binaries/src/ViennaRNA/doc/latex/gquad_8h_source.tex

   1 \hypertarget{gquad_8h}{\section{gquad.\-h}
   2 \label{gquad_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00005
  11 00006 \textcolor{preprocessor}{#ifndef INLINE}
  12 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline}
  14 00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  15 00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE}
  16 00011 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  17 00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  18 00013 \textcolor{preprocessor}{}
  19 00020 \textcolor{keywordtype}{int}         E\_gquad(\textcolor{keywordtype}{int} L,
  20 00021                     \textcolor{keywordtype}{int} l[3],
  21 00022                     \hyperlink{structparamT}{paramT} *P);
  22 00023
  23 00024 FLT\_OR\_DBL exp\_E\_gquad( \textcolor{keywordtype}{int} L,
  24 00025                         \textcolor{keywordtype}{int} l[3],
  25 00026                         \hyperlink{structpf__paramT}{pf\_paramT} *pf);
  26 00027
  27 00028 \textcolor{keywordtype}{int}         E\_gquad\_ali(\textcolor{keywordtype}{int} i,
  28 00029                         \textcolor{keywordtype}{int} L,
  29 00030                         \textcolor{keywordtype}{int} l[3],
  30 00031                         \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S,
  31 00032                         \textcolor{keywordtype}{int} n\_seq,
  32 00033                         \hyperlink{structparamT}{paramT} *P);
  33 00034
  34 00035
  35 00036 \textcolor{keywordtype}{void}        E\_gquad\_ali\_en( \textcolor{keywordtype}{int} i,
  36 00037                             \textcolor{keywordtype}{int} L,
  37 00038                             \textcolor{keywordtype}{int} l[3],
  38 00039                             \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S,
  39 00040                             \textcolor{keywordtype}{int} n\_seq,
  40 00041                             \textcolor{keywordtype}{int} en[2],
  41 00042                             \hyperlink{structparamT}{paramT} *P);
  42 00043
  43 00060 \textcolor{keywordtype}{int}         *\hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\_gquad\_matrix}(\textcolor{keywordtype}{short} *S, \hyperlink{structparamT}{paramT} *P);
  44 00061
  45 00062 \textcolor{keywordtype}{int}         *get\_gquad\_ali\_matrix(\textcolor{keywordtype}{short} *S\_cons,
  46 00063                                   \textcolor{keywordtype}{short} **S,
  47 00064                                   \textcolor{keywordtype}{int} n\_seq,
  48 00065                                   \hyperlink{structparamT}{paramT} *P);
  49 00066
  50 00067 FLT\_OR\_DBL  *get\_gquad\_pf\_matrix( \textcolor{keywordtype}{short} *S,
  51 00068                                   FLT\_OR\_DBL *scale,
  52 00069                                   \hyperlink{structpf__paramT}{pf\_paramT} *pf);
  53 00070
  54 00071 \textcolor{keywordtype}{int}         **get\_gquad\_L\_matrix( \textcolor{keywordtype}{short} *S,
  55 00072                                   \textcolor{keywordtype}{int} start,
  56 00073                                   \textcolor{keywordtype}{int} maxdist,
  57 00074                                   \textcolor{keywordtype}{int} **g,
  58 00075                                   \hyperlink{structparamT}{paramT} *P);
  59 00076
  60 00077 \textcolor{keywordtype}{void}        get\_gquad\_pattern\_mfe(\textcolor{keywordtype}{short} *S,
  61 00078                                   \textcolor{keywordtype}{int} i,
  62 00079                                   \textcolor{keywordtype}{int} j,
  63 00080                                   \hyperlink{structparamT}{paramT} *P,
  64 00081                                   \textcolor{keywordtype}{int} *L,
  65 00082                                   \textcolor{keywordtype}{int} l[3]);
  66 00083
  67 00084 \textcolor{keywordtype}{void}        get\_gquad\_pattern\_pf( \textcolor{keywordtype}{short} *S,
  68 00085                                   \textcolor{keywordtype}{int} i,
  69 00086                                   \textcolor{keywordtype}{int} j,
  70 00087                                   \hyperlink{structpf__paramT}{pf\_paramT} *pf,
  71 00088                                   \textcolor{keywordtype}{int} *L,
  72 00089                                   \textcolor{keywordtype}{int} l[3]);
  73 00090
  74 00091 \hyperlink{structplist}{plist}       *get\_plist\_gquad\_from\_pr( \textcolor{keywordtype}{short} *S,
  75 00092                                       \textcolor{keywordtype}{int} gi,
  76 00093                                       \textcolor{keywordtype}{int} gj,
  77 00094                                       FLT\_OR\_DBL *G,
  78 00095                                       FLT\_OR\_DBL *probs,
