binaries/src/ViennaRNA/doc/latex/data__structures_8h_source.tex

   1 \hypertarget{data__structures_8h}{\section{data\-\_\-structures.\-h}
   2 \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}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy\_const.h}"}
  10 00010 \textcolor{comment}{/* to use floats instead of doubles in pf\_fold() comment next line */}
  11 00011 \textcolor{preprocessor}{#define LARGE\_PF}
  12 00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef  LARGE\_PF}
  13 00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL double}
  14 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  15 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL float}
  16 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  17 00017 \textcolor{preprocessor}{}
  18 00018 \textcolor{preprocessor}{#ifndef NBASES}
  19 00019 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBASES 8}
  20 00020 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  21 00021 \textcolor{preprocessor}{}
  22 00022 \textcolor{preprocessor}{#ifndef MAXALPHA}
  23 00023 \textcolor{preprocessor}{}
  24 \hypertarget{data__structures_8h_source_l00026}{}\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{00026} \textcolor{preprocessor}{#define MAXALPHA              20}
  25 00027 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  26 00028 \textcolor{preprocessor}{}
  27 \hypertarget{data__structures_8h_source_l00032}{}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{00032} \textcolor{preprocessor}{#define MAXDOS                1000}
  28 00033 \textcolor{preprocessor}{}
  29 00034 \textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_STACK\_SIZE     7}
  30 00035 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_STACK\_SIZE     2}
  31 00036 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_LINKER\_LENGTH  15}
  32 00037 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_LINKER\_LENGTH  1}
  33 00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_BOX\_SIZE       ((4*VRNA\_GQUAD\_MIN\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MIN\_LINKER\_LENGTH))}
  34 00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_BOX\_SIZE       ((4*VRNA\_GQUAD\_MAX\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH))}
  35 00040 \textcolor{preprocessor}{}
  36 00041
  37 00042 \textcolor{comment}{/*}
  38 00043 \textcolor{comment}{* ############################################################}
  39 00044 \textcolor{comment}{* Here are the type definitions of various datastructures}
  40 00045 \textcolor{comment}{* shared among the Vienna RNA Package}
  41 00046 \textcolor{comment}{* ############################################################}
  42 00047 \textcolor{comment}{*/}
  43 00048
  44 \hypertarget{data__structures_8h_source_l00052}{}\hyperlink{structplist}{00052} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structplist}{plist} \{
  45 00053   \textcolor{keywordtype}{int} i;
  46 00054   \textcolor{keywordtype}{int} j;
  47 00055   \textcolor{keywordtype}{float} p;
  48 00056   \textcolor{keywordtype}{int} type;
  49 00057 \} \hyperlink{structplist}{plist};
  50 00058
  51 \hypertarget{data__structures_8h_source_l00062}{}\hyperlink{structcpair}{00062} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcpair}{cpair} \{
  52 00063   \textcolor{keywordtype}{int} i,j,mfe;
  53 00064   \textcolor{keywordtype}{float} p, hue, sat;
  54 00065 \} \hyperlink{structcpair}{cpair};
  55 00066
  56 \hypertarget{data__structures_8h_source_l00071}{}\hyperlink{structCOORDINATE}{00071} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
  57 00072   \textcolor{keywordtype}{float} X; \textcolor{comment}{/* X coords */}
  58 00073   \textcolor{keywordtype}{float} Y; \textcolor{comment}{/* Y coords */}
  59 00074 \} \hyperlink{structCOORDINATE}{COORDINATE};
  60 00075
  61 \hypertarget{data__structures_8h_source_l00079}{}\hyperlink{structsect}{00079} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structsect}{sect} \{
  62 00080   \textcolor{keywordtype}{int}  i;
  63 00081   \textcolor{keywordtype}{int}  j;
  64 00082   \textcolor{keywordtype}{int} ml;
  65 00083 \} \hyperlink{structsect}{sect};
  66 00084
  67 \hypertarget{data__structures_8h_source_l00088}{}\hyperlink{structbondT}{00088} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondT}{bondT} \{
  68 00089    \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i;
  69 00090    \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} j;
  70 00091 \} \hyperlink{structbondT}{bondT};
  71 00092
  72 \hypertarget{data__structures_8h_source_l00096}{}\hyperlink{structbondTEn}{00096} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondTEn}{bondTEn} \{
  73 00097    \textcolor{keywordtype}{int} i;
  74 00098    \textcolor{keywordtype}{int} j;
  75 00099    \textcolor{keywordtype}{int} energy;
  76 00100 \} \hyperlink{structbondTEn}{bondTEn};
  77 00101
  78 \hypertarget{data__structures_8h_source_l00106}{}\hyperlink{structmodel__detailsT}{00106} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
  79 \hypertarget{data__structures_8h_source_l00107}{}\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{00107}   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
  80 \hypertarget{data__structures_8h_source_l00113}{}\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{00113}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp};
  81 \hypertarget{data__structures_8h_source_l00114}{}\hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{00114}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{noLP};
  82 \hypertarget{data__structures_8h_source_l00115}{}\hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{00115}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{noGU};
  83 \hypertarget{data__structures_8h_source_l00116}{}\hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{00116}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{noGUclosure};
  84 \hypertarget{data__structures_8h_source_l00117}{}\hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{00117}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{logML};
