIInit(void);
-void GKIFree(GKI *hash);
-int GKIHashValue(GKI *hash, char *key);
-int GKIStoreKey(GKI *hash, char *key);
-int GKIKeyIndex(GKI *hash, char *key);
-void GKIStatus(GKI *hash);
-
-#endif /* SQUID_GKI_INCLUDED */
diff --git a/algorithm-hmm/src/include/msa.h b/algorithm-hmm/src/include/msa.h
deleted file mode 100644
index 84c8e88..0000000
--- a/algorithm-hmm/src/include/msa.h
+++ /dev/null
@@ -1,286 +0,0 @@
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING 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,v 1.1.1.1 2003/07/20 20:30:07 cspencer 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.
- *****************************************************************/
-
-/* 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 tc1, tc2; /* trusted score cutoffs (per-seq, per-domain) */
- float nc1, nc2; /* noise score cutoffs (per-seq, per-domain) */
- float ga1, ga2; /* gathering cutoffs (per-seq, per-domain) */
-
- /* 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_TC (1 << 0)
-#define MSA_SET_NC (1 << 1)
-#define MSA_SET_GA (1 << 2)
-#define MSA_SET_WGT (1 << 3)
-
-/* 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) */
-
-#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);
-
-/* from a2m.c
- */
-extern MSA *ReadA2M(MSAFILE *afp);
-extern void WriteA2M(FILE *fp, MSA *msa);
-
-/* 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);
-
-/* 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*/
diff --git a/algorithm-hmm/src/include/rk.h b/algorithm-hmm/src/include/rk.h
deleted file mode 100644
index aebf50b..0000000
--- a/algorithm-hmm/src/include/rk.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SQRKH_INCLUDED
-#define SQRKH_INCLUDED
-
-/* rk.h
- *
- * Header file for Rabin-Karp pattern searching on encoded
- * sequence strings.
- *
- * Sean Eddy, Thu Oct 1 11:45:42 1992
- * RCS $Id: rk.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- */
-
-
- /* expect 32 bits for 8 nt */
-typedef unsigned long Hashseq;
- /* but we count to be sure...
- RK_HASHSIZE is the number of nt that fit
- in one probe */
-#define RK_HASHSIZE (sizeof(Hashseq)*2)
- /* empirically, how many nt minimum we require
- in a pattern before we abandon rk and
- go with something else */
-#define RK_REQUIRE 4
-
-extern int rkseq(Hashseq hashprobe, char *sequence);
-extern Hashseq rkcomp(char *probe); /* compile a Hashseq from a pattern */
-
-
-
-#endif /* SQRKH_INCLUDED */
diff --git a/algorithm-hmm/src/include/sqfuncs.h b/algorithm-hmm/src/include/sqfuncs.h
deleted file mode 100644
index 6f60c28..0000000
--- a/algorithm-hmm/src/include/sqfuncs.h
+++ /dev/null
@@ -1,293 +0,0 @@
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SQFUNCSH_INCLUDED
-#define SQFUNCSH_INCLUDED
-/* sqfuncs.h
- *
- * Prototypes for squid library functions;
- * also makes a good reference list for what the package contains.
- *
- * Warning: squid is a slowly evolving beast. Some functions are
- * obsolete. Some functions are probably just wrong, dating to
- * a primordial era before I knew anything about what I was doing.
- * Some functions are both obsolete and wrong but still necessary
- * to get legacy code to compile.
- *
- * RCS $Id: sqfuncs.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- */
-
-/*
- * from aligneval.c
- */
-extern float ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2);
-extern float CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2);
-extern float CompareMultAlignments(char **kseqs, char **tseqs, int N);
-extern float CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N);
-extern float PairwiseIdentity(char *s1, char *s2);
-extern float AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample);
-extern char *MajorityRuleConsensus(char **aseq, int nseq, int alen);
-
-/*
- * from alignio.c
- */
-extern void AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo);
-extern void InitAinfo(AINFO *ainfo);
-extern void FreeAlignment(char **aseqs, AINFO *ainfo);
-extern void SAMizeAlignment(char **aseq, int nseq, int alen);
-extern void SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap);
-extern int MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s);
-extern int MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s);
-extern int DealignedLength(char *aseq);
-extern int WritePairwiseAlignment(FILE *ofp, char *aseq1, char *name1, int spos1,
- char *aseq2, char *name2, int spos2,
- int **pam, int indent);
-extern int MingapAlignment(char **aseqs, AINFO *ainfo);
-extern int RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex,
- char ***ret_aseqs, AINFO *ainfo);
-extern void AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym);
-
-/* from cluster.c
- */
-extern int Cluster(float **mx, int N, enum clust_strategy mode, struct phylo_s **ret_tree);
-extern struct phylo_s *AllocPhylo(int N);
-extern void FreePhylo(struct phylo_s *tree, int N);
-extern void MakeDiffMx(char **aseqs, int num, float ***ret_dmx);
-extern void MakeIdentityMx(char **aseqs, int num, float ***ret_imx);
-extern void PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N);
