-\hypertarget{data__structures_8h}{\section{data\-\_\-structures.\-h}
-\label{data__structures_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h}}
+\hypertarget{data__structures_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\-structures.h}
}
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
00003 \textcolor{preprocessor}{}
-00004 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy\_const.h}"}
+00004 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy_const.h}"}
00010 \textcolor{comment}{/* to use floats instead of doubles in pf\_fold() comment next line */}
00011 \textcolor{preprocessor}{#define LARGE\_PF}
00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef LARGE\_PF}
00035 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_STACK\_SIZE 2}
00036 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_LINKER\_LENGTH 15}
00037 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_LINKER\_LENGTH 1}
-00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_BOX\_SIZE ((4*VRNA\_GQUAD\_MIN\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MIN\_LINKER\_LENGTH))}
-00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_BOX\_SIZE ((4*VRNA\_GQUAD\_MAX\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH))}
+00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_BOX\_SIZE ((4*VRNA\_GQUAD\_MIN\_STACK\_SIZE)+(3*VRNA\_GQ
+ UAD\_MIN\_LINKER\_LENGTH))}
+00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_BOX\_SIZE ((4*VRNA\_GQUAD\_MAX\_STACK\_SIZE)+(3*VRNA\_GQ
+ UAD\_MAX\_LINKER\_LENGTH))}
00040 \textcolor{preprocessor}{}
00041
00042 \textcolor{comment}{/*}
00101
\hypertarget{data__structures_8h_source_l00106}{}\hyperlink{structmodel__detailsT}{00106} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
\hypertarget{data__structures_8h_source_l00107}{}\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{00107} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
-\hypertarget{data__structures_8h_source_l00113}{}\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{00113} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp};
-\hypertarget{data__structures_8h_source_l00114}{}\hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{00114} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{noLP};
-\hypertarget{data__structures_8h_source_l00115}{}\hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{00115} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{noGU};
-\hypertarget{data__structures_8h_source_l00116}{}\hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{00116} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{noGUclosure};
-\hypertarget{data__structures_8h_source_l00117}{}\hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{00117} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{logML};
-\hypertarget{data__structures_8h_source_l00118}{}\hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{00118} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ};
-\hypertarget{data__structures_8h_source_l00119}{}\hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{00119} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad};
-00120 \} \hyperlink{structmodel__detailsT}{model\_detailsT};
+\hypertarget{data__structures_8h_source_l00113}{}\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{00113} \textcolor{keywordtype}{int} special\_hp;
+\hypertarget{data__structures_8h_source_l00114}{}\hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{00114} \textcolor{keywordtype}{int} noLP;
+\hypertarget{data__structures_8h_source_l00115}{}\hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{00115} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{noGU};
+\hypertarget{data__structures_8h_source_l00116}{}\hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{00116} \textcolor{keywordtype}{int} noGUclosure;
+\hypertarget{data__structures_8h_source_l00117}{}\hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{00117} \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML};
+\hypertarget{data__structures_8h_source_l00118}{}\hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{00118} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
+\hypertarget{data__structures_8h_source_l00119}{}\hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{00119} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad};
+00120 \} \hyperlink{structmodel__detailsT}{model_detailsT};
00121
\hypertarget{data__structures_8h_source_l00125}{}\hyperlink{structparamT}{00125} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00126 \textcolor{keywordtype}{int} id;
00158 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad} [VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
00159 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
00160
-\hypertarget{data__structures_8h_source_l00161}{}\hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{00161} \textcolor{keywordtype}{double} \hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{temperature};
-\hypertarget{data__structures_8h_source_l00163}{}\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{00163} \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details};
+\hypertarget{data__structures_8h_source_l00161}{}\hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{00161} \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};
+\hypertarget{data__structures_8h_source_l00163}{}\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{00163} \hyperlink{structmodel__detailsT}{model_detailsT} model\_details;
00165 \} \hyperlink{structparamT}{paramT};