  85 \hypertarget{data__structures_8h_source_l00118}{}\hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{00118}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ};
  86 \hypertarget{data__structures_8h_source_l00119}{}\hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{00119}   \textcolor{keywordtype}{int}     \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad};
  87 00120 \} \hyperlink{structmodel__detailsT}{model\_detailsT};
  88 00121
  89 \hypertarget{data__structures_8h_source_l00125}{}\hyperlink{structparamT}{00125} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
  90 00126   \textcolor{keywordtype}{int} id;
  91 00127   \textcolor{keywordtype}{int} stack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
  92 00128   \textcolor{keywordtype}{int} hairpin[31];
  93 00129   \textcolor{keywordtype}{int} bulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
  94 00130   \textcolor{keywordtype}{int} internal\_loop[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
  95 00131   \textcolor{keywordtype}{int} mismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  96 00132   \textcolor{keywordtype}{int} mismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  97 00133   \textcolor{keywordtype}{int} mismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  98 00134   \textcolor{keywordtype}{int} mismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  99 00135   \textcolor{keywordtype}{int} mismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 100 00136   \textcolor{keywordtype}{int} mismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 101 00137   \textcolor{keywordtype}{int} dangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
 102 00138   \textcolor{keywordtype}{int} dangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
 103 00139   \textcolor{keywordtype}{int} int11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 104 00140   \textcolor{keywordtype}{int} int21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
 105 00141   \textcolor{keywordtype}{int} int22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
 106 00142   \textcolor{keywordtype}{int} ninio[5];
 107 00143   \textcolor{keywordtype}{double}  lxc;
 108 00144   \textcolor{keywordtype}{int}     MLbase;
 109 00145   \textcolor{keywordtype}{int}     MLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
 110 00146   \textcolor{keywordtype}{int}     MLclosing;
 111 00147   \textcolor{keywordtype}{int}     TerminalAU;
 112 00148   \textcolor{keywordtype}{int}     DuplexInit;
 113 00149   \textcolor{keywordtype}{int}     Tetraloop\_E[200];
 114 00150   \textcolor{keywordtype}{char}    Tetraloops[1401];
 115 00151   \textcolor{keywordtype}{int}     Triloop\_E[40];
 116 00152   \textcolor{keywordtype}{char}    Triloops[241];
 117 00153   \textcolor{keywordtype}{int}     Hexaloop\_E[40];
 118 00154   \textcolor{keywordtype}{char}    Hexaloops[1801];
 119 00155   \textcolor{keywordtype}{int}     TripleC;
 120 00156   \textcolor{keywordtype}{int}     MultipleCA;
 121 00157   \textcolor{keywordtype}{int}     MultipleCB;
 122 00158   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad} [VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
 123 00159                 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
 124 00160
 125 \hypertarget{data__structures_8h_source_l00161}{}\hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{00161}   \textcolor{keywordtype}{double}  \hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{temperature};
 126 \hypertarget{data__structures_8h_source_l00163}{}\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{00163}   \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details};
 127 00165 \}  \hyperlink{structparamT}{paramT};
 128 00166
 129 \hypertarget{data__structures_8h_source_l00170}{}\hyperlink{structpf__paramT}{00170} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
 130 00171   \textcolor{keywordtype}{int}     id;
 131 00172   \textcolor{keywordtype}{double}  expstack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
 132 00173   \textcolor{keywordtype}{double}  exphairpin[31];
 133 00174   \textcolor{keywordtype}{double}  expbulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
 134 00175   \textcolor{keywordtype}{double}  expinternal[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
 135 00176   \textcolor{keywordtype}{double}  expmismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 136 00177   \textcolor{keywordtype}{double}  expmismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 137 00178   \textcolor{keywordtype}{double}  expmismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 138 00179   \textcolor{keywordtype}{double}  expmismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 139 00180   \textcolor{keywordtype}{double}  expmismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 140 00181   \textcolor{keywordtype}{double}  expmismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 141 00182   \textcolor{keywordtype}{double}  expdangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
 142 00183   \textcolor{keywordtype}{double}  expdangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
 143 00184   \textcolor{keywordtype}{double}  expint11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
 144 00185   \textcolor{keywordtype}{double}  expint21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
 145 00186   \textcolor{keywordtype}{double}  expint22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
 146 00187   \textcolor{keywordtype}{double}  expninio[5][\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
 147 00188   \textcolor{keywordtype}{double}  lxc;
 148 00189   \textcolor{keywordtype}{double}  expMLbase;
 149 00190   \textcolor{keywordtype}{double}  expMLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
 150 00191   \textcolor{keywordtype}{double}  expMLclosing;
 151 00192   \textcolor{keywordtype}{double}  expTermAU;
 152 00193   \textcolor{keywordtype}{double}  expDuplexInit;
 153 00194   \textcolor{keywordtype}{double}  exptetra[40];
 154 00195   \textcolor{keywordtype}{double}  exptri[40];
 155 00196   \textcolor{keywordtype}{double}  exphex[40];
 156 00197   \textcolor{keywordtype}{char}    Tetraloops[1401];
