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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / snoop_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex
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+\hypertarget{snoop_8h}{\section{snoop.\-h}
+\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}}
+}
+
+\begin{DoxyCode}
+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{DoxyCode}