--- /dev/null
+\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}}
+}
+
+\begin{DoxyCode}
+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}"}
+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}
+00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL double}
+00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
+00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL float}
+00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00017 \textcolor{preprocessor}{}
+00018 \textcolor{preprocessor}{#ifndef NBASES}
+00019 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBASES 8}
+00020 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00021 \textcolor{preprocessor}{}
+00022 \textcolor{preprocessor}{#ifndef MAXALPHA}
+00023 \textcolor{preprocessor}{}
+\hypertarget{data__structures_8h_source_l00026}{}\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{00026} \textcolor{preprocessor}{#define MAXALPHA 20}
+00027 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00028 \textcolor{preprocessor}{}
+\hypertarget{data__structures_8h_source_l00032}{}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{00032} \textcolor{preprocessor}{#define MAXDOS 1000}
+00033 \textcolor{preprocessor}{}
+00034 \textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_STACK\_SIZE 7}
+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))}
+00040 \textcolor{preprocessor}{}
+00041
+00042 \textcolor{comment}{/*}
+00043 \textcolor{comment}{* ############################################################}
+00044 \textcolor{comment}{* Here are the type definitions of various datastructures}
+00045 \textcolor{comment}{* shared among the Vienna RNA Package}
+00046 \textcolor{comment}{* ############################################################}
+00047 \textcolor{comment}{*/}
+00048
+\hypertarget{data__structures_8h_source_l00052}{}\hyperlink{structplist}{00052} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structplist}{plist} \{
+00053 \textcolor{keywordtype}{int} i;
+00054 \textcolor{keywordtype}{int} j;
+00055 \textcolor{keywordtype}{float} p;
+00056 \textcolor{keywordtype}{int} type;
+00057 \} \hyperlink{structplist}{plist};
+00058
+\hypertarget{data__structures_8h_source_l00062}{}\hyperlink{structcpair}{00062} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcpair}{cpair} \{
+00063 \textcolor{keywordtype}{int} i,j,mfe;
+00064 \textcolor{keywordtype}{float} p, hue, sat;
+00065 \} \hyperlink{structcpair}{cpair};
+00066
+\hypertarget{data__structures_8h_source_l00071}{}\hyperlink{structCOORDINATE}{00071} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
+00072 \textcolor{keywordtype}{float} X; \textcolor{comment}{/* X coords */}
+00073 \textcolor{keywordtype}{float} Y; \textcolor{comment}{/* Y coords */}
+00074 \} \hyperlink{structCOORDINATE}{COORDINATE};
+00075
+\hypertarget{data__structures_8h_source_l00079}{}\hyperlink{structsect}{00079} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structsect}{sect} \{
+00080 \textcolor{keywordtype}{int} i;
+00081 \textcolor{keywordtype}{int} j;
+00082 \textcolor{keywordtype}{int} ml;
+00083 \} \hyperlink{structsect}{sect};
+00084
+\hypertarget{data__structures_8h_source_l00088}{}\hyperlink{structbondT}{00088} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondT}{bondT} \{
+00089 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i;
+00090 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} j;
+00091 \} \hyperlink{structbondT}{bondT};
+00092
+\hypertarget{data__structures_8h_source_l00096}{}\hyperlink{structbondTEn}{00096} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondTEn}{bondTEn} \{
+00097 \textcolor{keywordtype}{int} i;
+00098 \textcolor{keywordtype}{int} j;
+00099 \textcolor{keywordtype}{int} energy;
+00100 \} \hyperlink{structbondTEn}{bondTEn};
+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};
+00121
+\hypertarget{data__structures_8h_source_l00125}{}\hyperlink{structparamT}{00125} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
+00126 \textcolor{keywordtype}{int} id;
+00127 \textcolor{keywordtype}{int} stack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
+00128 \textcolor{keywordtype}{int} hairpin[31];
+00129 \textcolor{keywordtype}{int} bulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
+00130 \textcolor{keywordtype}{int} internal\_loop[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
