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 const int fullStemEnergy);
00026
00032 snoopT *snoop_subopt( const char *s1,
00033 const char *s2,
00034 int delta,
00035 int w,
00036 const int penalty,
00037 const int threshloop,
00038 const int threshLE,
00039 const int threshRE,
00040 const int threshDE,
00041 const int threshTE,
00042 const int threshSE,
00043 const int threshD,
00044 const int distance,
00045 const int half_stem,
00046 const int max_half_stem,
00047 const int min_s2,
00048 const int max_s2,
00049 const int min_s1,
00050 const int max_s1,
00051 const int min_d1,
00052 const int min_d2,
00053 const int fullStemEnergy);
00054
00061 void Lsnoop_subopt( const char *s1,
00062 const char *s2,
00063 int delta,
00064 int w,
00065 const int penalty,
00066 const int threshloop,
00067 const int threshLE,
00068 const int threshRE,
00069 const int threshDE,
00070 const int threshTE,
00071 const int threshSE,
00072 const int threshD,
00073 const int distance,
00074 const int half_stem,
00075 const int max_half_stem,
00076 const int min_s2,
00077 const int max_s2,
00078 const int min_s1,
00079 const int max_s1,
00080 const int min_d1,
00081 const int min_d2,
00082 const int alignment_length,
00083 const char* name,
00084 const int fullStemEnergy);
00085
00092 void Lsnoop_subopt_list ( const char *s1,
00093 const char *s2,
00094 int delta,
00095 int w,
00096 const int penalty,
00097 const int threshloop,
00098 const int threshLE,
00099 const int threshRE,
00100 const int threshDE,
00101 const int threshTE,
00102 const int threshSE,
00103 const int threshD,
00104 const int distance,
00105 const int half_stem,
00106 const int max_half_stem,
00107 const int min_s2,
00108 const int max_s2,
00109 const int min_s1,
00110 const int max_s1,
00111 const int min_d1,
00112 const int min_d2,
00113 const int alignment_length,
00114 const char *name,
00115 const int fullStemEnergy);
00116
00122 void Lsnoop_subopt_list_XS (const char *s1,
00123 const char *s2,
00124 const int **access_s1,
00125 int delta,
00126 int w,
00127 const int penalty,
00128 const int threshloop,
00129 const int threshLE,
00130 const int threshRE,
00131 const int threshDE,
00132 const int threshTE,
00133 const int threshSE,
00134 const int threshD,
00135 const int distance,
00136 const int half_stem,
00137 const int max_half_stem,
00138 const int min_s2,
00139 const int max_s2,
00140 const int min_s1,
00141 const int max_s1,
00142 const int min_d1,
00143 const int min_d2,
00144 const int alignment_length,
00145 const char *name,
00146 const int fullStemEnergy);
00147
00148
00154 void snoop_subopt_XS (const char *s1,
00155 const char *s2,
00156 const int **access_s1,
00157 int delta,
00158 int w,
00159 const int penalty,
00160 const int threshloop,
00161 const int threshLE,
00162 const int threshRE,
00163 const int threshDE,
00164 const int threshTE,
00165 const int threshSE,
00166 const int threshD,
00167 const int distance,
00168 const int half_stem,
00169 const int max_half_stem,
00170 const int min_s2,
00171 const int max_s2,
00172 const int min_s1,
00173 const int max_s1,
00174 const int min_d1,
00175 const int min_d2,
00176 const int alignment_length,
00177 const char *name,
00178 const int fullStemEnergy);
00179
00184 snoopT *alisnoop_subopt(const char **s1,
00185 const char **s2,
00186 int delta,
00187 int w,
00188 const int penalty,
00189 const int threshloop,
00190 const int threshLE,
00191 const int threshRE,
00192 const int threshDE,
00193 const int threshTE,
00194 const int threshSE,
00195 const int threshD,
00196 const int distance,
00197 const int half_stem,
00198 const int max_half_stem,
00199 const int min_s2,
00200 const int max_s2,
00201 const int min_s1,
00202 const int max_s1,
00203 const int min_d1,
00204 const int min_d2);
00205
00212 snoopT *aliLsnoop_subopt_list ( const char **s1,
00213 const char **s2,
00214 int delta,
00215 int w,
00216 const int penalty,
00217 const int threshloop,
00218 const int threshLE,
00219 const int threshRE,
00220 const int threshDE,
00221 const int threshTE,
00222 const int threshSE,
00223 const int threshD,
00224 const int distance,
00225 const int half_stem,
00226 const int max_half_stem,
00227 const int min_s2,
00228 const int max_s2,
00229 const int min_s1,
00230 const int max_s1,
00231 const int min_d1,
00232 const int min_d2,
00233 const int alignment_length);
00239 snoopT alisnoopfold(const char **s1,
00240 const char **s2,
00241 const int penalty,
00242 const int threshloop,
00243 const int threshLE,
00244 const int threshRE,
00245 const int threshDE,
00246 const int threshD,
00247 const int half_stem,
00248 const int max_half_stem,
00249 const int min_s2,
00250 const int max_s2,
00251 const int min_s1,
00252 const int max_s1,
00253 const int min_d1,
00254 const int min_d2);
00259 snoopT snoopfold_XS(const char *s1,
00260 const char *s2,
00261 const int **access_s1,
00262 const int pos,
00263 const int max_pos_j,
00264 const int penalty,
00265 const int threshloop,
00266 const int threshLE,
00267 const int threshRE,
00268 const int threshDE,
00269 const int threshD,
00270 const int half_stem,
00271 const int max_half_stem,
00272 const int min_s2,
00273 const int max_s2,
00274 const int min_s1,
00275 const int max_s1,
00276 const int min_d1,
00277 const int min_d2,
00278 const int fullStemEnergy);
00279
00280
00281
00282
00283 extern int snoop_subopt_sorted;
00284 #endif
