Mercurial > repos > clustalomega > clustalomega
annotate clustalomega/clustal-omega-0.2.0/src/squid/sqfuncs.h @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 /***************************************************************** |
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2 * SQUID - a library of functions for biological sequence analysis |
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3 * Copyright (C) 1992-2002 Washington University School of Medicine |
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4 * |
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5 * This source code is freely distributed under the terms of the |
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6 * GNU General Public License. See the files COPYRIGHT and LICENSE |
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7 * for details. |
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8 *****************************************************************/ |
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9 |
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10 #ifndef SQFUNCSH_INCLUDED |
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11 #define SQFUNCSH_INCLUDED |
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12 /* sqfuncs.h |
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13 * |
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14 * Prototypes for squid library functions; |
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15 * also makes a good reference list for what the package contains. |
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16 * |
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17 * Warning: squid is a slowly evolving beast. Some functions are |
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18 * obsolete. Some functions are probably just wrong, dating to |
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19 * a primordial era before I knew anything about what I was doing. |
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20 * Some functions are both obsolete and wrong but still necessary |
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21 * to get legacy code to compile. |
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22 * |
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23 * CVS $Id: sqfuncs.h,v 1.28 2002/10/09 14:26:09 eddy Exp) |
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24 */ |
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25 |
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26 /* |
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27 * from aligneval.c |
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28 */ |
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29 extern float ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2); |
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30 extern float CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2); |
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31 extern float CompareMultAlignments(char **kseqs, char **tseqs, int N); |
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32 extern float CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N); |
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33 extern float PairwiseIdentity(char *s1, char *s2); |
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34 extern float AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample); |
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35 extern char *MajorityRuleConsensus(char **aseq, int nseq, int alen); |
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36 |
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37 /* |
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38 * from alignio.c |
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39 */ |
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40 extern void AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo); |
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41 extern void InitAinfo(AINFO *ainfo); |
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42 extern void FreeAlignment(char **aseqs, AINFO *ainfo); |
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43 extern void SAMizeAlignment(char **aseq, int nseq, int alen); |
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44 extern void SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap); |
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45 extern int MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s); |
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46 extern int MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s); |
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47 extern int DealignedLength(char *aseq); |
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48 extern int WritePairwiseAlignment(FILE *ofp, char *aseq1, char *name1, int spos1, |
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49 char *aseq2, char *name2, int spos2, |
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50 int **pam, int indent); |
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51 extern int MingapAlignment(char **aseqs, AINFO *ainfo); |
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52 extern int RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex, |
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53 char ***ret_aseqs, AINFO *ainfo); |
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54 extern void AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym); |
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55 |
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56 /* from cluster.c |
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57 */ |
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58 extern int Cluster(float **mx, int N, enum clust_strategy mode, struct phylo_s **ret_tree); |
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59 extern struct phylo_s *AllocPhylo(int N); |
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60 extern void FreePhylo(struct phylo_s *tree, int N); |
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61 extern void MakeDiffMx(char **aseqs, int num, float ***ret_dmx); |
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62 extern void MakeIdentityMx(char **aseqs, int num, float ***ret_imx); |
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63 extern void PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N); |
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64 extern void PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N); |
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65 |
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66 /* |
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67 * from dayhoff.c |
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68 */ |
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69 extern int ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale); |
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70 extern void ScalePAM(int **pam, int scale); |
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71 |
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72 |
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73 /* from file.c |
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74 */ |
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75 extern char *FileDirname(char *filename); |
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76 extern char *FileTail(char *file, int noextension); |
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77 extern char *FileSameDirectory(char *full, char *file); |
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78 extern char *FileConcat(char *dir, char *file); |
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79 extern char *FileAddSuffix(char *filename, char *sfx); |
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80 extern FILE *EnvFileOpen(char *fname, char *env, char **ret_dir); |
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81 extern int FileExists(char *filename); |
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82 |
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83 |
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84 /* from getopt.c |
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85 */ |
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86 extern int Getopt(int argc, char **argv, |
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87 struct opt_s *opt, int nopts, char *usage, |
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88 int *ret_optind, char **ret_optname, char **ret_optarg); |