-extern void PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N);
-
-/*
- * from dayhoff.c
- */
-extern int ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale);
-extern void ScalePAM(int **pam, int scale);
-
-
-/* from file.c
- */
-extern char *FileDirname(char *filename);
-extern char *FileTail(char *file, int noextension);
-extern char *FileConcat(char *dir, char *file);
-extern char *FileAddSuffix(char *filename, char *sfx);
-extern FILE *EnvFileOpen(char *fname, char *env, char **ret_dir);
-extern int FileExists(char *filename);
-
-
-/* from getopt.c
- */
-extern int Getopt(int argc, char **argv,
- struct opt_s *opt, int nopts, char *usage,
- int *ret_optind, char **ret_optname, char **ret_optarg);
-
-
-/* from hsregex.c
- * Henry Spencer's regex() code
- */
-extern int Strparse(char *rexp, char *s, int ntok);
-extern void SqdClean(void);
-extern sqd_regexp *sqd_regcomp(const char *re);
-extern int sqd_regexec(sqd_regexp *rp, const char *s);
-extern void sqd_regsub(const sqd_regexp *rp, const char *src, char *dst);
-extern void sqd_regerror(char *message);
-
-/* from interleaved.c
- */
-extern int IsInterleavedFormat(int format);
-extern int ReadInterleaved(char *seqfile,
- int (*skip_header)(FILE *),
- int (*parse_header)(FILE *, AINFO *),
- int (*is_dataline)(char *, char *),
- char ***ret_aseqs, AINFO *ainfo);
-extern int ReadAlignment(char *seqfile, int format, char ***ret_aseqs, AINFO *ainfo);
-
-
-/* from revcomp.c
- */
-extern char *revcomp(char *comp, char *seq);
-
-/*
- * from selex.c
- */
-extern int DealignAseqs(char **aseqs, int num, char ***ret_rseqs);
-extern int IsSELEXFormat(char *filename);
-extern int TruncateNames(char **names, int N); /* OBSOLETE? */
-
-/*
- * from seqencode.c
- */
-extern int seqcmp(char *s1, char *s2, int allow);
-extern int seqncmp(char *s1, char *s2, int n, int allow);
-extern int seqencode(char *codeseq,char *str);
-extern int coded_revcomp(char *comp, char *seq);
-extern int seqdecode(char *str, char *codeseq);
-extern int seqndecode(char *str, char *codeseq, int n);
-
-/*
- * from shuffle.c
- */
-extern int StrShuffle(char *s1, char *s2);
-extern int StrDPShuffle(char *s1, char *s2);
-extern int StrMarkov0(char *s1, char *s2);
-extern int StrMarkov1(char *s1, char *s2);
-extern int StrReverse(char *s1, char *s2);
-extern int StrRegionalShuffle(char *s1, char *s2, int w);
-extern int AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen);
-extern int AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen);
-
-/*
- * from sqerror.c
- */
-extern void Die(char *format, ...);
-extern void Warn(char *format, ...);
-extern void Panic(char *file, int line);
-
-
-/*
- * from sqio.c
- */
-extern void FreeSequence(char *seq, SQINFO *sqinfo);
-extern int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag);
-extern void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2);
-extern void ToDNA(char *seq);
-extern void ToRNA(char *seq);
-extern void ToIUPAC(char *seq);
-extern int ReadMultipleRseqs(char *seqfile, int fformat, char ***ret_rseqs,
- SQINFO **ret_sqinfo, int *ret_num);
-extern SQFILE *SeqfileOpen(char *filename, int format, char *env);
-extern SQFILE *SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode);
-extern int SeqfileFormat(FILE *fp);
-extern void SeqfilePosition(SQFILE *sfp, SSIOFFSET *offset);
-extern void SeqfileRewind(SQFILE *sfp);
-extern void SeqfileClose(SQFILE *sfp);
-
-extern int ReadSeq(SQFILE *fp, int format, char **ret_seq, SQINFO *sqinfo);
-extern int GCGBinaryToSequence(char *seq, int len);
-extern int GCGchecksum(char *seq, int seqlen);
-extern int GCGMultchecksum(char **seqs, int nseq);
-extern void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc);
-extern int WriteSeq(FILE *outf, int outfmt, char *seq, SQINFO *sqinfo);
-extern int Seqtype(char *seq);
-extern int GuessAlignmentSeqtype(char **aseq, int nseq);
-extern int String2SeqfileFormat(char *s);
-extern char *SeqfileFormat2String(int code);
-extern SQINFO *MSAToSqinfo(MSA *msa);
-
-/* from squidcore.c
- */
-extern void Banner(FILE *fp, char *banner);
-
-
-/* from sre_ctype.c
- */
-extern int sre_tolower(int c);
-extern int sre_toupper(int c);
-
-/* from sre_math.c
- */
-extern float ExponentialRandom(void);
-extern float Gaussrandom(float mean, float stddev);
-extern int Linefit(float *x, float *y, int N,
- float *ret_a, float *ret_b, float *ret_r);
-extern void WeightedLinefit(float *x, float *y, float *var, int N,
- float *ret_m, float *ret_b);
-extern double Gammln(double xx);
-extern int DNorm(double *vec, int n);
-extern int FNorm(float *vec, int n);
-extern void DScale(double *vec, int n, double scale);
-extern void FScale(float *vec, int n, float scale);
-extern void DSet(double *vec, int n, double value);
-extern void FSet(float *vec, int n, float value);
-extern double DSum(double *vec, int n);
-extern float FSum(float *vec, int n);
-extern void DAdd(double *vec1, double *vec2, int n);
-extern void FAdd(float *vec1, float *vec2, int n);
-extern void DCopy(double *vec1, double *vec2, int n);
-extern void FCopy(float *vec1, float *vec2, int n);
