Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / move__set_8h_source.tex

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+\hypertarget{move__set_8h}{\section{move\-\_\-set.\-h}
+\label{move__set_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/move\-\_\-set.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/move\-\_\-set.\-h}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_MOVE\_SET\_H}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_MOVE\_SET\_H}
+00003 \textcolor{preprocessor}{}
+00004 \textcolor{comment}{/* used data structure*/}
+\hypertarget{move__set_8h_source_l00005}{}\hyperlink{structstruct__en}{00005} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\_struct\_en\{
+00006   \textcolor{keywordtype}{int} energy;        \textcolor{comment}{/* energy in 10kcal/mol*/}
+00007   \textcolor{keywordtype}{short} *structure;  \textcolor{comment}{/* structure in energy\_of\_move format*/}
+00008 \} \hyperlink{structstruct__en}{struct\_en};
+00009 
+00010 \textcolor{comment}{/* prints structure*/}
+00011 \textcolor{keywordtype}{void} print\_stren(FILE *out, \hyperlink{structstruct__en}{struct\_en} *str);
+00012 \textcolor{keywordtype}{void} print\_str(FILE *out, \textcolor{keywordtype}{short} *str);
+00013 
+00014 \textcolor{comment}{/* copying functions*/}
+00015 \textcolor{keywordtype}{void} copy\_arr(\textcolor{keywordtype}{short} *dest, \textcolor{keywordtype}{short} *src); \textcolor{comment}{/*just copy*/}
+00016 \textcolor{keywordtype}{short} *allocopy(\textcolor{keywordtype}{short} *src);            \textcolor{comment}{/*copy and make space*/}
+00017 
+00018 \textcolor{comment}{/* walking methods (verbose\_lvl 0-2, shifts = use shift moves? noLP = no lone pairs? (not compatible with
+       shifts))}
+00019 \textcolor{comment}{    input:    seq - sequence}
+00020 \textcolor{comment}{              ptable - structure encoded with make\_pair\_table() from pair\_mat.h}
+00021 \textcolor{comment}{              s, s1 - sequence encoded with encode\_sequence from pair\_mat.h}
+00022 \textcolor{comment}{    methods:  deepest - lowest energy structure is used}
+00023 \textcolor{comment}{              first - first found lower energy structure is used}
+00024 \textcolor{comment}{              rand - random lower energy structure is used}
+00025 \textcolor{comment}{    returns local minima structure in ptable and its energy in 10kcal/mol as output */}
+00026 
+00027 \textcolor{keywordtype}{int} move\_deepest( \textcolor{keywordtype}{char} *seq,
+00028                   \textcolor{keywordtype}{short} *ptable,
+00029                   \textcolor{keywordtype}{short} *s,
+00030                   \textcolor{keywordtype}{short} *s1,
+00031                   \textcolor{keywordtype}{int} verbosity\_level,
+00032                   \textcolor{keywordtype}{int} shifts,
+00033                   \textcolor{keywordtype}{int} noLP);
+00034 \textcolor{keywordtype}{int} move\_first( \textcolor{keywordtype}{char} *seq,
+00035                 \textcolor{keywordtype}{short} *ptable,
+00036                 \textcolor{keywordtype}{short} *s,
+00037                 \textcolor{keywordtype}{short} *s1,
+00038                 \textcolor{keywordtype}{int} verbosity\_level,
+00039                 \textcolor{keywordtype}{int} shifts,
+00040                 \textcolor{keywordtype}{int} noLP);
+00041 \textcolor{keywordtype}{int} move\_rand(  \textcolor{keywordtype}{char} *seq,
+00042                 \textcolor{keywordtype}{short} *ptable,
+00043                 \textcolor{keywordtype}{short} *s,
+00044                 \textcolor{keywordtype}{short} *s1,
+00045                 \textcolor{keywordtype}{int} verbosity\_level);
+00046 
+00047 
+00048 \textcolor{comment}{/* browse\_neighbours and do funct function on each of them (used mainly for user specified flooding)}
+00049 \textcolor{comment}{    input:    seq - sequence}
+00050 \textcolor{comment}{              ptable - structure encoded with make\_pair\_table() from pair\_mat.h}
+00051 \textcolor{comment}{              s, s1 - sequence encoded with encode\_sequence from pair\_mat.h}
+00052 \textcolor{comment}{              funct - function (moved structure, current structure (or altered by funct)) to do with every
+       structure in neigbourhood}
+00053 \textcolor{comment}{    returns energy of the structure funct sets as second argument*/}
+00054 \textcolor{keywordtype}{int} browse\_neighs( \textcolor{keywordtype}{char} *seq,
+00055                    \textcolor{keywordtype}{short} *ptable,
+00056                    \textcolor{keywordtype}{short} *s,
+00057                    \textcolor{keywordtype}{short} *s1,
+00058                    \textcolor{keywordtype}{int} verbosity\_level,
+00059                    \textcolor{keywordtype}{int} shifts,
+00060                    \textcolor{keywordtype}{int} noLP,
+00061                    \textcolor{keywordtype}{int} (*funct) (\hyperlink{structstruct__en}{struct\_en}*, \hyperlink{structstruct__en}{struct\_en}*));
+00062 
+00063 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}