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89 |
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90 |
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91 /* from hsregex.c |
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92 * Henry Spencer's regex() code |
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93 */ |
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94 extern int Strparse(char *rexp, char *s, int ntok); |
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95 extern void SqdClean(void); |
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96 extern sqd_regexp *sqd_regcomp(const char *re); |
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97 extern int sqd_regexec(sqd_regexp *rp, const char *s); |
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98 extern void sqd_regsub(const sqd_regexp *rp, const char *src, char *dst); |
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99 extern void sqd_regerror(char *message); |
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100 |
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101 /* from interleaved.c |
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102 */ |
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103 extern int IsInterleavedFormat(int format); |
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104 extern int ReadInterleaved(char *seqfile, |
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105 int (*skip_header)(FILE *), |
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106 int (*parse_header)(FILE *, AINFO *), |
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107 int (*is_dataline)(char *, char *), |
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108 char ***ret_aseqs, AINFO *ainfo); |
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109 extern int ReadAlignment(char *seqfile, int format, char ***ret_aseqs, AINFO *ainfo); |
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110 |
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111 |
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112 /* from revcomp.c |
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113 */ |
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114 extern char *revcomp(char *comp, char *seq); |
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115 |
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116 /* |
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117 * from selex.c |
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118 */ |
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119 extern int DealignAseqs(char **aseqs, int num, char ***ret_rseqs); |
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120 extern int IsSELEXFormat(char *filename); |
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121 extern int TruncateNames(char **names, int N); /* OBSOLETE? */ |
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122 |
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123 /* |
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124 * from seqencode.c |
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125 */ |
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126 extern int seqcmp(char *s1, char *s2, int allow); |
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127 extern int seqncmp(char *s1, char *s2, int n, int allow); |
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128 extern int seqencode(char *codeseq,char *str); |
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129 extern int coded_revcomp(char *comp, char *seq); |
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130 extern int seqdecode(char *str, char *codeseq); |
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131 extern int seqndecode(char *str, char *codeseq, int n); |
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132 |
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133 /* |
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134 * from shuffle.c |
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135 */ |
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136 extern int StrShuffle(char *s1, char *s2); |
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137 extern int StrDPShuffle(char *s1, char *s2); |
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138 extern int StrMarkov0(char *s1, char *s2); |
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139 extern int StrMarkov1(char *s1, char *s2); |
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140 extern int StrReverse(char *s1, char *s2); |
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141 extern int StrRegionalShuffle(char *s1, char *s2, int w); |
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142 extern int AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen); |
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143 extern int AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen); |
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144 extern int QRNAShuffle(char *xs, char *ys, char *x, char *y); |
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145 |
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146 /* |
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147 * from sqerror.c |
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148 */ |
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149 extern void Die(char *format, ...); |
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150 #ifdef CLUSTALO |
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151 extern void Warning(char *format, ...); |
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152 #else |
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153 extern void Warn(char *format, ...); |
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154 #endif |
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155 extern void Panic(char *file, int line); |
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156 |
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157 |
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158 /* |
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159 * from sqio.c |
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160 */ |
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161 extern void FreeSequence(char *seq, SQINFO *sqinfo); |
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162 extern int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag); |
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163 extern void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2); |
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164 extern void ToDNA(char *seq); |
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165 extern void ToRNA(char *seq); |
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166 extern void ToIUPAC(char *seq, int is_aseq); |
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167 extern int ReadMultipleRseqs(char *seqfile, int fformat, char ***ret_rseqs, |
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168 SQINFO **ret_sqinfo, int *ret_num); |
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169 extern SQFILE *SeqfileOpen(char *filename, int format, char *env); |
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170 extern SQFILE *SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode); |
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171 extern int SeqfileFormat(FILE *fp); |
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172 extern void SeqfilePosition(SQFILE *sfp, SSIOFFSET *offset); |
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173 extern void SeqfileRewind(SQFILE *sfp); |
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174 extern void SeqfileClose(SQFILE *sfp); |
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175 |
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176 extern int ReadSeq(SQFILE *fp, int format, char **ret_seq, SQINFO *sqinfo); |
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177 extern int GCGBinaryToSequence(char *seq, int len); |
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178 extern int GCGchecksum(char *seq, int seqlen); |
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179 extern int GCGMultchecksum(char **seqs, int nseq); |
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180 extern void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc); |
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181 extern int WriteSeq(FILE *outf, int outfmt, char *seq, SQINFO *sqinfo); |
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182 extern int Seqtype(char *seq); |