00166
\hypertarget{data__structures_8h_source_l00170}{}\hyperlink{structpf__paramT}{00170} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00205 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
00206
00207 \textcolor{keywordtype}{double} kT;
-\hypertarget{data__structures_8h_source_l00208}{}\hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{00208} \textcolor{keywordtype}{double} \hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{pf\_scale};
-\hypertarget{data__structures_8h_source_l00210}{}\hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{00210} \textcolor{keywordtype}{double} \hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{temperature};
+\hypertarget{data__structures_8h_source_l00208}{}\hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{00208} \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf_scale};
+\hypertarget{data__structures_8h_source_l00210}{}\hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{00210} \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};
\hypertarget{data__structures_8h_source_l00211}{}\hyperlink{structpf__paramT_a3d2af9040acfa08295efb50f0219149d}{00211} \textcolor{keywordtype}{double} alpha;
-\hypertarget{data__structures_8h_source_l00218}{}\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{00218} \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model\_details};
-00220 \} \hyperlink{structpf__paramT}{pf\_paramT};
+\hypertarget{data__structures_8h_source_l00218}{}\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{00218} \hyperlink{structmodel__detailsT}{model_detailsT} model\_details;
+00220 \} \hyperlink{structpf__paramT}{pf_paramT};
00221
00222
00223
00246 \} \hyperlink{structINTERVAL}{INTERVAL};
00247
\hypertarget{data__structures_8h_source_l00251}{}\hyperlink{structSOLUTION}{00251} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
-\hypertarget{data__structures_8h_source_l00252}{}\hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{00252} \textcolor{keywordtype}{float} \hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{energy};
-\hypertarget{data__structures_8h_source_l00253}{}\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{00253} \textcolor{keywordtype}{char} *\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{structure};
+\hypertarget{data__structures_8h_source_l00252}{}\hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{00252} \textcolor{keywordtype}{float} energy;
+\hypertarget{data__structures_8h_source_l00253}{}\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{00253} \textcolor{keywordtype}{char} *structure;
00254 \} \hyperlink{structSOLUTION}{SOLUTION};
00255
00256 \textcolor{comment}{/*}
00296 \}\hyperlink{structpairpro}{pairpro};
00297
\hypertarget{data__structures_8h_source_l00308}{}\hyperlink{structpair__info}{00308} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
-\hypertarget{data__structures_8h_source_l00309}{}\hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{00309} \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{i};
-\hypertarget{data__structures_8h_source_l00310}{}\hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{00310} \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{j};
-\hypertarget{data__structures_8h_source_l00311}{}\hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{00311} \textcolor{keywordtype}{float} \hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{p};
-\hypertarget{data__structures_8h_source_l00312}{}\hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{00312} \textcolor{keywordtype}{float} \hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{ent};
+\hypertarget{data__structures_8h_source_l00309}{}\hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{00309} \textcolor{keywordtype}{unsigned} i;
+\hypertarget{data__structures_8h_source_l00310}{}\hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{00310} \textcolor{keywordtype}{unsigned} j;
+\hypertarget{data__structures_8h_source_l00311}{}\hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{00311} \textcolor{keywordtype}{float} p;
+\hypertarget{data__structures_8h_source_l00312}{}\hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{00312} \textcolor{keywordtype}{float} ent;
\hypertarget{data__structures_8h_source_l00313}{}\hyperlink{structpair__info_a23fc316453d179474bed7f6ed2489723}{00313} \textcolor{keywordtype}{short} bp[8];
-\hypertarget{data__structures_8h_source_l00314}{}\hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{00314} \textcolor{keywordtype}{char} \hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{comp};
-00315 \} \hyperlink{structpair__info}{pair\_info};
+\hypertarget{data__structures_8h_source_l00314}{}\hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{00314} \textcolor{keywordtype}{char} comp;
+00315 \} \hyperlink{structpair__info}{pair_info};
00316
00317
00318 \textcolor{comment}{/*}
00329 \textcolor{keywordtype}{int} j;
00330 \textcolor{keywordtype}{int} when; \textcolor{comment}{/* 0 if still available, else resulting distance from start */}
00331 \textcolor{keywordtype}{int} E;
-00332 \} \hyperlink{structmove__t}{move\_t};
+00332 \} \hyperlink{structmove__t}{move_t};
00333
\hypertarget{data__structures_8h_source_l00337}{}\hyperlink{structintermediate__t}{00337} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }intermediate \{
-\hypertarget{data__structures_8h_source_l00338}{}\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{00338} \textcolor{keywordtype}{short} *\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{pt};
