\hypertarget{snoop_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snoop.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00009 \hyperlink{structsnoopT}{snoopT} snoopfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00010                   \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, 
00011                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00012                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00013                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00014                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00015                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00016                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00017                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00018                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00019                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00020                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00021                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00022                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00023                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00024                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00025       \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00026 
00032 \hyperlink{structsnoopT}{snoopT} *snoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00033                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00034                       \textcolor{keywordtype}{int} delta,
00035                       \textcolor{keywordtype}{int} w,
00036                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00037                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00038                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00039                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00040                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00041                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00042                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00043                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00044                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00045                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00046                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00047                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00048                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00049                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00050                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00051                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00052                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00053           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00054 
00061 \textcolor{keywordtype}{void} Lsnoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00062                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00063                     \textcolor{keywordtype}{int} delta,
00064                     \textcolor{keywordtype}{int} w, 
00065                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00066                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00067                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00068                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00069                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00070                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00071                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00072                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00073                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00074                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00075                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00076                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00077                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00078                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00079                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00080                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00081                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00082                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00083                     \textcolor{keyword}{const} \textcolor{keywordtype}{char}* name,
00084         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00085 
00092 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00093                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00094                           \textcolor{keywordtype}{int} delta,
00095                           \textcolor{keywordtype}{int} w, 
00096                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00097                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00098                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00099                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00100                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00101                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00102                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00103                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00104                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00105                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00106                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00107                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00108                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00109                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00110                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00111                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00112                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00113                           \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00114                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
00115         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00116 
00122 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00123                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00124                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00125                             \textcolor{keywordtype}{int} delta,
00126                             \textcolor{keywordtype}{int} w, 
00127                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00128                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00129                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00130                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00131                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00132                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00133                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00134                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00135                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00136                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00137                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00138                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00139                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00140                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00141                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00142                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00143                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00144                             \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00145                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
00146           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00147 
00148 
00154 \textcolor{keywordtype}{void} snoop\_subopt\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00155                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00156                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00157                       \textcolor{keywordtype}{int} delta,
00158                       \textcolor{keywordtype}{int} w, 
00159                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00160                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00161                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00162                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00163                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00164                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00165                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00166                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00167                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00168                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00169                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00170                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00171                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00172                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00173                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00174                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00175                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00176                       \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length,
00177                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name,
00178           \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00179 
00184 \hyperlink{structsnoopT}{snoopT} *alisnoop\_subopt(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
00185                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2,
00186                         \textcolor{keywordtype}{int} delta,
00187                         \textcolor{keywordtype}{int} w,
00188                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00189                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00190                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00191                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00192                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00193                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00194                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00195                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00196                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00197                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00198                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00199                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00200                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00201                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00202                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00203                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00204                         \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2);
00205 
00212 \hyperlink{structsnoopT}{snoopT} *aliLsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
00213                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2,
00214                                 \textcolor{keywordtype}{int} delta,
00215                                 \textcolor{keywordtype}{int} w, 
00216                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00217                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00218                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00219                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00220                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00221                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE,
00222                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE,
00223                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00224                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance,
00225                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00226                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00227                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00228                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00229                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00230                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00231                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00232                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00233                                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length);
00239 \hyperlink{structsnoopT}{snoopT} alisnoopfold(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1,
00240                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2, 
00241                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00242                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
00243                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00244                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00245                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00246                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00247                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00248                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00249                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00250                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00251                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00252                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00253                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00254                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2);
00259 \hyperlink{structsnoopT}{snoopT} snoopfold\_XS(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
00260                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2,
00261                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1,
00262                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} pos,
00263                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_pos\_j,
00264                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty,
00265                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00266                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE,
00267                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE,
00268                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE,
00269                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD,
00270                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00271                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem,
00272                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00273                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00274                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1,
00275                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1,
00276                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1,
00277                     \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2,
00278         \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy);
00279 
00280 
00281 
00282 
00283 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} snoop\_subopt\_sorted;
00284 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