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183 extern int GuessAlignmentSeqtype(char **aseq, int nseq); |
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184 extern int String2SeqfileFormat(char *s); |
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185 extern char *SeqfileFormat2String(int code); |
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186 extern SQINFO *MSAToSqinfo(MSA *msa); |
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187 |
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188 /* from squidcore.c |
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189 */ |
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190 extern void Banner(FILE *fp, char *banner); |
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191 |
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192 |
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193 /* from sre_ctype.c |
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194 */ |
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195 extern int sre_tolower(int c); |
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196 extern int sre_toupper(int c); |
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197 |
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198 /* from sre_math.c |
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199 */ |
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200 extern int Linefit(float *x, float *y, int N, |
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201 float *ret_a, float *ret_b, float *ret_r); |
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202 extern void WeightedLinefit(float *x, float *y, float *var, int N, |
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203 float *ret_m, float *ret_b); |
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204 extern double Gammln(double xx); |
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205 extern float **FMX2Alloc(int rows, int cols); |
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206 extern void FMX2Free(float **mx); |
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207 extern double **DMX2Alloc(int rows, int cols); |
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208 extern void DMX2Free(double **mx); |
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209 extern void FMX2Multiply(float **A, float **B, float **C, int m, int p, int n); |
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210 extern double IncompleteGamma(double a, double x); |
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211 |
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212 /* from sre_string.c |
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213 */ |
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214 #ifdef NOSTR |
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215 extern char *strstr(char *s, char *subs); |
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216 #endif |
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217 extern char *Strdup(char *s); |
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218 extern void StringChop(char *s); |
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219 extern int Strinsert(char *s1, char c, int pos); |
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220 extern int Strdelete(char *s1, int pos); |
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221 extern void s2lower(char *s); |
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222 extern void s2upper(char *s); |
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223 extern void *sre_malloc(char *file, int line, size_t size); |
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224 extern void *sre_realloc(char *file, int line, void *p, size_t size); |
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225 extern void Free2DArray(void **p, int dim1); |
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226 extern void Free3DArray(void ***p, int dim1, int dim2); |
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227 extern char *RandomSequence(char *alphabet, float *p, int n, int len); |
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228 extern char *sre_fgets(char **buf, int *n, FILE *fp); |
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229 extern int sre_strcat(char **dest, int ldest, char *src, int lsrc); |
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230 extern char *sre_strtok(char **s, char *delim, int *len); |
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231 extern char *sre_strdup(char *s, int n); |
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232 extern char *sre_strncat(char *s1, char *s2, int n); |
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233 extern int IsBlankline(char *s); |
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234 |
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235 /* from stack.c |
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236 */ |
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237 extern struct intstack_s *InitIntStack(void); |
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238 extern void PushIntStack(struct intstack_s *stack, int data); |
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239 extern int PopIntStack(struct intstack_s *stack, int *ret_data); |
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240 extern void ReverseIntStack(struct intstack_s *stack); |
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241 extern int FreeIntStack( struct intstack_s *stack ); |
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242 |
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243 /* |
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244 * from translate.c |
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245 */ |
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246 extern char *Translate(char *seq, char **code); |
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247 |
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248 /* |
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249 * from types.c |
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250 */ |
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251 extern int IsInt(char *s); |
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252 extern int IsReal(char *s); |
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253 extern void Byteswap(char *swap, int nbytes); |
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254 #ifndef USE_HOST_BYTESWAP_FUNCTIONS |
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255 extern sqd_uint16 sre_ntoh16(sqd_uint16 netshort); |
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256 extern sqd_uint32 sre_ntoh32(sqd_uint32 netlong); |
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257 extern sqd_uint16 sre_hton16(sqd_uint16 hostshort); |
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258 extern sqd_uint32 sre_hton32(sqd_uint32 hostlong); |
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259 #endif /*!USE_HOST_BYTESWAP_FUNCTIONS*/ |
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260 extern sqd_uint64 sre_ntoh64(sqd_uint64 net_int64); |
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261 extern sqd_uint64 sre_hton64(sqd_uint64 host_int64); |
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262 |
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263 /* |
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264 * from weight.c |
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265 */ |
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266 extern void GSCWeights(char **aseq, int nseq, int alen, float *wgt); |
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267 extern void VoronoiWeights(char **aseq, int nseq, int alen, float *wgt); |
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268 extern void BlosumWeights(char **aseq, int nseq, int alen, float blosumlevel, float *wgt); |
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269 extern void PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt); |
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270 extern void FilterAlignment(MSA *msa, float cutoff, MSA **ret_new); |
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271 extern void SampleAlignment(MSA *msa, int sample, MSA **ret_new); |
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272 extern void SingleLinkCluster(char **aseq, int nseq, int alen, float maxid, |
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273 int **ret_c, int *ret_nc); |
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274 #endif /* SQFUNCSH_INCLUDED */ |