+00131 \textcolor{keywordtype}{int} mismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00132 \textcolor{keywordtype}{int} mismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00133 \textcolor{keywordtype}{int} mismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00134 \textcolor{keywordtype}{int} mismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00135 \textcolor{keywordtype}{int} mismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00136 \textcolor{keywordtype}{int} mismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00137 \textcolor{keywordtype}{int} dangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
+00138 \textcolor{keywordtype}{int} dangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
+00139 \textcolor{keywordtype}{int} int11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00140 \textcolor{keywordtype}{int} int21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
+00141 \textcolor{keywordtype}{int} int22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
+00142 \textcolor{keywordtype}{int} ninio[5];
+00143 \textcolor{keywordtype}{double} lxc;
+00144 \textcolor{keywordtype}{int} MLbase;
+00145 \textcolor{keywordtype}{int} MLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
+00146 \textcolor{keywordtype}{int} MLclosing;
+00147 \textcolor{keywordtype}{int} TerminalAU;
+00148 \textcolor{keywordtype}{int} DuplexInit;
+00149 \textcolor{keywordtype}{int} Tetraloop\_E[200];
+00150 \textcolor{keywordtype}{char} Tetraloops[1401];
+00151 \textcolor{keywordtype}{int} Triloop\_E[40];
+00152 \textcolor{keywordtype}{char} Triloops[241];
+00153 \textcolor{keywordtype}{int} Hexaloop\_E[40];
+00154 \textcolor{keywordtype}{char} Hexaloops[1801];
+00155 \textcolor{keywordtype}{int} TripleC;
+00156 \textcolor{keywordtype}{int} MultipleCA;
+00157 \textcolor{keywordtype}{int} MultipleCB;
+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};
+00165 \} \hyperlink{structparamT}{paramT};
+00166
+\hypertarget{data__structures_8h_source_l00170}{}\hyperlink{structpf__paramT}{00170} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
+00171 \textcolor{keywordtype}{int} id;
+00172 \textcolor{keywordtype}{double} expstack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
+00173 \textcolor{keywordtype}{double} exphairpin[31];
+00174 \textcolor{keywordtype}{double} expbulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
+00175 \textcolor{keywordtype}{double} expinternal[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
+00176 \textcolor{keywordtype}{double} expmismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00177 \textcolor{keywordtype}{double} expmismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00178 \textcolor{keywordtype}{double} expmismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00179 \textcolor{keywordtype}{double} expmismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00180 \textcolor{keywordtype}{double} expmismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00181 \textcolor{keywordtype}{double} expmismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00182 \textcolor{keywordtype}{double} expdangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
+00183 \textcolor{keywordtype}{double} expdangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
+00184 \textcolor{keywordtype}{double} expint11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00185 \textcolor{keywordtype}{double} expint21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
+00186 \textcolor{keywordtype}{double} expint22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
+00187 \textcolor{keywordtype}{double} expninio[5][\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
+00188 \textcolor{keywordtype}{double} lxc;
+00189 \textcolor{keywordtype}{double} expMLbase;
+00190 \textcolor{keywordtype}{double} expMLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
+00191 \textcolor{keywordtype}{double} expMLclosing;
+00192 \textcolor{keywordtype}{double} expTermAU;
+00193 \textcolor{keywordtype}{double} expDuplexInit;
+00194 \textcolor{keywordtype}{double} exptetra[40];
+00195 \textcolor{keywordtype}{double} exptri[40];
+00196 \textcolor{keywordtype}{double} exphex[40];
+00197 \textcolor{keywordtype}{char} Tetraloops[1401];
+00198 \textcolor{keywordtype}{double} expTriloop[40];
+00199 \textcolor{keywordtype}{char} Triloops[241];