-\hypertarget{data__structures_8h_source_l00339}{}\hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{00339} \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{Sen};
-\hypertarget{data__structures_8h_source_l00340}{}\hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{00340} \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{curr\_en};
-\hypertarget{data__structures_8h_source_l00341}{}\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{00341} \hyperlink{structmove__t}{move\_t} *\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{moves};
-00342 \} \hyperlink{structintermediate__t}{intermediate\_t};
+\hypertarget{data__structures_8h_source_l00338}{}\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{00338} \textcolor{keywordtype}{short} *pt;
+\hypertarget{data__structures_8h_source_l00339}{}\hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{00339} \textcolor{keywordtype}{int} Sen;
+\hypertarget{data__structures_8h_source_l00340}{}\hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{00340} \textcolor{keywordtype}{int} curr\_en;
+\hypertarget{data__structures_8h_source_l00341}{}\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{00341} \hyperlink{structmove__t}{move_t} *moves;
+00342 \} \hyperlink{structintermediate__t}{intermediate_t};
00343
\hypertarget{data__structures_8h_source_l00347}{}\hyperlink{structpath__t}{00347} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }path \{
00348 \textcolor{keywordtype}{double} en;
00349 \textcolor{keywordtype}{char} *s;
-00350 \} \hyperlink{structpath__t}{path\_t};
+00350 \} \hyperlink{structpath__t}{path_t};
00351
00352 \textcolor{comment}{/*}
00353 \textcolor{comment}{* ############################################################}
00355 \textcolor{comment}{* ############################################################}
00356 \textcolor{comment}{*/}
00357
-\hypertarget{data__structures_8h_source_l00361}{}\hyperlink{structpu__contrib}{00361} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__contrib}{pu\_contrib} \{
+\hypertarget{data__structures_8h_source_l00361}{}\hyperlink{structpu__contrib}{00361} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__contrib}{pu_contrib} \{
\hypertarget{data__structures_8h_source_l00362}{}\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{00362} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{H};
\hypertarget{data__structures_8h_source_l00363}{}\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{00363} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{I};
\hypertarget{data__structures_8h_source_l00364}{}\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{00364} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{M};
\hypertarget{data__structures_8h_source_l00365}{}\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{00365} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{E};
\hypertarget{data__structures_8h_source_l00366}{}\hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{00366} \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{length};
\hypertarget{data__structures_8h_source_l00367}{}\hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{00367} \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{w};
-00368 \} \hyperlink{structpu__contrib}{pu\_contrib};
+00368 \} \hyperlink{structpu__contrib}{pu_contrib};
00369
\hypertarget{data__structures_8h_source_l00373}{}\hyperlink{structinteract}{00373} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structinteract}{interact} \{
\hypertarget{data__structures_8h_source_l00374}{}\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{00374} \textcolor{keywordtype}{double} *\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{Pi};
\hypertarget{data__structures_8h_source_l00375}{}\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{00375} \textcolor{keywordtype}{double} *\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{Gi};
\hypertarget{data__structures_8h_source_l00376}{}\hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{00376} \textcolor{keywordtype}{double} \hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{Gikjl};
-\hypertarget{data__structures_8h_source_l00378}{}\hyperlink{structinteract_a41793812abae560805414761fec398fe}{00378} \textcolor{keywordtype}{double} \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl\_wo};
+\hypertarget{data__structures_8h_source_l00378}{}\hyperlink{structinteract_a41793812abae560805414761fec398fe}{00378} \textcolor{keywordtype}{double} \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl_wo};
\hypertarget{data__structures_8h_source_l00379}{}\hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{00379} \textcolor{keywordtype}{int} \hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{i};
\hypertarget{data__structures_8h_source_l00380}{}\hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{00380} \textcolor{keywordtype}{int} \hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{k};
\hypertarget{data__structures_8h_source_l00381}{}\hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{00381} \textcolor{keywordtype}{int} \hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{j};
\hypertarget{data__structures_8h_source_l00383}{}\hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{00383} \textcolor{keywordtype}{int} \hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{length};
00384 \} \hyperlink{structinteract}{interact};
00385
-\hypertarget{data__structures_8h_source_l00389}{}\hyperlink{structpu__out}{00389} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__out}{pu\_out} \{
