binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex

   1 \hypertarget{snoop_8h}{\section{snoop.\-h}
   2 \label{snoop_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snoop.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snoop.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00009 \hyperlink{structsnoopT}{snoopT} snoopfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
  11 00010                   \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
  12 00011                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
  13 00012                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
  14 00013                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
  15 00014                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
  16 00015                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
  17 00016                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
  18 00017                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  19 00018                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
  20 00019                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  21 00020                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  22 00021                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
  23 00022                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
  24 00023                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
  25 00024                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
  26 00025       \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
  27 00026
  28 00032 \hyperlink{structsnoopT}{snoopT} *snoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
  29 00033                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
  30 00034                       \textcolor{keywordtype}{int} delta,
  31 00035                       \textcolor{keywordtype}{int} w,
  32 00036                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
  33 00037                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
  34 00038                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
  35 00039                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
  36 00040                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
  37 00041                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
  38 00042                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
  39 00043                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
  40 00044                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
  41 00045                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  42 00046                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
  43 00047                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  44 00048                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  45 00049                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
  46 00050                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
  47 00051                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
  48 00052                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
  49 00053           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
  50 00054
  51 00061 \textcolor{keywordtype}{void} Lsnoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
  52 00062                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
  53 00063                     \textcolor{keywordtype}{int} delta,
  54 00064                     \textcolor{keywordtype}{int} w,
  55 00065                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
  56 00066                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
  57 00067                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
  58 00068                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
  59 00069                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
  60 00070                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
  61 00071                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
  62 00072                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
  63 00073                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
  64 00074                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  65 00075                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
  66 00076                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  67 00077                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  68 00078                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
  69 00079                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
  70 00080                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
  71 00081                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
  72 00082                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
  73 00083                     \textcolor{keyword}{const} \textcolor{keywordtype}{char}* name,
  74 00084         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
  75 00085
  76 00092 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
  77 00093                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
  78 00094                           \textcolor{keywordtype}{int} delta,
  79 00095                           \textcolor{keywordtype}{int} w,
  80 00096                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
  81 00097                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
  82 00098                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
  83 00099                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
  84 00100                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
  85 00101                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
  86 00102                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
  87 00103                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
  88 00104                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
  89 00105                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  90 00106                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
  91 00107                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  92 00108                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  93 00109                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
  94 00110                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
  95 00111                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
  96 00112                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
  97 00113                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
  98 00114                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
  99 00115         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
 100 00116
 101 00122 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
 102 00123                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
 103 00124                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
 104 00125                             \textcolor{keywordtype}{int} delta,
 105 00126                             \textcolor{keywordtype}{int} w,
 106 00127                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 107 00128                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 108 00129                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 109 00130                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 110 00131                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 111 00132                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
 112 00133                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
 113 00134                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 114 00135                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
 115 00136                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 116 00137                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 117 00138                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 118 00139                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 119 00140                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 120 00141                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 121 00142                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 122 00143                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
 123 00144                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
 124 00145                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
 125 00146           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
 126 00147
 127 00148
 128 00154 \textcolor{keywordtype}{void} snoop\_subopt\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
 129 00155                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
 130 00156                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
 131 00157                       \textcolor{keywordtype}{int} delta,
 132 00158                       \textcolor{keywordtype}{int} w,
 133 00159                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 134 00160                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 135 00161                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 136 00162                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 137 00163                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 138 00164                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
 139 00165                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
 140 00166                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 141 00167                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
 142 00168                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 143 00169                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 144 00170                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 145 00171                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 146 00172                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 147 00173                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 148 00174                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 149 00175                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
 150 00176                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
 151 00177                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
 152 00178           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
 153 00179
 154 00184 \hyperlink{structsnoopT}{snoopT} *alisnoop\_subopt(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
 155 00185                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2,
 156 00186                         \textcolor{keywordtype}{int} delta,
 157 00187                         \textcolor{keywordtype}{int} w,
 158 00188                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 159 00189                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 160 00190                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 161 00191                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 162 00192                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 163 00193                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
 164 00194                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
 165 00195                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 166 00196                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
 167 00197                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 168 00198                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 169 00199                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 170 00200                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 171 00201                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 172 00202                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 173 00203                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 174 00204                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2);
 175 00205
 176 00212 \hyperlink{structsnoopT}{snoopT} *aliLsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
 177 00213                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2,
 178 00214                                 \textcolor{keywordtype}{int} delta,
 179 00215                                 \textcolor{keywordtype}{int} w,
 180 00216                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 181 00217                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 182 00218                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 183 00219                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 184 00220                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 185 00221                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
 186 00222                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
 187 00223                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 188 00224                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
 189 00225                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 190 00226                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 191 00227                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 192 00228                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 193 00229                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 194 00230                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 195 00231                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 196 00232                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
 197 00233                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length);
 198 00239 \hyperlink{structsnoopT}{snoopT} alisnoopfold(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
 199 00240                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2,
 200 00241                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 201 00242                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 202 00243                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 203 00244                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 204 00245                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 205 00246                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 206 00247                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 207 00248                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 208 00249                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 209 00250                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 210 00251                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 211 00252                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 212 00253                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 213 00254                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2);
 214 00259 \hyperlink{structsnoopT}{snoopT} snoopfold\_XS(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
 215 00260                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
 216 00261                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
 217 00262                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} pos,
 218 00263                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_pos\_j,
 219 00264                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
 220 00265                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
 221 00266                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
 222 00267                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
 223 00268                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
 224 00269                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
 225 00270                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
 226 00271                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
 227 00272                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
 228 00273                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
 229 00274                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
 230 00275                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
 231 00276                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
 232 00277                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
 233 00278         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
 234 00279
 235 00280
 236 00281
 237 00282
 238 00283 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} snoop\_subopt\_sorted;
 239 00284 \textcolor{preprocessor}{#endif}
 240 \end{DoxyCode}