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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/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       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