  79 00096                                       FLT\_OR\_DBL *scale,
  80 00097                                       \hyperlink{structpf__paramT}{pf\_paramT} *pf);
  81 00098 \hyperlink{structplist}{plist}       *get\_plist\_gquad\_from\_pr\_max(\textcolor{keywordtype}{short} *S,
  82 00099                                       \textcolor{keywordtype}{int} gi,
  83 00100                                       \textcolor{keywordtype}{int} gj,
  84 00101                                       FLT\_OR\_DBL *G,
  85 00102                                       FLT\_OR\_DBL *probs,
  86 00103                                       FLT\_OR\_DBL *scale,
  87 00104                                       \textcolor{keywordtype}{int} *L,
  88 00105                                       \textcolor{keywordtype}{int} l[3],
  89 00106                                       \hyperlink{structpf__paramT}{pf\_paramT} *pf);
  90 00107
  91 00108 \hyperlink{structplist}{plist}       *get\_plist\_gquad\_from\_db( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  92 00109                                       \textcolor{keywordtype}{float} pr);
  93 00110
  94 00121 \textcolor{keywordtype}{int}         \hyperlink{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{parse\_gquad}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc, \textcolor{keywordtype}{int} *L, \textcolor{keywordtype}{int} l[3]);
  95 00122
  96 00123
  97 00124
  98 \hypertarget{gquad_8h_source_l00142}{}\hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{00142} INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{backtrack\_GQuad\_IntLoop}(\textcolor{keywordtype}{int} c,
  99 00143                                             \textcolor{keywordtype}{int} i,
 100 00144                                             \textcolor{keywordtype}{int} j,
 101 00145                                             \textcolor{keywordtype}{int} type,
 102 00146                                             \textcolor{keywordtype}{short} *S,
 103 00147                                             \textcolor{keywordtype}{int} *ggg,
 104 00148                                             \textcolor{keywordtype}{int} *index,
 105 00149                                             \textcolor{keywordtype}{int} *p,
 106 00150                                             \textcolor{keywordtype}{int} *q,
 107 00151                                             \hyperlink{structparamT}{paramT} *P)\{
 108 00152
 109 00153   \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1;
 110 00154   \textcolor{keywordtype}{short} si, sj;
 111 00155
 112 00156   dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
 113 00157   si      = S[i + 1];
 114 00158   sj      = S[j - 1];
 115 00159   energy  = 0;
 116 00160
 117 00161   \textcolor{keywordflow}{if}(dangles == 2)
 118 00162     energy += P->mismatchI[type][si][sj];
 119 00163
 120 00164   \textcolor{keywordflow}{if}(type > 2)
 121 00165     energy += P->TerminalAU;
 122 00166
 123 00167   k = i + 1;
 124 00168   \textcolor{keywordflow}{if}(S[k] == 3)\{
 125 00169     \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 126 00170       minl  = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
 127 00171       c0    = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 128 00172       minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
 129 00173       c0    = j - 3;
 130 00174       maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 131 00175       maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
 132 00176       \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 133 00177         \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 134 00178         \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[j - l - 1])\{
 135 00179           *p = k; *q = l;
 136 00180           \textcolor{keywordflow}{return} 1;
 137 00181         \}
 138 00182       \}
 139 00183     \}
 140 00184   \}
 141 00185
 142 00186   \textcolor{keywordflow}{for}(k = i + 2;
 143 00187       k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 144 00188       k++)\{
 145 00189     l1    = k - i - 1;
 146 00190     \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
 147 00191     \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 148 00192     minl  = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
 149 00193     c0    = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 150 00194     minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
 151 00195     c0    = j - 1;
 152 00196     maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 153 00197     maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
 154 00198     \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 155 00199       \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 156 00200       \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1 + j - l - 1])\{