+00200 \textcolor{keywordtype}{char} Hexaloops[1801];
+00201 \textcolor{keywordtype}{double} expTripleC;
+00202 \textcolor{keywordtype}{double} expMultipleCA;
+00203 \textcolor{keywordtype}{double} expMultipleCB;
+00204 \textcolor{keywordtype}{double} expgquad[VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
+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_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};
+00221
+00222
+00223
+00224 \textcolor{comment}{/*}
+00225 \textcolor{comment}{* ############################################################}
+00226 \textcolor{comment}{* SUBOPT data structures}
+00227 \textcolor{comment}{* ############################################################}
+00228 \textcolor{comment}{*/}
+00229
+00230
+\hypertarget{data__structures_8h_source_l00234}{}\hyperlink{structPAIR}{00234} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
+00235 \textcolor{keywordtype}{int} i;
+00236 \textcolor{keywordtype}{int} j;
+00237 \} \hyperlink{structPAIR}{PAIR};
+00238
+\hypertarget{data__structures_8h_source_l00242}{}\hyperlink{structINTERVAL}{00242} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
+00243 \textcolor{keywordtype}{int} i;
+00244 \textcolor{keywordtype}{int} j;
+00245 \textcolor{keywordtype}{int} array\_flag;
+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};
+00254 \} \hyperlink{structSOLUTION}{SOLUTION};
+00255
+00256 \textcolor{comment}{/*}
+00257 \textcolor{comment}{* ############################################################}
+00258 \textcolor{comment}{* COFOLD data structures}
+00259 \textcolor{comment}{* ############################################################}
+00260 \textcolor{comment}{*/}
+00261
+\hypertarget{data__structures_8h_source_l00265}{}\hyperlink{structcofoldF}{00265} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcofoldF}{cofoldF} \{
+00266 \textcolor{comment}{/* free energies for: */}
+\hypertarget{data__structures_8h_source_l00267}{}\hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{00267} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{F0AB};
+\hypertarget{data__structures_8h_source_l00268}{}\hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{00268} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{FAB};
+\hypertarget{data__structures_8h_source_l00269}{}\hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{00269} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{FcAB};
+\hypertarget{data__structures_8h_source_l00270}{}\hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{00270} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{FA};
+\hypertarget{data__structures_8h_source_l00271}{}\hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{00271} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{FB};
+00272 \} \hyperlink{structcofoldF}{cofoldF};
+00273
+\hypertarget{data__structures_8h_source_l00277}{}\hyperlink{structConcEnt}{00277} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structConcEnt}{ConcEnt} \{
+\hypertarget{data__structures_8h_source_l00278}{}\hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{00278} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{A0};
+\hypertarget{data__structures_8h_source_l00279}{}\hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{00279} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{B0};
+\hypertarget{data__structures_8h_source_l00280}{}\hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{00280} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{ABc};
+00281 \textcolor{keywordtype}{double} AAc;
+00282 \textcolor{keywordtype}{double} BBc;
+00283 \textcolor{keywordtype}{double} Ac;
+00284 \textcolor{keywordtype}{double} Bc;
+00285 \} \hyperlink{structConcEnt}{ConcEnt};
+00286
+\hypertarget{data__structures_8h_source_l00290}{}\hyperlink{structpairpro}{00290} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpairpro}{pairpro}\{
+00291 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AB;
+00292 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AA;
+00293 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *A;
+00294 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *B;
+00295 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *BB;
+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_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};
+00316
+00317
+00318 \textcolor{comment}{/*}