-extern int DMax(double *vec, int n);
-extern int FMax(float *vec, int n);
-extern double DDot(double *vec1, double *vec2, int n);
-extern float FDot(float *vec1, float *vec2, int n);
-extern float **FMX2Alloc(int rows, int cols);
-extern void FMX2Free(float **mx);
-extern double **DMX2Alloc(int rows, int cols);
-extern void DMX2Free(double **mx);
-extern void FMX2Multiply(float **A, float **B, float **C, int m, int p, int n);
-extern float sre_random(void);
-extern void sre_srandom(int seed);
-extern int DChoose(double *p, int n);
-extern int FChoose(float *p, int n);
-extern double DLogSum(double *logp, int n);
-extern float FLogSum(float *logp, int n);
-extern double IncompleteGamma(double a, double x);
-
-/* from sre_string.c
- */
-#ifdef NOSTR
-extern char *strstr(char *s, char *subs);
-#endif
-extern char *Strdup(char *s);
-extern void StringChop(char *s);
-extern int Strinsert(char *s1, char c, int pos);
-extern int Strdelete(char *s1, int pos);
-extern void s2lower(char *s);
-extern void s2upper(char *s);
-extern void *sre_malloc(char *file, int line, size_t size);
-extern void *sre_realloc(char *file, int line, void *p, size_t size);
-extern void Free2DArray(void **p, int dim1);
-extern void Free3DArray(void ***p, int dim1, int dim2);
-extern char *RandomSequence(char *alphabet, float *p, int n, int len);
-extern char *sre_fgets(char **buf, int *n, FILE *fp);
-extern int sre_strcat(char **dest, int ldest, char *src, int lsrc);
-extern char *sre_strtok(char **s, char *delim, int *len);
-extern char *sre_strdup(char *s, int n);
-extern char *sre_strncat(char *s1, char *s2, int n);
-extern int IsBlankline(char *s);
-
-/* from stack.c
- */
-extern struct intstack_s *InitIntStack(void);
-extern void PushIntStack(struct intstack_s *stack, int data);
-extern int PopIntStack(struct intstack_s *stack, int *ret_data);
-extern void ReverseIntStack(struct intstack_s *stack);
-extern int FreeIntStack( struct intstack_s *stack );
-
-/*
- * from translate.c
- */
-extern char *Translate(char *seq, char **code);
-
-/*
- * from types.c
- */
-extern int IsInt(char *s);
-extern int IsReal(char *s);
-extern void Byteswap(char *swap, int nbytes);
-#ifndef USE_HOST_BYTESWAP_FUNCTIONS
-extern sqd_uint16 sre_ntoh16(sqd_uint16 netshort);
-extern sqd_uint32 sre_ntoh32(sqd_uint32 netlong);
-extern sqd_uint16 sre_hton16(sqd_uint16 hostshort);
-extern sqd_uint32 sre_hton32(sqd_uint32 hostlong);
-#endif /*!USE_HOST_BYTESWAP_FUNCTIONS*/
-extern sqd_uint64 sre_ntoh64(sqd_uint64 net_int64);
-extern sqd_uint64 sre_hton64(sqd_uint64 host_int64);
-
-/*
- * from weight.c
- */
-extern void GSCWeights(char **aseq, int nseq, int alen, float *wgt);
-extern void VoronoiWeights(char **aseq, int nseq, int alen, float *wgt);
-extern void BlosumWeights(char **aseq, int nseq, int alen, float blosumlevel, float *wgt);
-extern void PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt);
-extern void FilterAlignment(MSA *msa, float cutoff, MSA **ret_new);
-extern void SampleAlignment(MSA *msa, int sample, MSA **ret_new);
-extern void SingleLinkCluster(char **aseq, int nseq, int alen, float maxid,
- int **ret_c, int *ret_nc);
-#endif /* SQFUNCSH_INCLUDED */
diff --git a/algorithm-hmm/src/include/squid.h b/algorithm-hmm/src/include/squid.h
deleted file mode 100644
index 4806fa5..0000000
--- a/algorithm-hmm/src/include/squid.h
+++ /dev/null
@@ -1,473 +0,0 @@
-/* Generated automatically from squid.h.in by configure. */
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SQUIDH_INCLUDED
-#define SQUIDH_INCLUDED
-
-/* squid.h
- * Header file for my library of sequence functions.
- *
- * CVS $Id: squid.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- */
-
-#include <stdio.h>
-#include <math.h>
-#include <stdlib.h>
-#include <unistd.h> /* for sysconf() #define's */
-
-
-#if DEBUGLEVEL > 0
-#include <assert.h> /* for SQD_DASSERT1(), etc. */
-#endif
-
-#include "squidconf.h" /* #define's generated by ./configure script */
-
-/*****************************************************************
- * Integers of guaranteed size. (used for instance in gsi.c, gsi2.c)
- * These are set by the ./configure script; if they show up as FIXME,
- * they must be manually edited to appropriate type definitions. You
- * do need 64-bit integers in the current code; email me if this
- * prevents you from compiling SQUID and tell me your system (I don't
- * know of any systems that don't have 64-bit integers these days).
- *****************************************************************/
-typedef unsigned short sqd_uint16;
-typedef unsigned int sqd_uint32;
-typedef unsigned long long sqd_uint64;
-
-#ifdef USE_HOST_BYTESWAP_FUNCTIONS
-#include <sys/types.h> /* only for ntohl() and friends. */
-#include <netinet/in.h> /* only for ntohl() and friends. */
-#define sre_ntoh16(x) ntohs(x);
-#define sre_ntoh32(x) ntohl(x);
-#define sre_hton16(x) htons(x);
-#define sre_hton32(x) htonl(x);
-#endif /* USE_HOST_BYTESWAP_FUNCTIONS */
-
-/* Library version info is made available as a global to
- * any interested program. These are defined in iupac.c
- * with the other globals.