+\hypertarget{data__structures_8h_source_l00389}{}\hyperlink{structpu__out}{00389} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__out}{pu_out} \{
\hypertarget{data__structures_8h_source_l00390}{}\hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{00390} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{len};
-\hypertarget{data__structures_8h_source_l00391}{}\hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{00391} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u\_vals};
+\hypertarget{data__structures_8h_source_l00391}{}\hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{00391} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u_vals};
\hypertarget{data__structures_8h_source_l00392}{}\hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{00392} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{contribs};
\hypertarget{data__structures_8h_source_l00393}{}\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{00393} \textcolor{keywordtype}{char} **\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{header};
-\hypertarget{data__structures_8h_source_l00394}{}\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{00394} \textcolor{keywordtype}{double} **\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u\_values};
-00395 \} \hyperlink{structpu__out}{pu\_out};
+\hypertarget{data__structures_8h_source_l00394}{}\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{00394} \textcolor{keywordtype}{double} **\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u_values};
+00395 \} \hyperlink{structpu__out}{pu_out};
00396
\hypertarget{data__structures_8h_source_l00400}{}\hyperlink{structconstrain}{00400} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structconstrain}{constrain}\{
00401 \textcolor{keywordtype}{int} *indx;
00510 \textcolor{comment}{*/}
00511
\hypertarget{data__structures_8h_source_l00526}{}\hyperlink{structTwoDfold__solution}{00526} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
-\hypertarget{data__structures_8h_source_l00527}{}\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{00527} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{k};
-\hypertarget{data__structures_8h_source_l00528}{}\hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{00528} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{l};
-\hypertarget{data__structures_8h_source_l00529}{}\hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{00529} \textcolor{keywordtype}{float} \hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{en};
-\hypertarget{data__structures_8h_source_l00530}{}\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{00530} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{s};
-00531 \} \hyperlink{structTwoDfold__solution}{TwoDfold\_solution};
+\hypertarget{data__structures_8h_source_l00527}{}\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{00527} \textcolor{keywordtype}{int} k;
+\hypertarget{data__structures_8h_source_l00528}{}\hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{00528} \textcolor{keywordtype}{int} l;
+\hypertarget{data__structures_8h_source_l00529}{}\hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{00529} \textcolor{keywordtype}{float} en;
+\hypertarget{data__structures_8h_source_l00530}{}\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{00530} \textcolor{keywordtype}{char} *s;
+00531 \} \hyperlink{structTwoDfold__solution}{TwoDfold_solution};
00532
\hypertarget{data__structures_8h_source_l00538}{}\hyperlink{structTwoDfold__vars}{00538} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
-\hypertarget{data__structures_8h_source_l00539}{}\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{00539} \hyperlink{structparamT}{paramT} *\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P};
-\hypertarget{data__structures_8h_source_l00540}{}\hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{00540} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\_backtrack};
-\hypertarget{data__structures_8h_source_l00541}{}\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{00541} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype};
-\hypertarget{data__structures_8h_source_l00542}{}\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{00542} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence};
-\hypertarget{data__structures_8h_source_l00543}{}\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{00543} \textcolor{keywordtype}{short} *S, *\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1};
-\hypertarget{data__structures_8h_source_l00544}{}\hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{00544} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{maxD1};
-\hypertarget{data__structures_8h_source_l00545}{}\hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{00545} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{maxD2};
-\hypertarget{data__structures_8h_source_l00548}{}\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{00548} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1};
-\hypertarget{data__structures_8h_source_l00549}{}\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{00549} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2};
-\hypertarget{data__structures_8h_source_l00551}{}\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{00551} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\_iindx};
+\hypertarget{data__structures_8h_source_l00539}{}\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{00539} \hyperlink{structparamT}{paramT} *P;
