00001 #ifndef __VIENNA_RNA_PACKAGE_SNOOP_H__
00002 #define __VIENNA_RNA_PACKAGE_SNOOP_H__
00003
00004 #include "data_structures.h"
00009 snoopT snoopfold( const char *s1,
00010 const char *s2,
00011 const int penalty,
00012 const int threshloop,
00013 const int threshLE,
00014 const int threshRE,
00015 const int threshDE,
00016 const int threshD,
00017 const int half_stem,
00018 const int max_half_stem,
00019 const int min_s2,
00020 const int max_s2,
00021 const int min_s1,
00022 const int max_s1,
00023 const int min_d1,
00024 const int min_d2);
00025
00031 snoopT *snoop_subopt( const char *s1,
00032 const char *s2,
00033 int delta,
00034 int w,
00035 const int penalty,
00036 const int threshloop,
00037 const int threshLE,
00038 const int threshRE,
00039 const int threshDE,
00040 const int threshTE,
00041 const int threshSE,
00042 const int threshD,
00043 const int distance,
00044 const int half_stem,
00045 const int max_half_stem,
00046 const int min_s2,
00047 const int max_s2,
00048 const int min_s1,
00049 const int max_s1,
00050 const int min_d1,
00051 const int min_d2);
00052
00059 void Lsnoop_subopt( const char *s1,
00060 const char *s2,
00061 int delta,
00062 int w,
00063 const int penalty,
00064 const int threshloop,
00065 const int threshLE,
00066 const int threshRE,
00067 const int threshDE,
00068 const int threshTE,
00069 const int threshSE,
00070 const int threshD,
00071 const int distance,
00072 const int half_stem,
00073 const int max_half_stem,
00074 const int min_s2,
00075 const int max_s2,
00076 const int min_s1,
00077 const int max_s1,
00078 const int min_d1,
00079 const int min_d2,
00080 const int alignment_length,
00081 const char* name);
00082
00089 void Lsnoop_subopt_list ( const char *s1,
00090 const char *s2,
00091 int delta,
00092 int w,
00093 const int penalty,
00094 const int threshloop,
00095 const int threshLE,
00096 const int threshRE,
00097 const int threshDE,
00098 const int threshTE,
00099 const int threshSE,
00100 const int threshD,
00101 const int distance,
00102 const int half_stem,
00103 const int max_half_stem,
00104 const int min_s2,
00105 const int max_s2,
00106 const int min_s1,
00107 const int max_s1,
00108 const int min_d1,
00109 const int min_d2,
00110 const int alignment_length,
00111 const char *name);
00112
00118 void Lsnoop_subopt_list_XS (const char *s1,
00119 const char *s2,
00120 const int **access_s1,
00121 int delta,
00122 int w,
00123 const int penalty,
00124 const int threshloop,
00125 const int threshLE,
00126 const int threshRE,
00127 const int threshDE,
00128 const int threshTE,
00129 const int threshSE,
00130 const int threshD,
00131 const int distance,
00132 const int half_stem,
00133 const int max_half_stem,
00134 const int min_s2,
00135 const int max_s2,
00136 const int min_s1,
00137 const int max_s1,
00138 const int min_d1,
00139 const int min_d2,
00140 const int alignment_length,
00141 const char *name);
00142
00143
00149 void snoop_subopt_XS (const char *s1,
00150 const char *s2,
00151 const int **access_s1,
00152 int delta,
00153 int w,
00154 const int penalty,
00155 const int threshloop,
00156 const int threshLE,
00157 const int threshRE,
00158 const int threshDE,
00159 const int threshTE,
00160 const int threshSE,
00161 const int threshD,
00162 const int distance,
00163 const int half_stem,
00164 const int max_half_stem,
00165 const int min_s2,
00166 const int max_s2,
00167 const int min_s1,
00168 const int max_s1,
00169 const int min_d1,
00170 const int min_d2,
00171 const int alignment_length,
00172 const char *name);
00173
00178 snoopT *alisnoop_subopt(const char **s1,
00179 const char **s2,
00180 int delta,
00181 int w,
00182 const int penalty,
00183 const int threshloop,
00184 const int threshLE,
00185 const int threshRE,
00186 const int threshDE,
00187 const int threshTE,
00188 const int threshSE,
00189 const int threshD,
00190 const int distance,
00191 const int half_stem,
00192 const int max_half_stem,
00193 const int min_s2,
00194 const int max_s2,
00195 const int min_s1,
00196 const int max_s1,
00197 const int min_d1,
00198 const int min_d2);
00199
00206 snoopT *aliLsnoop_subopt_list ( const char **s1,
00207 const char **s2,
00208 int delta,
00209 int w,
00210 const int penalty,
00211 const int threshloop,
00212 const int threshLE,
00213 const int threshRE,
00214 const int threshDE,
00215 const int threshTE,
00216 const int threshSE,
00217 const int threshD,
00218 const int distance,
00219 const int half_stem,
00220 const int max_half_stem,
00221 const int min_s2,
00222 const int max_s2,
00223 const int min_s1,
00224 const int max_s1,
00225 const int min_d1,
00226 const int min_d2,
00227 const int alignment_length);
00233 snoopT alisnoopfold(const char **s1,
00234 const char **s2,
00235 const int penalty,
00236 const int threshloop,
00237 const int threshLE,
00238 const int threshRE,
00239 const int threshDE,
00240 const int threshD,
00241 const int half_stem,
00242 const int max_half_stem,
00243 const int min_s2,
00244 const int max_s2,
00245 const int min_s1,
00246 const int max_s1,
00247 const int min_d1,
00248 const int min_d2);
00253 snoopT snoopfold_XS(const char *s1,
00254 const char *s2,
00255 const int **access_s1,
00256 const int pos,
00257 const int max_pos_j,
00258 const int penalty,
00259 const int threshloop,
00260 const int threshLE,
00261 const int threshRE,
00262 const int threshDE,
00263 const int threshD,
00264 const int half_stem,
00265 const int max_half_stem,
00266 const int min_s2,
00267 const int max_s2,
00268 const int min_s1,
00269 const int max_s1,
00270 const int min_d1,
00271 const int min_d2);
00272
00273
00274
00275
00276 extern int snoop_subopt_sorted;
00277 #endif