- */
-extern char squid_version[]; /* version number */
-extern char squid_date[]; /* date of release */
-extern int squid_errno; /* error codes */
-
-
-
-/****************************************************
- * Error codes returned by squid library functions (squid_errno)
- ****************************************************/
-
-#define SQERR_OK 0 /* no error */
-#define SQERR_UNKNOWN 1 /* generic error, unidentified */
-#define SQERR_NODATA 2 /* unexpectedly NULL stream */
-#define SQERR_MEM 3 /* malloc or realloc failed */
-#define SQERR_NOFILE 4 /* file not found */
-#define SQERR_FORMAT 5 /* file format not recognized */
-#define SQERR_PARAMETER 6 /* bad parameter passed to func */
-#define SQERR_DIVZERO 7 /* error in sre_math.c */
-#define SQERR_INCOMPAT 8 /* incompatible parameters */
-#define SQERR_EOD 9 /* end-of-data (often normal) */
-
-/****************************************************
- * Single sequence information
- ****************************************************/
-#define SQINFO_NAMELEN 64
-#define SQINFO_DESCLEN 128
-
-struct seqinfo_s {
- int flags; /* what extra data are available */
- char name[SQINFO_NAMELEN];/* up to 63 characters of name */
- char id[SQINFO_NAMELEN]; /* up to 63 char of database identifier */
- char acc[SQINFO_NAMELEN]; /* up to 63 char of database accession # */
- char desc[SQINFO_DESCLEN];/* up to 127 char of description */
- int len; /* length of this seq */
- int start; /* (1..len) start position on source seq */
- int stop; /* (1..len) end position on source seq */
- int olen; /* original length of source seq */
- int type; /* kRNA, kDNA, kAmino, or kOther */
- char *ss; /* 0..len-1 secondary structure string */
- char *sa; /* 0..len-1 % side chain surface access. */
-};
-typedef struct seqinfo_s SQINFO;
-
-#define SQINFO_NAME (1 << 0)
-#define SQINFO_ID (1 << 1)
-#define SQINFO_ACC (1 << 2)
-#define SQINFO_DESC (1 << 3)
-#define SQINFO_START (1 << 4)
-#define SQINFO_STOP (1 << 5)
-#define SQINFO_LEN (1 << 6)
-#define SQINFO_TYPE (1 << 7)
-#define SQINFO_OLEN (1 << 8)
-#define SQINFO_SS (1 << 9)
-#define SQINFO_SA (1 << 10)
-
-
-/****************************************************
- * Sequence alphabet: see also iupac.c
- ****************************************************/
- /* IUPAC symbols defined globally in iupac.c */
-struct iupactype {
- char sym; /* character representation */
- char symcomp; /* complement (regular char */
- char code; /* my binary rep */
- char comp; /* binary encoded complement */
-};
-extern struct iupactype iupac[];
-#define IUPACSYMNUM 17
-
-extern char *stdcode1[]; /* 1-letter amino acid translation code */
-extern char *stdcode3[]; /* 3-letter amino acid translation code */
-extern float dnafq[]; /* nucleotide occurrence frequencies */
-extern float aafq[]; /* amino acid occurrence frequencies */
-extern char aa_alphabet[]; /* amino acid alphabet */
-extern int aa_index[]; /* convert 0..19 indices to 0..26 */
-
- /* valid symbols in IUPAC code */
-#define NUCLEOTIDES "ACGTUNRYMKSWHBVDacgtunrymkswhbvd"
-#define AMINO_ALPHABET "ACDEFGHIKLMNPQRSTVWY"
-#define DNA_ALPHABET "ACGT"
-#define RNA_ALPHABET "ACGU"
-#define WHITESPACE " \t\n"
-
-#define isgap(c) ((c) == ' ' || (c) == '.' || (c) == '_' || (c) == '-' || (c) == '~')
-
-
-/****************************************************
- * Sequence i/o: originally from Don Gilbert's readseq
- ****************************************************/
-#include "msa.h" /* for multiple sequence alignment support */
-
- /* buffer size for reading in lines from sequence files*/
-#define LINEBUFLEN 4096
-
-/* sequence types parsed by Seqtype() */
-/* note that these must match hmmAMINO and hmmNUCLEIC in HMMER */
-#define kOtherSeq 0 /* hmmNOTSETYET */
-#define kDNA 1
-#define kRNA 2 /* hmmNUCLEIC */
-#define kAmino 3 /* hmmAMINO */
-
-/* Unaligned sequence file formats recognized
- * Coexists with definitions of multiple alignment formats in msa.h:
- * >100 reserved for alignment formats
- * <100 reserved for unaligned formats
- * 0 reserved for unknown
- *
- * Some "legacy" formats are supported only when explicitly
- * requested; not autodetected by SeqfileFormat().
- *
- * DON'T REASSIGN THESE CODES. They're written into
- * GSI index files. You can use new ones, but reassigning
- * the sense of old ones will break GSI indices.
- * Alignment format codes were reassigned with the creation
- * of msa.c, but before Stockholm format, there were no
- * indexed alignment databases.
- */
-#define SQFILE_UNKNOWN 0 /* unknown format */
-#define SQFILE_IG 1 /* Intelligenetics (!) */
-#define SQFILE_GENBANK 2 /* GenBank flatfile */
- /* 3 was A2M. Now an alignment format */
-#define SQFILE_EMBL 4 /* EMBL or Swissprot flatfile */
-#define SQFILE_GCG 5 /* GCG single sequence files */
-#define SQFILE_STRIDER 6 /* MacStrider (!!) */
-#define SQFILE_FASTA 7 /* FASTA format: default */
-#define SQFILE_ZUKER 8 /* Zuker MFOLD format (legacy) */
-#define SQFILE_IDRAW 9 /* Idraw-style PostScript (legacy) */
- /* 10 was SELEX. Now alignment format */
- /* 11 was MSF. Now alignment format */
-#define SQFILE_PIR 12 /* PIR format */
-#define SQFILE_RAW 13 /* raw sequence */
-#define SQFILE_SQUID 14 /* my obsolete squid format */
- /* 15 was kXPearson, extended FASTA; withdrawn */
-#define SQFILE_GCGDATA 16 /* GCG data library file */
- /* 17 was Clustal. Now alignment format*/
-
-#define IsUnalignedFormat(fmt) ((fmt) && (fmt) < 100)
-
-#include "ssi.h"
-
-struct ReadSeqVars {
- FILE *f; /* open file pointer */
- char *fname; /* name of file; used for diagnostics */
- int linenumber; /* what line are we on in the file */
-
- char *buf; /* dynamically allocated sre_fgets() buffer */
- int buflen; /* allocation length for buf */
-
- int ssimode; /* SSI_OFFSET_I32 or SSI_OFFSET_I64 */
- SSIOFFSET ssioffset; /* disk offset to last line read into buf */
- SSIOFFSET r_off; /* offset to start of record */
- SSIOFFSET d_off; /* offset to start of sequence data */
-
- int rpl; /* residues per data line for this file; -1 if unset, 0 if invalid */
- int lastrpl; /* rpl on last line seen */
- int maxrpl; /* max rpl on any line of the file */
- int bpl; /* bytes per data line; -1 if unset, 0 if invalid */
- int lastbpl; /* bpl on last line seen */
- int maxbpl; /* max bpl on any line of the file */
-
- char *seq; /* growing sequence during parse */
- SQINFO *sqinfo; /* name, id, etc, gathered during parse */
- char *sp;
- int seqlen; /* current sequence length */
- int maxseq; /* current allocation length for seq */
-
- int format; /* format of seqfile we're reading. */
- int do_gzip; /* TRUE if f is a pipe from gzip -dc */
- int do_stdin; /* TRUE if f is stdin */
-
- /* An (important) hack for sequential access of multiple alignment files:
- * we read the whole alignment in,
- * and then copy it one sequence at a time into seq and sqinfo.
