git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / utils_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/utils_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/utils_8h_source.tex
index 1e47672..f4ce9ad 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/utils_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/utils_8h_source.tex
@@ -1,8 +1,9 @@
-\hypertarget{utils_8h}{\section{utils.\-h}
-\label{utils_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h}}
+\hypertarget{utils_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_UTILS\_H\_\_}
 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_UTILS\_H\_\_}
 00003 \textcolor{preprocessor}{}
@@ -96,46 +97,47 @@
 00196 
 00204 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@notnull@*/}
 00205 \textcolor{keywordtype}{void}  *\hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc}(\textcolor{comment}{/*@null@*/} \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@out@*/} \textcolor{comment}{/*@returned@*/} \textcolor{keywordtype}{void} *p,
-00206                 \textcolor{keywordtype}{unsigned} size) \textcolor{comment}{/*@modifies *p @*/} \textcolor{comment}{/*@ensures MaxSet(result) == (size-1) @*/};
+00206                 \textcolor{keywordtype}{unsigned} size) \textcolor{comment}{/*@modifies *p @*/} \textcolor{comment}{/*@ensures MaxSet(result) == (s
+      ize-1) @*/};
 00207 \textcolor{preprocessor}{#endif}
 00208 \textcolor{preprocessor}{}
 00215 \textcolor{comment}{/*@exits@*/}
 00216 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]);
 00217 
-00225 \textcolor{keywordtype}{void} \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]);
+00225 \textcolor{keywordtype}{void} \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn_user}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]);
 00226 
-00230 \textcolor{keywordtype}{void}   \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand}(\textcolor{keywordtype}{void});
+00230 \textcolor{keywordtype}{void}   \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init_rand}(\textcolor{keywordtype}{void});
 00231 
 00240 \textcolor{keyword}{extern} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi}[3];
 00241 
 00248 \textcolor{keywordtype}{double} \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn}(\textcolor{keywordtype}{void});
 00249 
-00257 \textcolor{keywordtype}{int}    \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn}(\textcolor{keywordtype}{int} from, \textcolor{keywordtype}{int} to);
+00257 \textcolor{keywordtype}{int}    \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int_urn}(\textcolor{keywordtype}{int} from, \textcolor{keywordtype}{int} to);
 00258 
 00259 \textcolor{keywordtype}{void}   filecopy(FILE *from, FILE *to); \textcolor{comment}{/* inefficient `cp' */}
 00260 
 00269 \textcolor{comment}{/*@observer@*/}
-00270 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp}(\textcolor{keywordtype}{void});
+00270 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time_stamp}(\textcolor{keywordtype}{void});
 00271 
 00279 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@notnull@*/}
-00280 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string}(\textcolor{keywordtype}{int} l, \textcolor{keyword}{const} \textcolor{keywordtype}{char} symbols[]);
+00280 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random_string}(\textcolor{keywordtype}{int} l, \textcolor{keyword}{const} \textcolor{keywordtype}{char} symbols[]);
 00281 
 00290 \textcolor{keywordtype}{int}   \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2);
 00291 
-00301 \textcolor{keywordtype}{int}   \hyperlink{utils_8h_a96d3c36717d624514055ce201cab1542}{hamming\_bound}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, \textcolor{keywordtype}{int} n);
+00301 \textcolor{keywordtype}{int}   \hyperlink{utils_8h_a96d3c36717d624514055ce201cab1542}{hamming_bound}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, \textcolor{keywordtype}{int} n);
 00302 
 00313 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@null@*/}
-00314 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}(FILE *fp);
+00314 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get_line}(FILE *fp);
 00315 
 00316 \textcolor{keywordtype}{int} skip\_comment\_lines(\textcolor{keywordtype}{char} **line);
 00317 
-00338 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\_input\_line}(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string},
+00338 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get_input_line}(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string},
 00339                             \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);
 00340 
 00341 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} get\_multi\_input\_line(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string},
 00342                                   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);
 00343 
-00396 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}( \textcolor{keywordtype}{char} **header,
+00396 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read_record}( \textcolor{keywordtype}{char} **header,
 00397                           \textcolor{keywordtype}{char} **sequence,
 00398                           \textcolor{keywordtype}{char}  ***rest,
 00399                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);
@@ -143,65 +145,68 @@
 00401 
 00402 \textcolor{comment}{/* \(\backslash\)brief Extract a dot-bracket structure string from (multiline)character array}
 00403 \textcolor{comment}{ *}
-00404 \textcolor{comment}{ * This function extracts a dot-bracket structure string from the 'rest' array as}
-00405 \textcolor{comment}{ * returned by read\_record() and returns it. All occurences of comments within the}
-00406 \textcolor{comment}{ * 'lines' array will be skipped as long as they do not break the structure string.}
+00404 \textcolor{comment}{ * This function extracts a dot-bracket structure string from the 'rest' array as
+      }
+00405 \textcolor{comment}{ * returned by read\_record() and returns it. All occurences of comments within th
+      e}