 157 00201         *p = k; *q = l;
 158 00202         \textcolor{keywordflow}{return} 1;
 159 00203       \}
 160 00204     \}
 161 00205   \}
 162 00206
 163 00207   l = j - 1;
 164 00208   \textcolor{keywordflow}{if}(S[l] == 3)
 165 00209     \textcolor{keywordflow}{for}(k = i + 4;
 166 00210         k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 167 00211         k++)\{
 168 00212       l1    = k - i - 1;
 169 00213       \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
 170 00214       \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 171 00215       \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1])\{
 172 00216         *p = k; *q = l;
 173 00217         \textcolor{keywordflow}{return} 1;
 174 00218       \}
 175 00219     \}
 176 00220
 177 00221   \textcolor{keywordflow}{return} 0;
 178 00222 \}
 179 00223
 180 \hypertarget{gquad_8h_source_l00240}{}\hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{00240} INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{backtrack\_GQuad\_IntLoop\_L}(\textcolor{keywordtype}{int} c,
 181 00241                                               \textcolor{keywordtype}{int} i,
 182 00242                                               \textcolor{keywordtype}{int} j,
 183 00243                                               \textcolor{keywordtype}{int} type,
 184 00244                                               \textcolor{keywordtype}{short} *S,
 185 00245                                               \textcolor{keywordtype}{int} **ggg,
 186 00246                                               \textcolor{keywordtype}{int} maxdist,
 187 00247                                               \textcolor{keywordtype}{int} *p,
 188 00248                                               \textcolor{keywordtype}{int} *q,
 189 00249                                               \hyperlink{structparamT}{paramT} *P)\{
 190 00250
 191 00251   \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1;
 192 00252   \textcolor{keywordtype}{short} si, sj;
 193 00253
 194 00254   dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
 195 00255   si      = S[i + 1];
 196 00256   sj      = S[j - 1];
 197 00257   energy  = 0;
 198 00258
 199 00259   \textcolor{keywordflow}{if}(dangles == 2)
 200 00260     energy += P->mismatchI[type][si][sj];
 201 00261
 202 00262   \textcolor{keywordflow}{if}(type > 2)
 203 00263     energy += P->TerminalAU;
 204 00264
 205 00265   k = i + 1;
 206 00266   \textcolor{keywordflow}{if}(S[k] == 3)\{
 207 00267     \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 208 00268       minl  = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
 209 00269       c0    = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 210 00270       minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
 211 00271       c0    = j - 3;
 212 00272       maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 213 00273       maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
 214 00274       \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 215 00275         \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 216 00276         \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[j - l - 1])\{
 217 00277           *p = k; *q = l;
 218 00278           \textcolor{keywordflow}{return} 1;
 219 00279         \}
 220 00280       \}
 221 00281     \}
 222 00282   \}
 223 00283
 224 00284   \textcolor{keywordflow}{for}(k = i + 2;
 225 00285       k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 226 00286       k++)\{
 227 00287     l1    = k - i - 1;
 228 00288     \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
 229 00289     \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 230 00290     minl  = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
 231 00291     c0    = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 232 00292     minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
 233 00293     c0    = j - 1;
 234 00294     maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 235 00295     maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
 236 00296     \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 237 00297       \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 238 00298       \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1 + j - l - 1])\{
 239 00299         *p = k; *q = l;
 240 00300         \textcolor{keywordflow}{return} 1;
 241 00301       \}
 242 00302     \}
 243 00303   \}
 244 00304
 245 00305   l = j - 1;
 246 00306   \textcolor{keywordflow}{if}(S[l] == 3)
 247 00307     \textcolor{keywordflow}{for}(k = i + 4;
 248 00308         k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 249 00309         k++)\{
 250 00310       l1    = k - i - 1;
 251 00311       \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