- * It is active if msa is non NULL.
- * msa->lastidx is reused/overloaded: used to keep track of what
- * seq we'll return next.
- * afp->format is the real format, while SQFILE->format is kMSA.
- * Because we keep it in the SQFILE structure,
- * ReadSeq() and friends are always reentrant for multiple seqfiles.
- */
- MSA *msa;
- MSAFILE *afp;
-};
-typedef struct ReadSeqVars SQFILE;
-
-
-/****************************************************
- * Cluster analysis and phylogenetic tree support
- ****************************************************/
-
-/* struct phylo_s - a phylogenetic tree
- *
- * For N sequences, there will generally be an array of 0..N-2
- * phylo_s structures representing the nodes of a tree.
- * [0] is the root. The indexes of left and
- * right children are somewhat confusing so be careful. The
- * indexes can have values of 0..2N-2. If they are 0..N-1, they
- * represent pointers to individual sequences. If they are
- * >= N, they represent pointers to a phylo_s structure
- * at (index - N).
- */
-struct phylo_s {
- int parent; /* index of parent, N..2N-2, or -1 for root */
- int left; /* index of one of the branches, 0..2N-2 */
- int right; /* index of other branch, 0..2N-2 */
- float diff; /* difference score between seqs */
- float lblen; /* left branch length */
- float rblen; /* right branch length */
- char *is_in; /* 0..N-1 flag array, 1 if seq included */
- int incnum; /* number of seqs included at this node */
-};
-
-
-/* Strategies for cluster analysis; cluster by mean distance,
- * minimum distance, or maximum distance.
- */
-enum clust_strategy { CLUSTER_MEAN, CLUSTER_MAX, CLUSTER_MIN };
-
-/****************************************************
- * Generic data structure support
- ****************************************************/
-
-/* a struct intstack_s implements a pushdown stack for storing
- * single integers.
- */
-struct intstack_s {
- int data;
- struct intstack_s *nxt;
-};
-
-/****************************************************
- * Binary nucleotide alphabet support
- ****************************************************/
-
-/* Binary encoding of the IUPAC code for nucleotides
- *
- * four-bit "word", permitting rapid degenerate matching
- * A C G T/U
- * 0 0 1 0
- */
-#define NTA 8
-#define NTC 4
-#define NTG 2
-#define NTT 1
-#define NTU 1
-#define NTN 15 /* A|C|G|T */
-#define NTR 10 /* A|G */
-#define NTY 5 /* C|T */
-#define NTM 12 /* A|C */
-#define NTK 3 /* G|T */
-#define NTS 6 /* C|G */
-#define NTW 9 /* A|T */
-#define NTH 13 /* A|C|T */
-#define NTB 7 /* C|G|T */
-#define NTV 14 /* A|C|G */
-#define NTD 11 /* A|G|T */
-#define NTGAP 16 /* GAP */
-#define NTEND 0 /* null string terminator */
-
-/* ntmatch(): bitwise comparison of two nuc's
- * note that it's sensitive to the order;
- * probe may be degenerate but target should not be
- */
-#define ntmatch(probe, target) ((probe & target) == target)
-
-/****************************************************
- * Support for a portable, flexible Getopt()
- ****************************************************/
-
-/* Structure: opt_s
- *
- * Structure for declaring options to a main().
- */
-struct opt_s {
- char *name; /* name of option, e.g. "--option1" or "-o" */
- int single; /* TRUE if a single letter option */
- int argtype; /* for typechecking, e.g. sqdARG_INT */
-};
- /* acceptable argtype's... */
-#define sqdARG_NONE 0 /* no argument */
-#define sqdARG_INT 1 /* something that atoi() can grok */
-#define sqdARG_FLOAT 2 /* something that atof() can grok */
-#define sqdARG_CHAR 3 /* require single character or digit */
-#define sqdARG_STRING 4 /* anything goes */
-
-/****************************************************
- * Support for convenient Perl-y regexp matching
- * See hsregexp.c for copyright notice: this code is derived
- * from Henry Spencer's freely distributed regexp library.
- ****************************************************/
-
-#define NSUBEXP 10
-typedef struct sqd_regexp {
- char *startp[NSUBEXP];
- char *endp[NSUBEXP];
- char regstart; /* Internal use only. */
- char reganch; /* Internal use only. */
- char *regmust; /* Internal use only. */
- int regmlen; /* Internal use only. */
- char program[1]; /* Unwarranted chumminess with compiler. */
-} sqd_regexp;
-
-/* Strparse() defines and manages these.
- * sqd_parse[0] contains the substring that matched the pattern.
- * sqd_parse[1-9] contain substrings matched with ()'s.
- */
-extern char *sqd_parse[10];
-
-/****************************************************
- * Portable detection of multiprocessor # of CPUs.
- * #include <unistd.h>
- * long foo = SQD_NPROC;
- * returns the number of available processors.
- * if foo == -1, we failed.
- ****************************************************/
-
-/* Our problem here is that POSIX apparently doesn't specify
- * a standard for how to get sysconf() to report the number of
- * processors on-line. _SC_NPROCESSORS_ONLN is specified
- * by SVR4.0MP. Thanks to W. Gish for help here.