+00406 \textcolor{comment}{ * 'lines' array will be skipped as long as they do not break the structure strin
+      g.}
 00407 \textcolor{comment}{ * If no structure could be read, this function returns NULL.}
 00408 \textcolor{comment}{ *}
 00409 \textcolor{comment}{ * \(\backslash\)see read\_record()}
 00410 \textcolor{comment}{ *}
 00411 \textcolor{comment}{ * \(\backslash\)param lines   The (multiline) character array to be parsed}
-00412 \textcolor{comment}{ * \(\backslash\)param length  The assumed length of the dot-bracket string (passing a value < 1 results in no length
-       limit)}
-00413 \textcolor{comment}{ * \(\backslash\)param option  Some options which may be passed to alter the behavior of the function, use 0 for no
-       options}
+00412 \textcolor{comment}{ * \(\backslash\)param length  The assumed length of the dot-bracket string (passing a value <
+       1 results in no length limit)}
+00413 \textcolor{comment}{ * \(\backslash\)param option  Some options which may be passed to alter the behavior of the f
+      unction, use 0 for no options}
 00414 \textcolor{comment}{ * \(\backslash\)return        The dot-bracket string read from lines or NULL}
 00415 \textcolor{comment}{ */}
 00416 \textcolor{keywordtype}{char} *extract\_record\_rest\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines,
 00417                                     \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length,
 00418                                     \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option);
 00419 
-00431 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc);
+00431 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc);
 00432 
-00442 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *packed);
+00442 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *packed);
 00443 
-00453 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
+00453 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make_pair_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
 00454 
 00455 \textcolor{keywordtype}{short} *make\_pair\_table\_pk(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
 00456 
-00463 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{short} *pt);
+00463 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy_pair_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{short} *pt);
 00464 
-00470 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{alimake\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
+00470 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{alimake_pair_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
 00471 
-00477 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{make\_pair\_table\_snoop}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
+00477 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{make_pair_table_snoop}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure);
 00478 
-00491 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{make\_loop\_index\_pt}(\textcolor{keywordtype}{short} *pt);
+00491 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{make_loop_index_pt}(\textcolor{keywordtype}{short} *pt);
 00492 
 00493 
 00494 \textcolor{keywordtype}{int} bp\_distance(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *str1,
 00495                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *str2);
 00496 
-00502 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq}(\textcolor{keywordtype}{void});
+00502 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print_tty_input_seq}(\textcolor{keywordtype}{void});
 00503 
-00512 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{print\_tty\_input\_seq\_str}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s);
+00512 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{print_tty_input_seq_str}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s);
 00513 
-00519 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full}(\textcolor{keywordtype}{void});
+00519 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print_tty_constraint_full}(\textcolor{keywordtype}{void});
 00520 
-00537 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option);
+00537 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print_tty_constraint}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option);
 00538 
-00546 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}(\textcolor{keywordtype}{char} *sequence);
+00546 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str_DNA2RNA}(\textcolor{keywordtype}{char} *sequence);
 00547 
-00553 \textcolor{keywordtype}{void}  \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}(\textcolor{keywordtype}{char} *sequence);
+00553 \textcolor{keywordtype}{void}  \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str_uppercase}(\textcolor{keywordtype}{char} *sequence);
 00554 
-00568 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
+00568 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get_iindx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
 00569 
-00584 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
+00584 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get_indx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
 00585 
 00586 \textcolor{keywordtype}{void} getConstraint( \textcolor{keywordtype}{char} **cstruc,
 00587                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines,
 00588                     \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option);
 00589 
-00601 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *constraint,
+00601 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain_ptypes}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *constraint,
 00602                       \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length,
 00603                       \textcolor{keywordtype}{char} *ptype,
 00604                       \textcolor{keywordtype}{int} *BP,
@@ -216,4 +221,4 @@
 00613                                       \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} turn);
 00614 
 00615 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}