 157 00198   \textcolor{keywordtype}{double}  expTriloop[40];
 158 00199   \textcolor{keywordtype}{char}    Triloops[241];
 159 00200   \textcolor{keywordtype}{char}    Hexaloops[1801];
 160 00201   \textcolor{keywordtype}{double}  expTripleC;
 161 00202   \textcolor{keywordtype}{double}  expMultipleCA;
 162 00203   \textcolor{keywordtype}{double}  expMultipleCB;
 163 00204   \textcolor{keywordtype}{double}  expgquad[VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
 164 00205                   [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
 165 00206
 166 00207   \textcolor{keywordtype}{double}  kT;
 167 \hypertarget{data__structures_8h_source_l00208}{}\hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{00208}   \textcolor{keywordtype}{double}  \hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{pf\_scale};
 168 \hypertarget{data__structures_8h_source_l00210}{}\hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{00210}   \textcolor{keywordtype}{double}  \hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{temperature};
 169 \hypertarget{data__structures_8h_source_l00211}{}\hyperlink{structpf__paramT_a3d2af9040acfa08295efb50f0219149d}{00211}   \textcolor{keywordtype}{double}  alpha;
 170 \hypertarget{data__structures_8h_source_l00218}{}\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{00218}   \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model\_details};
 171 00220 \}  \hyperlink{structpf__paramT}{pf\_paramT};
 172 00221
 173 00222
 174 00223
 175 00224 \textcolor{comment}{/*}
 176 00225 \textcolor{comment}{* ############################################################}
 177 00226 \textcolor{comment}{* SUBOPT data structures}
 178 00227 \textcolor{comment}{* ############################################################}
 179 00228 \textcolor{comment}{*/}
 180 00229
 181 00230
 182 \hypertarget{data__structures_8h_source_l00234}{}\hyperlink{structPAIR}{00234} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 183 00235   \textcolor{keywordtype}{int} i;
 184 00236   \textcolor{keywordtype}{int} j;
 185 00237 \} \hyperlink{structPAIR}{PAIR};
 186 00238
 187 \hypertarget{data__structures_8h_source_l00242}{}\hyperlink{structINTERVAL}{00242} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 188 00243     \textcolor{keywordtype}{int} i;
 189 00244     \textcolor{keywordtype}{int} j;
 190 00245     \textcolor{keywordtype}{int} array\_flag;
 191 00246 \} \hyperlink{structINTERVAL}{INTERVAL};
 192 00247
 193 \hypertarget{data__structures_8h_source_l00251}{}\hyperlink{structSOLUTION}{00251} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 194 \hypertarget{data__structures_8h_source_l00252}{}\hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{00252}   \textcolor{keywordtype}{float} \hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{energy};
 195 \hypertarget{data__structures_8h_source_l00253}{}\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{00253}   \textcolor{keywordtype}{char} *\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{structure};
 196 00254 \} \hyperlink{structSOLUTION}{SOLUTION};
 197 00255
 198 00256 \textcolor{comment}{/*}
 199 00257 \textcolor{comment}{* ############################################################}
 200 00258 \textcolor{comment}{* COFOLD data structures}
 201 00259 \textcolor{comment}{* ############################################################}
 202 00260 \textcolor{comment}{*/}
 203 00261
 204 \hypertarget{data__structures_8h_source_l00265}{}\hyperlink{structcofoldF}{00265} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcofoldF}{cofoldF} \{
 205 00266   \textcolor{comment}{/* free energies for: */}
 206 \hypertarget{data__structures_8h_source_l00267}{}\hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{00267}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{F0AB};
 207 \hypertarget{data__structures_8h_source_l00268}{}\hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{00268}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{FAB};
 208 \hypertarget{data__structures_8h_source_l00269}{}\hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{00269}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{FcAB};
 209 \hypertarget{data__structures_8h_source_l00270}{}\hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{00270}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{FA};
 210 \hypertarget{data__structures_8h_source_l00271}{}\hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{00271}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{FB};
 211 00272 \} \hyperlink{structcofoldF}{cofoldF};
 212 00273
 213 \hypertarget{data__structures_8h_source_l00277}{}\hyperlink{structConcEnt}{00277} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structConcEnt}{ConcEnt} \{
 214 \hypertarget{data__structures_8h_source_l00278}{}\hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{00278}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{A0};
 215 \hypertarget{data__structures_8h_source_l00279}{}\hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{00279}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{B0};
 216 \hypertarget{data__structures_8h_source_l00280}{}\hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{00280}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{ABc};
 217 00281   \textcolor{keywordtype}{double} AAc;
 218 00282   \textcolor{keywordtype}{double} BBc;
 219 00283   \textcolor{keywordtype}{double} Ac;
 220 00284   \textcolor{keywordtype}{double} Bc;
 221 00285 \} \hyperlink{structConcEnt}{ConcEnt};
 222 00286
 223 \hypertarget{data__structures_8h_source_l00290}{}\hyperlink{structpairpro}{00290} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpairpro}{pairpro}\{
 224 00291   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AB;
 225 00292   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AA;
 226 00293   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *A;
 227 00294   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *B;
 228 00295   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *BB;
 229 00296 \}\hyperlink{structpairpro}{pairpro};
 230 00297