+\hypertarget{data__structures_8h_source_l00540}{}\hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{00540} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do_backtrack};
+\hypertarget{data__structures_8h_source_l00541}{}\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{00541} \textcolor{keywordtype}{char} *ptype;
+\hypertarget{data__structures_8h_source_l00542}{}\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{00542} \textcolor{keywordtype}{char} *sequence;
+\hypertarget{data__structures_8h_source_l00543}{}\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{00543} \textcolor{keywordtype}{short} *S, *S1;
+\hypertarget{data__structures_8h_source_l00544}{}\hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{00544} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} maxD1;
+\hypertarget{data__structures_8h_source_l00545}{}\hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{00545} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} maxD2;
+\hypertarget{data__structures_8h_source_l00548}{}\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{00548} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *mm1;
+\hypertarget{data__structures_8h_source_l00549}{}\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{00549} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *mm2;
+\hypertarget{data__structures_8h_source_l00551}{}\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{00551} \textcolor{keywordtype}{int} *my\_iindx;
00553 \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};
00554
-\hypertarget{data__structures_8h_source_l00555}{}\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{00555} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{referenceBPs1};
-\hypertarget{data__structures_8h_source_l00556}{}\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{00556} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{referenceBPs2};
-\hypertarget{data__structures_8h_source_l00557}{}\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{00557} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist};
+\hypertarget{data__structures_8h_source_l00555}{}\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{00555} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *referenceBPs1;
+\hypertarget{data__structures_8h_source_l00556}{}\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{00556} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *referenceBPs2;
+\hypertarget{data__structures_8h_source_l00557}{}\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{00557} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *bpdist;
00559 \textcolor{keywordtype}{short} *reference\_pt1;
00560 \textcolor{keywordtype}{short} *reference\_pt2;
00561 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
00624 \textcolor{keywordtype}{int} k\_min\_values\_fcM;
00625 \textcolor{keywordtype}{int} k\_max\_values\_fcM;
00626
-00627 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */}
+00627 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max)
+ */}
00628 \textcolor{keywordtype}{int} *E\_F5\_rem;
00629 \textcolor{keywordtype}{int} *E\_F3\_rem;
00630 \textcolor{keywordtype}{int} *E\_C\_rem;
00643 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_M;
00644 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_M1;
00645 \textcolor{preprocessor}{#endif}
-00646 \textcolor{preprocessor}{}\} \hyperlink{structTwoDfold__vars}{TwoDfold\_vars};
+00646 \textcolor{preprocessor}{}\} \hyperlink{structTwoDfold__vars}{TwoDfold_vars};
00647
\hypertarget{data__structures_8h_source_l00660}{}\hyperlink{structTwoDpfold__solution}{00660} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
-\hypertarget{data__structures_8h_source_l00661}{}\hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{00661} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{k};
-\hypertarget{data__structures_8h_source_l00662}{}\hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{00662} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{l};
-\hypertarget{data__structures_8h_source_l00663}{}\hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{00663} FLT\_OR\_DBL \hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{q};
-00664 \} \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution};
+\hypertarget{data__structures_8h_source_l00661}{}\hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{00661} \textcolor{keywordtype}{int} k;
+\hypertarget{data__structures_8h_source_l00662}{}\hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{00662} \textcolor{keywordtype}{int} l;
+\hypertarget{data__structures_8h_source_l00663}{}\hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{00663} FLT\_OR\_DBL q;
+00664 \} \hyperlink{structTwoDpfold__solution}{TwoDpfold_solution};
00665
\hypertarget{data__structures_8h_source_l00672}{}\hyperlink{structTwoDpfold__vars}{00672} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00673
00674 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} alloc;
-\hypertarget{data__structures_8h_source_l00675}{}\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{00675} \textcolor{keywordtype}{char} *\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype};
-\hypertarget{data__structures_8h_source_l00676}{}\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{00676} \textcolor{keywordtype}{char} *\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence};
-\hypertarget{data__structures_8h_source_l00677}{}\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{00677} \textcolor{keywordtype}{short} *S, *\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1};