+00319 \textcolor{comment}{* ############################################################}
+00320 \textcolor{comment}{* FINDPATH data structures}
+00321 \textcolor{comment}{* ############################################################}
+00322 \textcolor{comment}{*/}
+00323
+\hypertarget{data__structures_8h_source_l00327}{}\hyperlink{structmove__t}{00327} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }move \{
+00328 \textcolor{keywordtype}{int} i; \textcolor{comment}{/* i,j>0 insert; i,j<0 delete */}
+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};
+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};
+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};
+00351
+00352 \textcolor{comment}{/*}
+00353 \textcolor{comment}{* ############################################################}
+00354 \textcolor{comment}{* RNAup data structures}
+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_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};
+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_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_l00382}{}\hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{00382} \textcolor{keywordtype}{int} \hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{l};
+\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_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_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};
+00396
+\hypertarget{data__structures_8h_source_l00400}{}\hyperlink{structconstrain}{00400} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structconstrain}{constrain}\{
+00401 \textcolor{keywordtype}{int} *indx;
+00402 \textcolor{keywordtype}{char} *ptype;
+00403 \} \hyperlink{structconstrain}{constrain};
+00404
+00405 \textcolor{comment}{/*}
+00406 \textcolor{comment}{* ############################################################}
+00407 \textcolor{comment}{* RNAduplex data structures}
+00408 \textcolor{comment}{* ############################################################}
+00409 \textcolor{comment}{*/}
+00410
+\hypertarget{data__structures_8h_source_l00414}{}\hyperlink{structduplexT}{00414} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
+00415 \textcolor{keywordtype}{int} i;
+00416 \textcolor{keywordtype}{int} j;
+00417 \textcolor{keywordtype}{int} end;
+00418 \textcolor{keywordtype}{char} *structure;
+00419 \textcolor{keywordtype}{double} energy;
+00420 \textcolor{keywordtype}{double} energy\_backtrack;
+00421 \textcolor{keywordtype}{double} opening\_backtrack\_x;
+00422 \textcolor{keywordtype}{double} opening\_backtrack\_y;
+00423 \textcolor{keywordtype}{int} offset;
+00424 \textcolor{keywordtype}{double} dG1;
+00425 \textcolor{keywordtype}{double} dG2;
+00426 \textcolor{keywordtype}{double} ddG;
+00427 \textcolor{keywordtype}{int} tb;
+00428 \textcolor{keywordtype}{int} te;
+00429 \textcolor{keywordtype}{int} qb;
+00430 \textcolor{keywordtype}{int} qe;
+00431 \} \hyperlink{structduplexT}{duplexT};
+00432
+00433 \textcolor{comment}{/*}
+00434 \textcolor{comment}{* ############################################################}
+00435 \textcolor{comment}{* RNAsnoop data structures}
+00436 \textcolor{comment}{* ############################################################}
+00437 \textcolor{comment}{*/}
+00438
+\hypertarget{data__structures_8h_source_l00442}{}\hyperlink{structfolden}{00442} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }node \{
+00443 \textcolor{keywordtype}{int} k;
+00444 \textcolor{keywordtype}{int} energy;
+00445 \textcolor{keyword}{struct }node *next;
+00446 \} \hyperlink{structfolden}{folden};
+00447
+\hypertarget{data__structures_8h_source_l00451}{}\hyperlink{structsnoopT}{00451} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
+00452 \textcolor{keywordtype}{int} i;
+00453 \textcolor{keywordtype}{int} j;
+00454 \textcolor{keywordtype}{int} u;
+00455 \textcolor{keywordtype}{char} *structure;
+00456 \textcolor{keywordtype}{float} energy;
+00457 \textcolor{keywordtype}{float} Duplex\_El;
+00458 \textcolor{keywordtype}{float} Duplex\_Er;
+00459 \textcolor{keywordtype}{float} Loop\_E;
+00460 \textcolor{keywordtype}{float} Loop\_D;
+00461 \textcolor{keywordtype}{float} pscd;
+00462 \textcolor{keywordtype}{float} psct;
+00463 \textcolor{keywordtype}{float} pscg;
+00464 \textcolor{keywordtype}{float} Duplex\_Ol;
+00465 \textcolor{keywordtype}{float} Duplex\_Or;
+00466 \textcolor{keywordtype}{float} Duplex\_Ot;