 231 \hypertarget{data__structures_8h_source_l00308}{}\hyperlink{structpair__info}{00308} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 232 \hypertarget{data__structures_8h_source_l00309}{}\hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{00309}    \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{i};
 233 \hypertarget{data__structures_8h_source_l00310}{}\hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{00310}    \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{j};
 234 \hypertarget{data__structures_8h_source_l00311}{}\hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{00311}    \textcolor{keywordtype}{float} \hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{p};
 235 \hypertarget{data__structures_8h_source_l00312}{}\hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{00312}    \textcolor{keywordtype}{float} \hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{ent};
 236 \hypertarget{data__structures_8h_source_l00313}{}\hyperlink{structpair__info_a23fc316453d179474bed7f6ed2489723}{00313}    \textcolor{keywordtype}{short} bp[8];
 237 \hypertarget{data__structures_8h_source_l00314}{}\hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{00314}    \textcolor{keywordtype}{char} \hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{comp};
 238 00315 \} \hyperlink{structpair__info}{pair\_info};
 239 00316
 240 00317
 241 00318 \textcolor{comment}{/*}
 242 00319 \textcolor{comment}{* ############################################################}
 243 00320 \textcolor{comment}{* FINDPATH data structures}
 244 00321 \textcolor{comment}{* ############################################################}
 245 00322 \textcolor{comment}{*/}
 246 00323
 247 \hypertarget{data__structures_8h_source_l00327}{}\hyperlink{structmove__t}{00327} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }move \{
 248 00328   \textcolor{keywordtype}{int} i;  \textcolor{comment}{/* i,j>0 insert; i,j<0 delete */}
 249 00329   \textcolor{keywordtype}{int} j;
 250 00330   \textcolor{keywordtype}{int} when;  \textcolor{comment}{/* 0 if still available, else resulting distance from start */}
 251 00331   \textcolor{keywordtype}{int} E;
 252 00332 \} \hyperlink{structmove__t}{move\_t};
 253 00333
 254 \hypertarget{data__structures_8h_source_l00337}{}\hyperlink{structintermediate__t}{00337} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }intermediate \{
 255 \hypertarget{data__structures_8h_source_l00338}{}\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{00338}   \textcolor{keywordtype}{short} *\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{pt};
 256 \hypertarget{data__structures_8h_source_l00339}{}\hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{00339}   \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{Sen};
 257 \hypertarget{data__structures_8h_source_l00340}{}\hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{00340}   \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{curr\_en};
 258 \hypertarget{data__structures_8h_source_l00341}{}\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{00341}   \hyperlink{structmove__t}{move\_t} *\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{moves};
 259 00342 \} \hyperlink{structintermediate__t}{intermediate\_t};
 260 00343
 261 \hypertarget{data__structures_8h_source_l00347}{}\hyperlink{structpath__t}{00347} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }path \{
 262 00348   \textcolor{keywordtype}{double} en;
 263 00349   \textcolor{keywordtype}{char} *s;
 264 00350 \} \hyperlink{structpath__t}{path\_t};
 265 00351
 266 00352 \textcolor{comment}{/*}
 267 00353 \textcolor{comment}{* ############################################################}
 268 00354 \textcolor{comment}{* RNAup data structures}
 269 00355 \textcolor{comment}{* ############################################################}
 270 00356 \textcolor{comment}{*/}
 271 00357
 272 \hypertarget{data__structures_8h_source_l00361}{}\hyperlink{structpu__contrib}{00361} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__contrib}{pu\_contrib} \{
 273 \hypertarget{data__structures_8h_source_l00362}{}\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{00362}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{H};
 274 \hypertarget{data__structures_8h_source_l00363}{}\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{00363}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{I};
 275 \hypertarget{data__structures_8h_source_l00364}{}\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{00364}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{M};
 276 \hypertarget{data__structures_8h_source_l00365}{}\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{00365}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{E};
 277 \hypertarget{data__structures_8h_source_l00366}{}\hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{00366}   \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{length};
 278 \hypertarget{data__structures_8h_source_l00367}{}\hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{00367}   \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{w};
 279 00368 \} \hyperlink{structpu__contrib}{pu\_contrib};
 280 00369
 281 \hypertarget{data__structures_8h_source_l00373}{}\hyperlink{structinteract}{00373} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structinteract}{interact} \{
 282 \hypertarget{data__structures_8h_source_l00374}{}\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{00374}   \textcolor{keywordtype}{double} *\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{Pi};
 283 \hypertarget{data__structures_8h_source_l00375}{}\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{00375}   \textcolor{keywordtype}{double} *\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{Gi};
 284 \hypertarget{data__structures_8h_source_l00376}{}\hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{00376}   \textcolor{keywordtype}{double} \hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{Gikjl};
 285 \hypertarget{data__structures_8h_source_l00378}{}\hyperlink{structinteract_a41793812abae560805414761fec398fe}{00378}   \textcolor{keywordtype}{double} \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl\_wo};