-\hypertarget{data__structures_8h_source_l00678}{}\hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{00678} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{maxD1};
-\hypertarget{data__structures_8h_source_l00679}{}\hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{00679} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{maxD2};
-00681 \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}; \textcolor{comment}{/* temperature in last call to scale\_pf\_params */}
-00682 \textcolor{keywordtype}{double} init\_temp; \textcolor{comment}{/* temperature in last call to scale\_pf\_params */}
+\hypertarget{data__structures_8h_source_l00675}{}\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{00675} \textcolor{keywordtype}{char} *ptype;
+\hypertarget{data__structures_8h_source_l00676}{}\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{00676} \textcolor{keywordtype}{char} *sequence;
+\hypertarget{data__structures_8h_source_l00677}{}\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{00677} \textcolor{keywordtype}{short} *S, *S1;
+\hypertarget{data__structures_8h_source_l00678}{}\hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{00678} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} maxD1;
+\hypertarget{data__structures_8h_source_l00679}{}\hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{00679} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} maxD2;
+00681 \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}; \textcolor{comment}{/* temperature in last call to scale\_pf\_params
+ */}
+00682 \textcolor{keywordtype}{double} init\_temp; \textcolor{comment}{/* temperature in last call to scale\_pf\_params
+ */}
00683 FLT\_OR\_DBL *scale;
-00684 FLT\_OR\_DBL \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale};
-00685 \hyperlink{structpf__paramT}{pf\_paramT} *pf\_params; \textcolor{comment}{/* holds all [unscaled] pf parameters */}
+00684 FLT\_OR\_DBL \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf_scale};
+00685 \hyperlink{structpf__paramT}{pf_paramT} *pf\_params; \textcolor{comment}{/* holds all [unscaled] pf parameters */}
00686
-\hypertarget{data__structures_8h_source_l00687}{}\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{00687} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\_iindx};
-\hypertarget{data__structures_8h_source_l00688}{}\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{00688} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx};
+\hypertarget{data__structures_8h_source_l00687}{}\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{00687} \textcolor{keywordtype}{int} *my\_iindx;
+\hypertarget{data__structures_8h_source_l00688}{}\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{00688} \textcolor{keywordtype}{int} *jindx;
00690 \textcolor{keywordtype}{short} *reference\_pt1;
00691 \textcolor{keywordtype}{short} *reference\_pt2;
00692
-\hypertarget{data__structures_8h_source_l00693}{}\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{00693} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{referenceBPs1};
-\hypertarget{data__structures_8h_source_l00694}{}\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{00694} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{referenceBPs2};
-\hypertarget{data__structures_8h_source_l00695}{}\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{00695} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist};
-\hypertarget{data__structures_8h_source_l00697}{}\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{00697} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1};
-\hypertarget{data__structures_8h_source_l00698}{}\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{00698} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2};
+\hypertarget{data__structures_8h_source_l00693}{}\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{00693} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *referenceBPs1;
+\hypertarget{data__structures_8h_source_l00694}{}\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{00694} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *referenceBPs2;
+\hypertarget{data__structures_8h_source_l00695}{}\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{00695} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *bpdist;
+\hypertarget{data__structures_8h_source_l00697}{}\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{00697} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *mm1;
+\hypertarget{data__structures_8h_source_l00698}{}\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{00698} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *mm2;
00700 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
00701 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
00702 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} seq\_length;
00757 \textcolor{keywordtype}{int} k\_min\_values\_qcM;
00758 \textcolor{keywordtype}{int} k\_max\_values\_qcM;
00759
-00760 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */}
+00760 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max)
+ */}
00761 FLT\_OR\_DBL *Q\_rem;
00762 FLT\_OR\_DBL *Q\_B\_rem;
00763 FLT\_OR\_DBL *Q\_M\_rem;
00769 FLT\_OR\_DBL Q\_cI\_rem;
00770 FLT\_OR\_DBL Q\_cM\_rem;
00771
-00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars};
+00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars};
00773
00774 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}
git://source.jalview.org / jabaws.git / blobdiff