+00467 \textcolor{keywordtype}{float} fullStemEnergy;
+00468 \} \hyperlink{structsnoopT}{snoopT};
+00469
+00470
+00471
+00472
+00473
+00474
+00475
+00476 \textcolor{comment}{/*}
+00477 \textcolor{comment}{* ############################################################}
+00478 \textcolor{comment}{* PKplex data structures}
+00479 \textcolor{comment}{* ############################################################}
+00480 \textcolor{comment}{*/}
+00481
+\hypertarget{data__structures_8h_source_l00485}{}\hyperlink{structdupVar}{00485} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structdupVar}{dupVar}\{
+00486 \textcolor{keywordtype}{int} i;
+00487 \textcolor{keywordtype}{int} j;
+00488 \textcolor{keywordtype}{int} end;
+00489 \textcolor{keywordtype}{char} *pk\_helix;
+00490 \textcolor{keywordtype}{char} *structure;
+00491 \textcolor{keywordtype}{double} energy;
+00492 \textcolor{keywordtype}{int} offset;
+00493 \textcolor{keywordtype}{double} dG1;
+00494 \textcolor{keywordtype}{double} dG2;
+00495 \textcolor{keywordtype}{double} ddG;
+00496 \textcolor{keywordtype}{int} tb;
+00497 \textcolor{keywordtype}{int} te;
+00498 \textcolor{keywordtype}{int} qb;
+00499 \textcolor{keywordtype}{int} qe;
+00500 \textcolor{keywordtype}{int} inactive;
+00501 \textcolor{keywordtype}{int} processed;
+00502 \} \hyperlink{structdupVar}{dupVar};
+00503
+00504
+00505
+00506 \textcolor{comment}{/*}
+00507 \textcolor{comment}{* ############################################################}
+00508 \textcolor{comment}{* 2Dfold data structures}
+00509 \textcolor{comment}{* ############################################################}
+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};
+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};
+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};
+00559 \textcolor{keywordtype}{short} *reference\_pt1;
+00560 \textcolor{keywordtype}{short} *reference\_pt2;
+00561 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
+00562 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
+00563 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} seq\_length;
+00564
+00565 \textcolor{keywordtype}{int} ***E\_F5;
+00566 \textcolor{keywordtype}{int} ***E\_F3;
+00567 \textcolor{keywordtype}{int} ***E\_C;
+00568 \textcolor{keywordtype}{int} ***E\_M;
+00569 \textcolor{keywordtype}{int} ***E\_M1;
+00570 \textcolor{keywordtype}{int} ***E\_M2;
+00571
+00572 \textcolor{keywordtype}{int} **E\_Fc;
+00573 \textcolor{keywordtype}{int} **E\_FcH;
+00574 \textcolor{keywordtype}{int} **E\_FcI;
+00575 \textcolor{keywordtype}{int} **E\_FcM;
+00576
+00577 \textcolor{keywordtype}{int} **l\_min\_values;
+00578 \textcolor{keywordtype}{int} **l\_max\_values;
+00579 \textcolor{keywordtype}{int} *k\_min\_values;
+00580 \textcolor{keywordtype}{int} *k\_max\_values;
+00581
+00582 \textcolor{keywordtype}{int} **l\_min\_values\_m;
+00583 \textcolor{keywordtype}{int} **l\_max\_values\_m;
+00584 \textcolor{keywordtype}{int} *k\_min\_values\_m;
+00585 \textcolor{keywordtype}{int} *k\_max\_values\_m;
+00586
+00587 \textcolor{keywordtype}{int} **l\_min\_values\_m1;
+00588 \textcolor{keywordtype}{int} **l\_max\_values\_m1;
+00589 \textcolor{keywordtype}{int} *k\_min\_values\_m1;
+00590 \textcolor{keywordtype}{int} *k\_max\_values\_m1;
+00591
+00592 \textcolor{keywordtype}{int} **l\_min\_values\_f;
+00593 \textcolor{keywordtype}{int} **l\_max\_values\_f;
+00594 \textcolor{keywordtype}{int} *k\_min\_values\_f;
+00595 \textcolor{keywordtype}{int} *k\_max\_values\_f;
+00596
+00597 \textcolor{keywordtype}{int} **l\_min\_values\_f3;
+00598 \textcolor{keywordtype}{int} **l\_max\_values\_f3;
+00599 \textcolor{keywordtype}{int} *k\_min\_values\_f3;
+00600 \textcolor{keywordtype}{int} *k\_max\_values\_f3;
+00601
+00602 \textcolor{keywordtype}{int} **l\_min\_values\_m2;
+00603 \textcolor{keywordtype}{int} **l\_max\_values\_m2;
+00604 \textcolor{keywordtype}{int} *k\_min\_values\_m2;
+00605 \textcolor{keywordtype}{int} *k\_max\_values\_m2;
+00606
+00607 \textcolor{keywordtype}{int} *l\_min\_values\_fc;
+00608 \textcolor{keywordtype}{int} *l\_max\_values\_fc;
+00609 \textcolor{keywordtype}{int} k\_min\_values\_fc;
+00610 \textcolor{keywordtype}{int} k\_max\_values\_fc;
+00611
+00612 \textcolor{keywordtype}{int} *l\_min\_values\_fcH;
+00613 \textcolor{keywordtype}{int} *l\_max\_values\_fcH;
+00614 \textcolor{keywordtype}{int} k\_min\_values\_fcH;