 286 \hypertarget{data__structures_8h_source_l00379}{}\hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{00379}   \textcolor{keywordtype}{int} \hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{i};
 287 \hypertarget{data__structures_8h_source_l00380}{}\hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{00380}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{k};
 288 \hypertarget{data__structures_8h_source_l00381}{}\hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{00381}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{j};
 289 \hypertarget{data__structures_8h_source_l00382}{}\hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{00382}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{l};
 290 \hypertarget{data__structures_8h_source_l00383}{}\hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{00383}   \textcolor{keywordtype}{int} \hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{length};
 291 00384 \} \hyperlink{structinteract}{interact};
 292 00385
 293 \hypertarget{data__structures_8h_source_l00389}{}\hyperlink{structpu__out}{00389} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__out}{pu\_out} \{
 294 \hypertarget{data__structures_8h_source_l00390}{}\hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{00390}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{len};
 295 \hypertarget{data__structures_8h_source_l00391}{}\hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{00391}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u\_vals};
 296 \hypertarget{data__structures_8h_source_l00392}{}\hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{00392}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{contribs};
 297 \hypertarget{data__structures_8h_source_l00393}{}\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{00393}   \textcolor{keywordtype}{char} **\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{header};
 298 \hypertarget{data__structures_8h_source_l00394}{}\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{00394}   \textcolor{keywordtype}{double} **\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u\_values};
 299 00395 \} \hyperlink{structpu__out}{pu\_out};
 300 00396
 301 \hypertarget{data__structures_8h_source_l00400}{}\hyperlink{structconstrain}{00400} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structconstrain}{constrain}\{
 302 00401   \textcolor{keywordtype}{int} *indx;
 303 00402   \textcolor{keywordtype}{char} *ptype;
 304 00403 \} \hyperlink{structconstrain}{constrain};
 305 00404
 306 00405 \textcolor{comment}{/*}
 307 00406 \textcolor{comment}{* ############################################################}
 308 00407 \textcolor{comment}{* RNAduplex data structures}
 309 00408 \textcolor{comment}{* ############################################################}
 310 00409 \textcolor{comment}{*/}
 311 00410
 312 \hypertarget{data__structures_8h_source_l00414}{}\hyperlink{structduplexT}{00414} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 313 00415   \textcolor{keywordtype}{int} i;
 314 00416   \textcolor{keywordtype}{int} j;
 315 00417   \textcolor{keywordtype}{int} end;
 316 00418   \textcolor{keywordtype}{char} *structure;
 317 00419   \textcolor{keywordtype}{double} energy;
 318 00420   \textcolor{keywordtype}{double} energy\_backtrack;
 319 00421   \textcolor{keywordtype}{double} opening\_backtrack\_x;
 320 00422   \textcolor{keywordtype}{double} opening\_backtrack\_y;
 321 00423   \textcolor{keywordtype}{int} offset;
 322 00424   \textcolor{keywordtype}{double} dG1;
 323 00425   \textcolor{keywordtype}{double} dG2;
 324 00426   \textcolor{keywordtype}{double} ddG;
 325 00427   \textcolor{keywordtype}{int} tb;
 326 00428   \textcolor{keywordtype}{int} te;
 327 00429   \textcolor{keywordtype}{int} qb;
 328 00430   \textcolor{keywordtype}{int} qe;
 329 00431 \} \hyperlink{structduplexT}{duplexT};
 330 00432
 331 00433 \textcolor{comment}{/*}
 332 00434 \textcolor{comment}{* ############################################################}
 333 00435 \textcolor{comment}{* RNAsnoop data structures}
 334 00436 \textcolor{comment}{* ############################################################}
 335 00437 \textcolor{comment}{*/}
 336 00438
 337 \hypertarget{data__structures_8h_source_l00442}{}\hyperlink{structfolden}{00442} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }node \{
 338 00443   \textcolor{keywordtype}{int} k;
 339 00444   \textcolor{keywordtype}{int} energy;
 340 00445   \textcolor{keyword}{struct }node *next;
 341 00446 \} \hyperlink{structfolden}{folden};
 342 00447
 343 \hypertarget{data__structures_8h_source_l00451}{}\hyperlink{structsnoopT}{00451} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
 344 00452   \textcolor{keywordtype}{int} i;
 345 00453   \textcolor{keywordtype}{int} j;
 346 00454   \textcolor{keywordtype}{int} u;
 347 00455   \textcolor{keywordtype}{char} *structure;
 348 00456   \textcolor{keywordtype}{float} energy;
 349 00457   \textcolor{keywordtype}{float} Duplex\_El;
 350 00458   \textcolor{keywordtype}{float} Duplex\_Er;
 351 00459   \textcolor{keywordtype}{float} Loop\_E;
 352 00460   \textcolor{keywordtype}{float} Loop\_D;
 353 00461   \textcolor{keywordtype}{float} pscd;
 354 00462   \textcolor{keywordtype}{float} psct;
 355 00463   \textcolor{keywordtype}{float} pscg;
 356 00464   \textcolor{keywordtype}{float} Duplex\_Ol;
 357 00465   \textcolor{keywordtype}{float} Duplex\_Or;
 358 00466   \textcolor{keywordtype}{float} Duplex\_Ot;
 359 00467   \textcolor{keywordtype}{float} fullStemEnergy;
 360 00468 \} \hyperlink{structsnoopT}{snoopT};
 361 00469
 362 00470
 363 00471
 364 00472
 365 00473
 366 00474
 367 00475
 368 00476 \textcolor{comment}{/*}
 369 00477 \textcolor{comment}{* ############################################################}
 370 00478 \textcolor{comment}{* PKplex data structures}
 371 00479 \textcolor{comment}{* ############################################################}
 372 00480 \textcolor{comment}{*/}
 373 00481
 374 \hypertarget{data__structures_8h_source_l00485}{}\hyperlink{structdupVar}{00485} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structdupVar}{dupVar}\{
 375 00486   \textcolor{keywordtype}{int} i;
 376 00487   \textcolor{keywordtype}{int} j;
 377 00488   \textcolor{keywordtype}{int} end;
 378 00489   \textcolor{keywordtype}{char} *pk\_helix;
 379 00490   \textcolor{keywordtype}{char} *structure;
 380 00491   \textcolor{keywordtype}{double} energy;
 381 00492   \textcolor{keywordtype}{int} offset;
 382 00493   \textcolor{keywordtype}{double} dG1;
 383 00494   \textcolor{keywordtype}{double} dG2;
 384 00495   \textcolor{keywordtype}{double} ddG;
 385 00496   \textcolor{keywordtype}{int} tb;
 386 00497   \textcolor{keywordtype}{int} te;
 387 00498   \textcolor{keywordtype}{int} qb;
 388 00499   \textcolor{keywordtype}{int} qe;
 389 00500   \textcolor{keywordtype}{int} inactive;
 390 00501   \textcolor{keywordtype}{int} processed;
 391 00502 \} \hyperlink{structdupVar}{dupVar};
 392 00503
 393 00504
 394 00505
 395 00506 \textcolor{comment}{/*}
 396 00507 \textcolor{comment}{* ############################################################}
 397 00508 \textcolor{comment}{* 2Dfold data structures}
 398 00509 \textcolor{comment}{* ############################################################}
 399 00510 \textcolor{comment}{*/}
 400 00511
 401 \hypertarget{data__structures_8h_source_l00526}{}\hyperlink{structTwoDfold__solution}{00526} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
 402 \hypertarget{data__structures_8h_source_l00527}{}\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{00527}   \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{k};
 403 \hypertarget{data__structures_8h_source_l00528}{}\hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{00528}   \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{l};
 404 \hypertarget{data__structures_8h_source_l00529}{}\hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{00529}   \textcolor{keywordtype}{float} \hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{en};
 405 \hypertarget{data__structures_8h_source_l00530}{}\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{00530}   \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{s};
 406 00531 \} \hyperlink{structTwoDfold__solution}{TwoDfold\_solution};
 407 00532
 408 \hypertarget{data__structures_8h_source_l00538}{}\hyperlink{structTwoDfold__vars}{00538} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
 409 \hypertarget{data__structures_8h_source_l00539}{}\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{00539}   \hyperlink{structparamT}{paramT}          *\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P};
 410 \hypertarget{data__structures_8h_source_l00540}{}\hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{00540}   \textcolor{keywordtype}{int}             \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\_backtrack};
 411 \hypertarget{data__structures_8h_source_l00541}{}\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{00541}   \textcolor{keywordtype}{char}            *\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype};
 412 \hypertarget{data__structures_8h_source_l00542}{}\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{00542}   \textcolor{keywordtype}{char}            *\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence};
 413 \hypertarget{data__structures_8h_source_l00543}{}\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{00543}   \textcolor{keywordtype}{short}           *S, *\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1};
 414 \hypertarget{data__structures_8h_source_l00544}{}\hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{00544}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{maxD1};
 415 \hypertarget{data__structures_8h_source_l00545}{}\hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{00545}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{maxD2};
 416 \hypertarget{data__structures_8h_source_l00548}{}\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{00548}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1};
 417 \hypertarget{data__structures_8h_source_l00549}{}\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{00549}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2};
 418 \hypertarget{data__structures_8h_source_l00551}{}\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{00551}   \textcolor{keywordtype}{int}             *\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\_iindx};
 419 00553   \textcolor{keywordtype}{double}          \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};
 420 00554
 421 \hypertarget{data__structures_8h_source_l00555}{}\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{00555}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{referenceBPs1};
 422 \hypertarget{data__structures_8h_source_l00556}{}\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{00556}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{referenceBPs2};
 423 \hypertarget{data__structures_8h_source_l00557}{}\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{00557}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist};
 424 00559   \textcolor{keywordtype}{short}           *reference\_pt1;
 425 00560   \textcolor{keywordtype}{short}           *reference\_pt2;
 426 00561   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
 427 00562   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
 428 00563   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    seq\_length;
 429 00564
 430 00565   \textcolor{keywordtype}{int}             ***E\_F5;
 431 00566   \textcolor{keywordtype}{int}             ***E\_F3;
 432 00567   \textcolor{keywordtype}{int}             ***E\_C;
 433 00568   \textcolor{keywordtype}{int}             ***E\_M;
 434 00569   \textcolor{keywordtype}{int}             ***E\_M1;
 435 00570   \textcolor{keywordtype}{int}             ***E\_M2;
 436 00571
 437 00572   \textcolor{keywordtype}{int}             **E\_Fc;
 438 00573   \textcolor{keywordtype}{int}             **E\_FcH;
 439 00574   \textcolor{keywordtype}{int}             **E\_FcI;
 440 00575   \textcolor{keywordtype}{int}             **E\_FcM;
 441 00576
 442 00577   \textcolor{keywordtype}{int}             **l\_min\_values;
 443 00578   \textcolor{keywordtype}{int}             **l\_max\_values;
 444 00579   \textcolor{keywordtype}{int}             *k\_min\_values;
 445 00580   \textcolor{keywordtype}{int}             *k\_max\_values;
 446 00581
 447 00582   \textcolor{keywordtype}{int}             **l\_min\_values\_m;
 448 00583   \textcolor{keywordtype}{int}             **l\_max\_values\_m;
 449 00584   \textcolor{keywordtype}{int}             *k\_min\_values\_m;
 450 00585   \textcolor{keywordtype}{int}             *k\_max\_values\_m;
 451 00586
 452 00587   \textcolor{keywordtype}{int}             **l\_min\_values\_m1;
 453 00588   \textcolor{keywordtype}{int}             **l\_max\_values\_m1;
 454 00589   \textcolor{keywordtype}{int}             *k\_min\_values\_m1;
 455 00590   \textcolor{keywordtype}{int}             *k\_max\_values\_m1;
 456 00591
 457 00592   \textcolor{keywordtype}{int}             **l\_min\_values\_f;
 458 00593   \textcolor{keywordtype}{int}             **l\_max\_values\_f;
 459 00594   \textcolor{keywordtype}{int}             *k\_min\_values\_f;
 460 00595   \textcolor{keywordtype}{int}             *k\_max\_values\_f;
 461 00596
 462 00597   \textcolor{keywordtype}{int}             **l\_min\_values\_f3;
 463 00598   \textcolor{keywordtype}{int}             **l\_max\_values\_f3;
 464 00599   \textcolor{keywordtype}{int}             *k\_min\_values\_f3;
 465 00600   \textcolor{keywordtype}{int}             *k\_max\_values\_f3;
 466 00601
 467 00602   \textcolor{keywordtype}{int}             **l\_min\_values\_m2;
 468 00603   \textcolor{keywordtype}{int}             **l\_max\_values\_m2;
 469 00604   \textcolor{keywordtype}{int}             *k\_min\_values\_m2;
 470 00605   \textcolor{keywordtype}{int}             *k\_max\_values\_m2;
 471 00606
 472 00607   \textcolor{keywordtype}{int}             *l\_min\_values\_fc;
 473 00608   \textcolor{keywordtype}{int}             *l\_max\_values\_fc;
 474 00609   \textcolor{keywordtype}{int}             k\_min\_values\_fc;
 475 00610   \textcolor{keywordtype}{int}             k\_max\_values\_fc;
 476 00611
 477 00612   \textcolor{keywordtype}{int}             *l\_min\_values\_fcH;
 478 00613   \textcolor{keywordtype}{int}             *l\_max\_values\_fcH;
 479 00614   \textcolor{keywordtype}{int}             k\_min\_values\_fcH;
 480 00615   \textcolor{keywordtype}{int}             k\_max\_values\_fcH;
 481 00616
 482 00617   \textcolor{keywordtype}{int}             *l\_min\_values\_fcI;
 483 00618   \textcolor{keywordtype}{int}             *l\_max\_values\_fcI;
 484 00619   \textcolor{keywordtype}{int}             k\_min\_values\_fcI;
 485 00620   \textcolor{keywordtype}{int}             k\_max\_values\_fcI;
 486 00621
 487 00622   \textcolor{keywordtype}{int}             *l\_min\_values\_fcM;
 488 00623   \textcolor{keywordtype}{int}             *l\_max\_values\_fcM;
 489 00624   \textcolor{keywordtype}{int}             k\_min\_values\_fcM;
 490 00625   \textcolor{keywordtype}{int}             k\_max\_values\_fcM;
 491 00626
 492 00627   \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */}
 493 00628   \textcolor{keywordtype}{int}             *E\_F5\_rem;
 494 00629   \textcolor{keywordtype}{int}             *E\_F3\_rem;
 495 00630   \textcolor{keywordtype}{int}             *E\_C\_rem;
 496 00631   \textcolor{keywordtype}{int}             *E\_M\_rem;
 497 00632   \textcolor{keywordtype}{int}             *E\_M1\_rem;
 498 00633   \textcolor{keywordtype}{int}             *E\_M2\_rem;
 499 00634
 500 00635   \textcolor{keywordtype}{int}             E\_Fc\_rem;
 501 00636   \textcolor{keywordtype}{int}             E\_FcH\_rem;
 502 00637   \textcolor{keywordtype}{int}             E\_FcI\_rem;
 503 00638   \textcolor{keywordtype}{int}             E\_FcM\_rem;
 504 00639
 505 00640 \textcolor{preprocessor}{#ifdef COUNT\_STATES}
 506 00641 \textcolor{preprocessor}{}  \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_F5;
 507 00642   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_C;
 508 00643   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_M;
 509 00644   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_M1;
 510 00645 \textcolor{preprocessor}{#endif}
 511 00646 \textcolor{preprocessor}{}\} \hyperlink{structTwoDfold__vars}{TwoDfold\_vars};
 512 00647
 513 \hypertarget{data__structures_8h_source_l00660}{}\hyperlink{structTwoDpfold__solution}{00660} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
 514 \hypertarget{data__structures_8h_source_l00661}{}\hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{00661}   \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{k};
 515 \hypertarget{data__structures_8h_source_l00662}{}\hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{00662}   \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{l};
 516 \hypertarget{data__structures_8h_source_l00663}{}\hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{00663}   FLT\_OR\_DBL  \hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{q};
 517 00664 \} \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution};
 518 00665
 519 \hypertarget{data__structures_8h_source_l00672}{}\hyperlink{structTwoDpfold__vars}{00672} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
 520 00673
 521 00674   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    alloc;
 522 \hypertarget{data__structures_8h_source_l00675}{}\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{00675}   \textcolor{keywordtype}{char}            *\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype};
 523 \hypertarget{data__structures_8h_source_l00676}{}\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{00676}   \textcolor{keywordtype}{char}            *\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence};
 524 \hypertarget{data__structures_8h_source_l00677}{}\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{00677}   \textcolor{keywordtype}{short}           *S, *\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1};
 525 \hypertarget{data__structures_8h_source_l00678}{}\hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{00678}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{maxD1};
 526 \hypertarget{data__structures_8h_source_l00679}{}\hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{00679}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{maxD2};
 527 00681   \textcolor{keywordtype}{double}          \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};    \textcolor{comment}{/* temperature in last call to scale\_pf\_params */}
 528 00682   \textcolor{keywordtype}{double}          init\_temp;      \textcolor{comment}{/* temperature in last call to scale\_pf\_params */}
 529 00683   FLT\_OR\_DBL      *scale;
 530 00684   FLT\_OR\_DBL      \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale};
 531 00685   \hyperlink{structpf__paramT}{pf\_paramT}       *pf\_params;     \textcolor{comment}{/* holds all [unscaled] pf parameters */}
 532 00686
 533 \hypertarget{data__structures_8h_source_l00687}{}\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{00687}   \textcolor{keywordtype}{int}             *\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\_iindx};
 534 \hypertarget{data__structures_8h_source_l00688}{}\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{00688}   \textcolor{keywordtype}{int}             *\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx};
 535 00690   \textcolor{keywordtype}{short}           *reference\_pt1;
 536 00691   \textcolor{keywordtype}{short}           *reference\_pt2;
 537 00692
 538 \hypertarget{data__structures_8h_source_l00693}{}\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{00693}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{referenceBPs1};
 539 \hypertarget{data__structures_8h_source_l00694}{}\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{00694}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{referenceBPs2};
 540 \hypertarget{data__structures_8h_source_l00695}{}\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{00695}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist};
 541 \hypertarget{data__structures_8h_source_l00697}{}\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{00697}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1};
 542 \hypertarget{data__structures_8h_source_l00698}{}\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{00698}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2};
 543 00700   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
 544 00701   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
 545 00702   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    seq\_length;
 546 00703
 547 00704   FLT\_OR\_DBL      ***Q;
 548 00705   FLT\_OR\_DBL      ***Q\_B;
 549 00706   FLT\_OR\_DBL      ***Q\_M;
 550 00707   FLT\_OR\_DBL      ***Q\_M1;
 551 00708   FLT\_OR\_DBL      ***Q\_M2;
 552 00709
 553 00710   FLT\_OR\_DBL      **Q\_c;
 554 00711   FLT\_OR\_DBL      **Q\_cH;
 555 00712   FLT\_OR\_DBL      **Q\_cI;
 556 00713   FLT\_OR\_DBL      **Q\_cM;
 557 00714
 558 00715   \textcolor{keywordtype}{int}             **l\_min\_values;
 559 00716   \textcolor{keywordtype}{int}             **l\_max\_values;
 560 00717   \textcolor{keywordtype}{int}             *k\_min\_values;
 561 00718   \textcolor{keywordtype}{int}             *k\_max\_values;
 562 00719
 563 00720   \textcolor{keywordtype}{int}             **l\_min\_values\_b;
 564 00721   \textcolor{keywordtype}{int}             **l\_max\_values\_b;
 565 00722   \textcolor{keywordtype}{int}             *k\_min\_values\_b;
 566 00723   \textcolor{keywordtype}{int}             *k\_max\_values\_b;
 567 00724
 568 00725   \textcolor{keywordtype}{int}             **l\_min\_values\_m;
 569 00726   \textcolor{keywordtype}{int}             **l\_max\_values\_m;
 570 00727   \textcolor{keywordtype}{int}             *k\_min\_values\_m;
 571 00728   \textcolor{keywordtype}{int}             *k\_max\_values\_m;
 572 00729
 573 00730   \textcolor{keywordtype}{int}             **l\_min\_values\_m1;
 574 00731   \textcolor{keywordtype}{int}             **l\_max\_values\_m1;
 575 00732   \textcolor{keywordtype}{int}             *k\_min\_values\_m1;
 576 00733   \textcolor{keywordtype}{int}             *k\_max\_values\_m1;
 577 00734
 578 00735   \textcolor{keywordtype}{int}             **l\_min\_values\_m2;
 579 00736   \textcolor{keywordtype}{int}             **l\_max\_values\_m2;
 580 00737   \textcolor{keywordtype}{int}             *k\_min\_values\_m2;
 581 00738   \textcolor{keywordtype}{int}             *k\_max\_values\_m2;
 582 00739
 583 00740   \textcolor{keywordtype}{int}             *l\_min\_values\_qc;
 584 00741   \textcolor{keywordtype}{int}             *l\_max\_values\_qc;
 585 00742   \textcolor{keywordtype}{int}             k\_min\_values\_qc;
 586 00743   \textcolor{keywordtype}{int}             k\_max\_values\_qc;
 587 00744
 588 00745   \textcolor{keywordtype}{int}             *l\_min\_values\_qcH;
 589 00746   \textcolor{keywordtype}{int}             *l\_max\_values\_qcH;
 590 00747   \textcolor{keywordtype}{int}             k\_min\_values\_qcH;
 591 00748   \textcolor{keywordtype}{int}             k\_max\_values\_qcH;
 592 00749
 593 00750   \textcolor{keywordtype}{int}             *l\_min\_values\_qcI;
 594 00751   \textcolor{keywordtype}{int}             *l\_max\_values\_qcI;
 595 00752   \textcolor{keywordtype}{int}             k\_min\_values\_qcI;
 596 00753   \textcolor{keywordtype}{int}             k\_max\_values\_qcI;
 597 00754
 598 00755   \textcolor{keywordtype}{int}             *l\_min\_values\_qcM;
 599 00756   \textcolor{keywordtype}{int}             *l\_max\_values\_qcM;
 600 00757   \textcolor{keywordtype}{int}             k\_min\_values\_qcM;
 601 00758   \textcolor{keywordtype}{int}             k\_max\_values\_qcM;
 602 00759
 603 00760   \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */}
 604 00761   FLT\_OR\_DBL      *Q\_rem;
 605 00762   FLT\_OR\_DBL      *Q\_B\_rem;
 606 00763   FLT\_OR\_DBL      *Q\_M\_rem;
 607 00764   FLT\_OR\_DBL      *Q\_M1\_rem;
 608 00765   FLT\_OR\_DBL      *Q\_M2\_rem;
 609 00766
 610 00767   FLT\_OR\_DBL      Q\_c\_rem;
 611 00768   FLT\_OR\_DBL      Q\_cH\_rem;
 612 00769   FLT\_OR\_DBL      Q\_cI\_rem;
 613 00770   FLT\_OR\_DBL      Q\_cM\_rem;
 614 00771
 615 00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars};
 616 00773
 617 00774 \textcolor{preprocessor}{#endif}
 618 \end{DoxyCode}