- */
-#undef SQD_NPROC
-#ifdef _SC_NPROCESSORS_ONLN /* Sun Solaris, Digital UNIX */
-#define SQD_NPROC sysconf(_SC_NPROCESSORS_ONLN)
-#else
-#ifdef _SC_NPROC_ONLN /* Silicon Graphics IRIX */
-#define SQD_NPROC sysconf(_SC_NPROC_ONLN)
-#else /* FreeBSD, Linux don't support getting ncpu via sysconf() */
-#define SQD_NPROC -1
-#endif
-#endif
-
-/****************************************************
- * Three levels of debugging printf's and assert's
- * level 1: little impact on verbosity or performance
- * level 2: moderate impact
- * level 3: high impact
- * Example:
- * SQD_DPRINTF3(("Matrix row %d col %d = %f\n", i, j, val));
- * Note the double parentheses; these are important.
- ****************************************************/
-
-#ifndef DEBUGLEVEL
-#define DEBUGLEVEL 0
-#endif
-
-#if (DEBUGLEVEL >= 1)
-#define SQD_DPRINTF1(x) printf x
-#define SQD_DASSERT1(x) assert x
-#else
-#define SQD_DPRINTF1(x)
-#define SQD_DASSERT1(x)
-#endif
-#if (DEBUGLEVEL >= 2)
-#define SQD_DPRINTF2(x) printf x
-#define SQD_DASSERT2(x) assert x
-#else
-#define SQD_DPRINTF2(x)
-#define SQD_DASSERT2(x)
-#endif
-#if (DEBUGLEVEL >= 3)
-#define SQD_DPRINTF3(x) printf x
-#define SQD_DASSERT3(x) assert x
-#else
-#define SQD_DPRINTF3(x)
-#define SQD_DASSERT3(x)
-#endif
-
-/* PANIC is called for failures of Std C/POSIX functions,
- * instead of my own functions. Panic() calls perror() and exits
- * abnormally.
- */
-#define PANIC Panic(__FILE__, __LINE__)
-
-/* Malloc/realloc calls are wrapped
- */
-#define MallocOrDie(x) sre_malloc(__FILE__, __LINE__, (x))
-#define ReallocOrDie(x,y) sre_realloc(__FILE__, __LINE__, (x), (y))
-
-/****************************************************
- * Miscellaneous macros and defines
- ****************************************************/
-
-#define CHOOSE(a) ((int) (sre_random() * (a)))
- /* must declare swapfoo to use SWAP() */
-#define SWAP(a,b) {swapfoo = b; b = a; a = swapfoo;}
-#define ScalarsEqual(a,b) (fabs((a)-(b)) < 1e-7)
-
-#ifndef MIN
-#define MIN(a,b) (((a)<(b))?(a):(b))
-#endif
-#ifndef MAX
-#define MAX(a,b) (((a)>(b))?(a):(b))
-#endif
-
-/* For convenience and (one hopes) clarity in boolean tests:
- */
-#ifndef TRUE
-#define TRUE 1
-#endif
-#ifndef FALSE
-#define FALSE 0
-#endif
-
-/* Somewhere, there is a universe in which Unix vendors comply
- * with the ANSI C standard. Unfortunately, it is not ours:
- */
-#ifndef EXIT_SUCCESS
-#define EXIT_SUCCESS 0
-#endif
-#ifndef EXIT_FAILURE
-#define EXIT_FAILURE 1
-#endif
-
-#include "sqfuncs.h" /* squid function declarations */
-#endif /* SQUIDH_INCLUDED */
diff --git a/algorithm-hmm/src/include/squidconf.h b/algorithm-hmm/src/include/squidconf.h
deleted file mode 100644
index 4155d62..0000000
--- a/algorithm-hmm/src/include/squidconf.h
+++ /dev/null
@@ -1,77 +0,0 @@
-/* squidconf.h. Generated automatically by configure. */
-/* @configure_input@ */
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SQUIDCONFH_INCLUDED
-#define SQUIDCONFH_INCLUDED
-
-/* squidconf.h
- * Captures #define's generated by the ./configure script;
- * this configuration information is #included at the start of
- * squid.h
- */
-
-/*****************************************************************
- * Sizes of integer types.
- * various things are set by ./configure; the code
- * uses WORDS_BIGENDIAN and USE_HOST_BYTESWAP_FUNCTIONS.
- *****************************************************************/
-/* #undef WORDS_BIGENDIAN */
-#define SIZEOF_UNSIGNED_SHORT 2
-#define SIZEOF_UNSIGNED_INT 4
-#define SIZEOF_UNSIGNED_LONG 4
-#define SIZEOF_UNSIGNED_LONG_LONG 8
-#define HAVE_NTOHS 1 /* if defined, system provides ntohs() */
-#define HAVE_NTOHL 1 /* if defined, system provides ntohl() */
-#define HAVE_HTONS 1 /* if defined, system provides htons() */
-#define HAVE_HTONL 1 /* if defined, system provides htonl() */
-#if defined HAVE_NTOHL && defined HAVE_NTOHS && defined HAVE_HTONS && defined HAVE_HTONL
-#define USE_HOST_BYTESWAP_FUNCTIONS 1
-#endif
-
-/*****************************************************************
- * Can we support arithmetic 64-bit file offsets?
- * four possible models checked for:
- * 1. ftello(), fseeko() with 64-bit off_t
- * 2. ftello64(), fseeko64() with 64-bit off64_t
- * 3. ftell64(), fseek64() with 64-bit integer
- * 4. fgetpos(), fsetpos() with an fpos_t that happens to be a
- * 64-bit integer, even though ANSI says we're not supposed to know
- * anything about fpos_t's internals.
- * Based on what ./configure tells us about these, we set
- * HAS_64BIT_FILE_OFFSETS or not.
- *****************************************************************/
-#define HAVE_FTELLO 1
-#define HAVE_FSEEKO 1
-#define HAVE_FTELLO64 1
-#define HAVE_FSEEKO64 1
-/* #undef HAVE_FTELL64 */
-/* #undef HAVE_FSEEK64 */
-/* #undef ARITHMETIC_FPOS_T */
-/* #undef HAVE_STAT64 */
-#define SIZEOF_FPOS_T 12
-#define SIZEOF_OFF_T 0
-#define SIZEOF_OFF64_T 0
-
-#if defined HAVE_FTELLO && defined HAVE_FSEEKO && SIZEOF_OFF_T == 8
-#define HAS_64BIT_FILE_OFFSETS 1
-#elif defined HAVE_FTELLO64 && defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8
-#define HAS_64BIT_FILE_OFFSETS 1
-#elif defined HAVE_FTELL64 && defined HAVE_FSEEK64
-#define HAS_64BIT_FILE_OFFSETS 1
-#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
-#define HAS_64BIT_FILE_OFFSETS 1
-#else
-/* #undef HAS_64BIT_FILE_OFFSETS */
-#endif
-
-
-#endif /* SQUIDCONFH_INCLUDED */
diff --git a/algorithm-hmm/src/include/ssi.h b/algorithm-hmm/src/include/ssi.h
deleted file mode 100644
index e976dfd..0000000
--- a/algorithm-hmm/src/include/ssi.h
+++ /dev/null
@@ -1,193 +0,0 @@
-/*****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************/
-
-#ifndef SSIH_INCLUDED
-#define SSIH_INCLUDED
-
-/* ssi.h
- * Database indexing (SSI format support)
- * CVS $Id: ssi.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- *
- * See: ssi_format.tex in Docs/
- */
-
-#include <stdio.h>
-#include "squid.h"
-
-/* Limits
- */
-#define SSI_MAXFILES 32767 /* 2^15-1 */
-#define SSI_MAXKEYS 2147483647L /* 2^31-1 */
-
-/* typedef: SSIOFFSET
- * Use the union to save space, since the two offset types are
- * mutually exclusive, controlled by "mode"
- */
-struct ssioffset_s {
- char mode; /* GSI_OFFSET_I32, for example */
- union {
- sqd_uint32 i32; /* an offset that fseek() can use */
- sqd_uint64 i64; /* an offset that e.g. fseeko64() can use */
- } off;
-};
-typedef struct ssioffset_s SSIOFFSET;
-#define SSI_OFFSET_I32 0
-#define SSI_OFFSET_I64 1
-
-/* Structure: SSIFILE
- * xref: SSI API documentation in ssi-format.tex
- */
-struct ssifile_s {
- FILE *fp; /* open SSI index file */
- sqd_uint32 flags; /* optional behavior flags */
- sqd_uint16 nfiles; /* number of files = 16 bit int */
- sqd_uint32 nprimary; /* number of primary keys */
- sqd_uint32 nsecondary; /* number of secondary keys */
- sqd_uint32 flen; /* length of filenames (inc '\0') */
- sqd_uint32 plen; /* length of primary keys (inc '\0') */
- sqd_uint32 slen; /* length of secondary keys (inc '\0') */
- sqd_uint32 frecsize; /* # bytes in a file record */
- sqd_uint32 precsize; /* # bytes in a primary key record */
- sqd_uint32 srecsize; /* # bytes in a secondary key record */
- SSIOFFSET foffset; /* disk offset, start of file records */
- SSIOFFSET poffset; /* disk offset, start of pri key recs */
- SSIOFFSET soffset; /* disk offset, start of sec key recs */
-
- char imode; /* mode for index file offsets, 32 v. 64 bit */
- char smode; /* mode for sequence file offsets, 32 v. 64 bit */
-
- /* File information:
- */
- char **filename; /* list of file names [0..nfiles-1] */
- sqd_uint32 *fileformat; /* file formats */
- sqd_uint32 *fileflags; /* optional per-file behavior flags */
- sqd_uint32 *bpl; /* bytes per line in file */
- sqd_uint32 *rpl; /* residues per line in file */
-};
-typedef struct ssifile_s SSIFILE;
-
-/* optional per-index behavior flags in SSIFILE structure's flags:
- */
-#define SSI_USE64 1<<0 /* seq offsets are 64-bit */
-#define SSI_USE64_INDEX 1<<1 /* index file offsets are 64-bit */
-
-/* optional per-file behavior flags in fileflags
- */
-#define SSI_FAST_SUBSEQ 1<<0 /* can do subseq lookup in this file */
-
-/* Structure: SSIINDEX
- *
- * Used when building up an index and writing it to disk
- */
-struct ssipkey_s { /* Primary key data: */
- char *key; /* key name */
- sqd_uint16 fnum; /* file number */
- SSIOFFSET r_off; /* record offset */
- SSIOFFSET d_off; /* data offset */
- sqd_uint32 len; /* sequence length */
- sqd_uint32 handle; /* handle on this key*/
-};
-struct ssiskey_s { /* Secondary key data: */
- char *key; /* secondary key name */
- char *pkey; /* primary key name */
-};
-struct ssiindex_s {
- int smode; /* sequence mode: SSI_OFFSET_I32 or _I64 */
- int imode; /* index mode: SSI_OFFSET_I32 or _I64 */
-
- char **filenames;
- sqd_uint32 *fileformat;
- sqd_uint32 *bpl;
- sqd_uint32 *rpl;
- sqd_uint32 flen; /* length of longest filename, inc '\0' */
- sqd_uint16 nfiles;
-
- struct ssipkey_s *pkeys;
- sqd_uint32 plen; /* length of longest pkey, including '\0' */
- sqd_uint32 nprimary;
- sqd_uint32 tot_primary;
-
- struct ssiskey_s *skeys;
- sqd_uint32 slen; /* length of longest skey, including '\0' */
- sqd_uint32 nsecondary;
- sqd_uint32 tot_secondary;
-
- /* The following stuff is for creating really big indexes, where
- * we have to write a tmp file to disk with multiple chunks, then
- * mergesort the chunks.
- */
- char *tmpbase; /* root name of tmp files: <tmpbase>.t1 and .t2 */
- FILE *t1; /* open tmp file for collecting chunks */
- fpos_t *chunkoffset; /* array of offsets to individual chunks; 0..nchunks-1 */
- int nchunks; /* total # of chunks in t1 */
- int max_chunk_size; /* maximum size of chunk to hold in memory at one time, in MB */
-};
-typedef struct ssiindex_s SSIINDEX;
-
-/* These control malloc and realloc chunk sizes in the index
- * construction code.
- */
-#define SSI_FILE_BLOCK 10
-#define SSI_KEY_BLOCK 100
-
-/* Error codes set by the API
- */
-#define SSI_ERR_OK 0
-#define SSI_ERR_NODATA 1 /* no data? an fread() failed */
-#define SSI_ERR_NO_SUCH_KEY 2 /* that key's not in the index */
-#define SSI_ERR_MALLOC 3
-#define SSI_ERR_NOFILE 4 /* no such file? an fopen() failed */
-#define SSI_ERR_BADMAGIC 5 /* magic number mismatch in GSIOpen() */
-#define SSI_ERR_BADFORMAT 6 /* didn't read what I expected to fread() */
-#define SSI_ERR_NO64BIT 7 /* needed 64-bit support and didn't have it */
-#define SSI_ERR_SEEK_FAILED 8 /* an fseek() (or similar) failed */
-#define SSI_ERR_TELL_FAILED 9 /* an ftell() (or similar) failed */
-#define SSI_ERR_NO_SUBSEQS 10 /* fast subseq is disallowed */
-#define SSI_ERR_RANGE 11 /* subseq requested is out of range */
-#define SSI_ERR_BADARG 12 /* something wrong with a function argument */
-
-#define SSI_ERR_TOOMANY_FILES 13 /* ran out of range for files in an index */
-#define SSI_ERR_TOOMANY_KEYS 14 /* ran out of range for keys in an index */
-#define SSI_ERR_FWRITE 15
-
-/* The SSI file reading API:
- */
-extern int SSIOpen(char *filename, SSIFILE **ret_sfp);
-extern int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
- SSIOFFSET *ret_offset);
-extern int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh,
- SSIOFFSET *ret_offset);
-extern int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
- int *ret_fh, SSIOFFSET *record_offset,
- SSIOFFSET *data_offset, int *ret_actual_start);
-extern int SSISetFilePosition(FILE *fp, SSIOFFSET *offset);
-extern int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format);
-extern void SSIClose(SSIFILE *sfp);
-
-/* The SSI index file writing API:
- */
-extern int SSIRecommendMode(char *file);
-extern SSIINDEX *SSICreateIndex(int mode);
-extern int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset);
-extern int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh);
-extern int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl);
-extern int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
- SSIOFFSET *r_off, SSIOFFSET *d_off,
- int L);
-extern int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey);
-extern int SSIWriteIndex(char *file, SSIINDEX *g);
-extern void SSIFreeIndex(SSIINDEX *g);
-
-/* The SSI misc. functions API:
- */
-extern char *SSIErrorString(int n);
-
-
-#endif /*SSIH_INCLUDED*/
diff --git a/algorithm-hmm/src/include/stopwatch.h b/algorithm-hmm/src/include/stopwatch.h
deleted file mode 100644
index 743e1a4..0000000
--- a/algorithm-hmm/src/include/stopwatch.h
+++ /dev/null
@@ -1,59 +0,0 @@
-/* stopwatch.h
- * SRE, Fri Nov 26 14:54:21 1999 [St. Louis] [HMMER]
- * SRE, Thu Aug 3 08:00:35 2000 [St. Louis] [moved to SQUID]
- * CVS $Id: stopwatch.h,v 1.1.1.1 2003/07/20 20:30:07 cspencer Exp $
- *
- * Header file for stopwatch.c module:
- * reporting of cpu/system/elapsed time used by a process.
- * See stopwatch.c comments for documentation of compile-time
- * configuration options and API.
- *
- *****************************************************************
- * HMMER - Biological sequence analysis with profile HMMs
- * Copyright (C) 1992-1999 Washington University School of Medicine
- * All Rights Reserved
- *
- * This source code is distributed under the terms of the
- * GNU General Public License. See the files COPYING and LICENSE
- * for details.
- *****************************************************************
- */
-#include <stdio.h>
-#include <time.h>
-#ifndef SRE_STRICT_ANSI
-#include <sys/times.h>
-#endif
-
-#ifndef STOPWATCH_H_INCLUDED
-#define STOPWATCH_H_INCLUDED
-
-struct stopwatch_s {
- time_t t0; /* Wall clock time, ANSI time() */
-#ifdef SRE_STRICT_ANSI
- clock_t cpu0; /* CPU time, ANSI clock() */
-#else
- struct tms cpu0; /* CPU/system time, POSIX times()*/
-#endif
-
- double elapsed; /* elapsed time, seconds */
- double user; /* CPU time, seconds */
- double sys; /* system time, seconds */
-};
-typedef struct stopwatch_s Stopwatch_t;
-
-extern void StopwatchStart(Stopwatch_t *w);
-extern void StopwatchStop(Stopwatch_t *w);
-extern void StopwatchInclude(Stopwatch_t *w1, Stopwatch_t *w2);
-extern Stopwatch_t *StopwatchCreate(void);
-extern void StopwatchZero(Stopwatch_t *w);
-extern void StopwatchCopy(Stopwatch_t *w1, Stopwatch_t *w2);
-extern void StopwatchFree(Stopwatch_t *w);
-extern void StopwatchDisplay(FILE *fp, char *s, Stopwatch_t *w);
-
-#ifdef HMMER_PVM
-extern void StopwatchPVMPack(Stopwatch_t *w);
-extern void StopwatchPVMUnpack(Stopwatch_t *w);
-#endif
-
-#endif /*STOPWATCH_H_INCLUDED*/
-
--
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