+00615 \textcolor{keywordtype}{int} k\_max\_values\_fcH;
+00616
+00617 \textcolor{keywordtype}{int} *l\_min\_values\_fcI;
+00618 \textcolor{keywordtype}{int} *l\_max\_values\_fcI;
+00619 \textcolor{keywordtype}{int} k\_min\_values\_fcI;
+00620 \textcolor{keywordtype}{int} k\_max\_values\_fcI;
+00621
+00622 \textcolor{keywordtype}{int} *l\_min\_values\_fcM;
+00623 \textcolor{keywordtype}{int} *l\_max\_values\_fcM;
+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) */}
+00628 \textcolor{keywordtype}{int} *E\_F5\_rem;
+00629 \textcolor{keywordtype}{int} *E\_F3\_rem;
+00630 \textcolor{keywordtype}{int} *E\_C\_rem;
+00631 \textcolor{keywordtype}{int} *E\_M\_rem;
+00632 \textcolor{keywordtype}{int} *E\_M1\_rem;
+00633 \textcolor{keywordtype}{int} *E\_M2\_rem;
+00634
+00635 \textcolor{keywordtype}{int} E\_Fc\_rem;
+00636 \textcolor{keywordtype}{int} E\_FcH\_rem;
+00637 \textcolor{keywordtype}{int} E\_FcI\_rem;
+00638 \textcolor{keywordtype}{int} E\_FcM\_rem;
+00639
+00640 \textcolor{preprocessor}{#ifdef COUNT\_STATES}
+00641 \textcolor{preprocessor}{} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_F5;
+00642 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_C;
+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};
+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};
+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 */}
+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 */}
+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};
+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};
+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;
+00703
+00704 FLT\_OR\_DBL ***Q;
+00705 FLT\_OR\_DBL ***Q\_B;
+00706 FLT\_OR\_DBL ***Q\_M;
+00707 FLT\_OR\_DBL ***Q\_M1;
+00708 FLT\_OR\_DBL ***Q\_M2;
+00709
+00710 FLT\_OR\_DBL **Q\_c;
+00711 FLT\_OR\_DBL **Q\_cH;
+00712 FLT\_OR\_DBL **Q\_cI;
+00713 FLT\_OR\_DBL **Q\_cM;
+00714
+00715 \textcolor{keywordtype}{int} **l\_min\_values;
+00716 \textcolor{keywordtype}{int} **l\_max\_values;
+00717 \textcolor{keywordtype}{int} *k\_min\_values;
+00718 \textcolor{keywordtype}{int} *k\_max\_values;
+00719
+00720 \textcolor{keywordtype}{int} **l\_min\_values\_b;
+00721 \textcolor{keywordtype}{int} **l\_max\_values\_b;
+00722 \textcolor{keywordtype}{int} *k\_min\_values\_b;
+00723 \textcolor{keywordtype}{int} *k\_max\_values\_b;
+00724
+00725 \textcolor{keywordtype}{int} **l\_min\_values\_m;
+00726 \textcolor{keywordtype}{int} **l\_max\_values\_m;
+00727 \textcolor{keywordtype}{int} *k\_min\_values\_m;
+00728 \textcolor{keywordtype}{int} *k\_max\_values\_m;
+00729
+00730 \textcolor{keywordtype}{int} **l\_min\_values\_m1;
+00731 \textcolor{keywordtype}{int} **l\_max\_values\_m1;
+00732 \textcolor{keywordtype}{int} *k\_min\_values\_m1;
+00733 \textcolor{keywordtype}{int} *k\_max\_values\_m1;
+00734
+00735 \textcolor{keywordtype}{int} **l\_min\_values\_m2;
+00736 \textcolor{keywordtype}{int} **l\_max\_values\_m2;
+00737 \textcolor{keywordtype}{int} *k\_min\_values\_m2;
+00738 \textcolor{keywordtype}{int} *k\_max\_values\_m2;
+00739
+00740 \textcolor{keywordtype}{int} *l\_min\_values\_qc;
+00741 \textcolor{keywordtype}{int} *l\_max\_values\_qc;
+00742 \textcolor{keywordtype}{int} k\_min\_values\_qc;
+00743 \textcolor{keywordtype}{int} k\_max\_values\_qc;
+00744
+00745 \textcolor{keywordtype}{int} *l\_min\_values\_qcH;
+00746 \textcolor{keywordtype}{int} *l\_max\_values\_qcH;
+00747 \textcolor{keywordtype}{int} k\_min\_values\_qcH;
+00748 \textcolor{keywordtype}{int} k\_max\_values\_qcH;
+00749
+00750 \textcolor{keywordtype}{int} *l\_min\_values\_qcI;
+00751 \textcolor{keywordtype}{int} *l\_max\_values\_qcI;
+00752 \textcolor{keywordtype}{int} k\_min\_values\_qcI;
+00753 \textcolor{keywordtype}{int} k\_max\_values\_qcI;
+00754
+00755 \textcolor{keywordtype}{int} *l\_min\_values\_qcM;
+00756 \textcolor{keywordtype}{int} *l\_max\_values\_qcM;
+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) */}
+00761 FLT\_OR\_DBL *Q\_rem;
+00762 FLT\_OR\_DBL *Q\_B\_rem;
+00763 FLT\_OR\_DBL *Q\_M\_rem;
+00764 FLT\_OR\_DBL *Q\_M1\_rem;
+00765 FLT\_OR\_DBL *Q\_M2\_rem;
+00766
+00767 FLT\_OR\_DBL Q\_c\_rem;
+00768 FLT\_OR\_DBL Q\_cH\_rem;
+00769 FLT\_OR\_DBL Q\_cI\_rem;
+00770 FLT\_OR\_DBL Q\_cM\_rem;
+00771
+00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars};
+00773
+00774 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff