--- /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 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.
+ *
+ * CVS $Id: sqfuncs.h,v 1.28 2002/10/09 14:26:09 eddy 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 *FileSameDirectory(char *full, char *file);
+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);
+extern int QRNAShuffle(char *xs, char *ys, char *x, char *y);
+
+/*
+ * from sqerror.c
+ */
+extern void Die(char *format, ...);
+#ifdef CLUSTALO
+extern void Warning(char *format, ...);
+#else
+extern void Warn(char *format, ...);
+#endif
+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, int is_aseq);
+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 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 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 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 */
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