 252 00312       \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 253 00313       \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1])\{
 254 00314         *p = k; *q = l;
 255 00315         \textcolor{keywordflow}{return} 1;
 256 00316       \}
 257 00317     \}
 258 00318
 259 00319   \textcolor{keywordflow}{return} 0;
 260 00320 \}
 261 00321
 262 00322 INLINE PRIVATE
 263 00323 \textcolor{keywordtype}{int}
 264 00324 E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i,
 265 00325                 \textcolor{keywordtype}{int} j,
 266 00326                 \textcolor{keywordtype}{int} type,
 267 00327                 \textcolor{keywordtype}{short} *S,
 268 00328                 \textcolor{keywordtype}{int} *ggg,
 269 00329                 \textcolor{keywordtype}{int} *index,
 270 00330                 \hyperlink{structparamT}{paramT} *P)\{
 271 00331
 272 00332   \textcolor{keywordtype}{int} energy, ge, en1, en2, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, p, q, l1, minq, maxq;
 273 00333   \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3;
 274 00334   \textcolor{keywordtype}{short} si, sj;
 275 00335
 276 00336   dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
 277 00337   si      = S[i + 1];
 278 00338   sj      = S[j - 1];
 279 00339   energy  = 0;
 280 00340
 281 00341   \textcolor{keywordflow}{if}(dangles == 2)
 282 00342     energy += P->mismatchI[type][si][sj];
 283 00343
 284 00344   \textcolor{keywordflow}{if}(type > 2)
 285 00345     energy += P->TerminalAU;
 286 00346
 287 00347   ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
 288 00348
 289 00349   p = i + 1;
 290 00350   \textcolor{keywordflow}{if}(S[p] == 3)\{
 291 00351     \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 292 00352       minq  = j - i + p - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
 293 00353       c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 294 00354       minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 295 00355       c0    = j - 3;
 296 00356       maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 297 00357       maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 298 00358       \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 299 00359         \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 300 00360         c0  = energy + ggg[index[q] + p] + P->internal\_loop[j - q - 1];
 301 00361         ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 302 00362       \}
 303 00363     \}
 304 00364   \}
 305 00365
 306 00366   \textcolor{keywordflow}{for}(p = i + 2;
 307 00367       p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 308 00368       p++)\{
 309 00369     l1    = p - i - 1;
 310 00370     \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 311 00371     \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 312 00372     minq  = j - i + p - MAXLOOP - 2;
 313 00373     c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 314 00374     minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 315 00375     c0    = j - 1;
 316 00376     maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 317 00377     maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 318 00378     \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 319 00379       \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 320 00380       c0  = energy + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1];
 321 00381       ge   = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 322 00382     \}
 323 00383   \}
 324 00384
 325 00385   q = j - 1;
 326 00386   \textcolor{keywordflow}{if}(S[q] == 3)
 327 00387     \textcolor{keywordflow}{for}(p = i + 4;
 328 00388         p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 329 00389         p++)\{
 330 00390       l1    = p - i - 1;
 331 00391       \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 332 00392       \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 333 00393       c0  = energy + ggg[index[q] + p] + P->internal\_loop[l1];
 334 00394       ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 335 00395     \}
 336 00396
 337 00397 \textcolor{preprocessor}{#if 0}
 338 00398 \textcolor{preprocessor}{}  \textcolor{comment}{/* here comes the additional stuff for the odd dangle models */}
 339 00399   \textcolor{keywordflow}{if}(dangles % 1)\{
 340 00400     en1 = energy + P->dangle5[type][si];
 341 00401     en2 = energy + P->dangle5[type][sj];
 342 00402     en3 = energy + P->mismatchI[type][si][sj];
 343 00403
 344 00404     \textcolor{comment}{/* first case with 5' dangle (i.e. j-1) onto enclosing pair */}
 345 00405     p = i + 1;
 346 00406     \textcolor{keywordflow}{if}(S[p] == 3)\{
 347 00407       \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 348 00408         minq  = j - i + p - MAXLOOP - 2;
 349 00409         c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 350 00410         minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 351 00411         c0    = j - 4;
 352 00412         maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 353 00413         maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 354 00414         \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 355 00415           \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 356 00416           c0  = en1 + ggg[index[q] + p] + P->internal\_loop[j - q - 1];
 357 00417           ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 358 00418         \}
 359 00419       \}
 360 00420     \}
 361 00421
 362 00422     \textcolor{keywordflow}{for}(p = i + 2; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{
 363 00423       l1    = p - i - 1;
 364 00424       \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 365 00425       \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 366 00426       minq  = j - i + p - MAXLOOP - 2;
 367 00427       c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 368 00428       minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 369 00429       c0    = j - 2;
 370 00430       maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 371 00431       maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 372 00432       \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 373 00433         \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 374 00434         c0  = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1];
 375 00435         ge   = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 376 00436       \}
 377 00437     \}
 378 00438
 379 00439     q = j - 2;
 380 00440     \textcolor{keywordflow}{if}(S[q] == 3)
 381 00441       \textcolor{keywordflow}{for}(p = i + 4; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{
 382 00442         l1    = p - i - 1;
 383 00443         \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 384 00444         \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 385 00445         c0  = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + 1];
 386 00446         ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 387 00447       \}
 388 00448
 389 00449     \textcolor{comment}{/* second case with 3' dangle (i.e. i+1) onto enclosing pair */}
 390 00450
 391 00451   \}
 392 00452 \textcolor{preprocessor}{#endif}
 393 00453 \textcolor{preprocessor}{}  \textcolor{keywordflow}{return} ge;
 394 00454 \}
 395 00455
 396 00456 INLINE PRIVATE
 397 00457 \textcolor{keywordtype}{int}
 398 00458 E\_GQuad\_IntLoop\_L(\textcolor{keywordtype}{int} i,
 399 00459                   \textcolor{keywordtype}{int} j,
 400 00460                   \textcolor{keywordtype}{int} type,
 401 00461                   \textcolor{keywordtype}{short} *S,
 402 00462                   \textcolor{keywordtype}{int} **ggg,
 403 00463                   \textcolor{keywordtype}{int} maxdist,
 404 00464                   \hyperlink{structparamT}{paramT} *P)\{
 405 00465
 406 00466   \textcolor{keywordtype}{int} energy, ge, en1, en2, dangles, p, q, l1, minq, maxq;
 407 00467   \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3;
 408 00468   \textcolor{keywordtype}{short} si, sj;
 409 00469
 410 00470   dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
 411 00471   si      = S[i + 1];
 412 00472   sj      = S[j - 1];
 413 00473   energy  = 0;
 414 00474
 415 00475   \textcolor{keywordflow}{if}(dangles == 2)
 416 00476     energy += P->mismatchI[type][si][sj];
 417 00477
 418 00478   \textcolor{keywordflow}{if}(type > 2)
 419 00479     energy += P->TerminalAU;
 420 00480
 421 00481   ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
 422 00482
 423 00483   p = i + 1;
 424 00484   \textcolor{keywordflow}{if}(S[p] == 3)\{
 425 00485     \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 426 00486       minq  = j - i + p - MAXLOOP - 2;
 427 00487       c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 428 00488       minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 429 00489       c0    = j - 3;
 430 00490       maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 431 00491       maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 432 00492       \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 433 00493         \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 434 00494         c0  = energy + ggg[p][q-p] + P->internal\_loop[j - q - 1];
 435 00495         ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 436 00496       \}
 437 00497     \}
 438 00498   \}
 439 00499
 440 00500   \textcolor{keywordflow}{for}(p = i + 2;
 441 00501       p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 442 00502       p++)\{
 443 00503     l1    = p - i - 1;
 444 00504     \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 445 00505     \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 446 00506     minq  = j - i + p - MAXLOOP - 2;
 447 00507     c0    = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 448 00508     minq  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
 449 00509     c0    = j - 1;
 450 00510     maxq  = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 451 00511     maxq  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
 452 00512     \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
 453 00513       \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
 454 00514       c0  = energy + ggg[p][q - p] + P->internal\_loop[l1 + j - q - 1];
 455 00515       ge   = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 456 00516     \}
 457 00517   \}
 458 00518
 459 00519   q = j - 1;
 460 00520   \textcolor{keywordflow}{if}(S[q] == 3)
 461 00521     \textcolor{keywordflow}{for}(p = i + 4;
 462 00522         p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 463 00523         p++)\{
 464 00524       l1    = p - i - 1;
 465 00525       \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
 466 00526       \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
 467 00527       c0  = energy + ggg[p][q - p] + P->internal\_loop[l1];
 468 00528       ge  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
 469 00529     \}
 470 00530
 471 00531   \textcolor{keywordflow}{return} ge;
 472 00532 \}
 473 00533
 474 00534 INLINE PRIVATE
 475 00535 FLT\_OR\_DBL
 476 00536 exp\_E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i,
 477 00537                     \textcolor{keywordtype}{int} j,
 478 00538                     \textcolor{keywordtype}{int} type,
 479 00539                     \textcolor{keywordtype}{short} *S,
 480 00540                     FLT\_OR\_DBL *G,
 481 00541                     \textcolor{keywordtype}{int} *index,
 482 00542                     \hyperlink{structpf__paramT}{pf\_paramT} *pf)\{
 483 00543
 484 00544   \textcolor{keywordtype}{int} k, l, minl, maxl, u, r;
 485 00545   FLT\_OR\_DBL q, qe, *expintern;
 486 00546   \textcolor{keywordtype}{short} si, sj;
 487 00547
 488 00548   q         = 0;
 489 00549   si        = S[i + 1];
 490 00550   sj        = S[j - 1];
 491 00551   qe        = pf->expmismatchI[type][si][sj];
 492 00552   expintern = pf->expinternal;
 493 00553
 494 00554   \textcolor{keywordflow}{if}(type > 2)
 495 00555     qe *= pf->expTermAU;
 496 00556
 497 00557   k = i + 1;
 498 00558   \textcolor{keywordflow}{if}(S[k] == 3)\{
 499 00559     \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
 500 00560       minl  = j - i + k - MAXLOOP - 2;
 501 00561       u     = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 502 00562       minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(u, minl);
 503 00563       u     = j - 3;
 504 00564       maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 505 00565       maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(u, maxl);
 506 00566       \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 507 00567         \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 508 00568         q += qe * G[index[k]-l] * expintern[j - l - 1];
 509 00569       \}
 510 00570     \}
 511 00571   \}
 512 00572
 513 00573
 514 00574   \textcolor{keywordflow}{for}(k = i + 2;
 515 00575       k <= j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
 516 00576       k++)\{
 517 00577     u = k - i - 1;
 518 00578     \textcolor{keywordflow}{if}(u > MAXLOOP) \textcolor{keywordflow}{break};
 519 00579     \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 520 00580     minl  = j - i + k - MAXLOOP - 2;
 521 00581     r     = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
 522 00582     minl  = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(r, minl);
 523 00583     maxl  = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
 524 00584     r     = j - 1;
 525 00585     maxl  = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(r, maxl);
 526 00586     \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
 527 00587       \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
 528 00588       q += qe * G[index[k]-l] * expintern[u + j - l - 1];
 529 00589     \}
 530 00590   \}
 531 00591
 532 00592   l = j - 1;
 533 00593   \textcolor{keywordflow}{if}(S[l] == 3)
 534 00594     \textcolor{keywordflow}{for}(k = i + 4; k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; k++)\{
 535 00595       u    = k - i - 1;
 536 00596       \textcolor{keywordflow}{if}(u>MAXLOOP) \textcolor{keywordflow}{break};
 537 00597       \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
 538 00598       q += qe * G[index[k]-l] * expintern[u];
 539 00599     \}
 540 00600
 541 00601   \textcolor{keywordflow}{return} q;
 542 00602 \}
 543 00603
 544 00604 \textcolor{preprocessor}{#endif}
 545 \end{DoxyCode}