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# H/snoop.h

    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