--- /dev/null
+\hypertarget{gquad_8h}{\section{gquad.\-h}
+\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}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_}
+00003 \textcolor{preprocessor}{}
+00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
+00005
+00006 \textcolor{preprocessor}{#ifndef INLINE}
+00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
+00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline}
+00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
+00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE}
+00011 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00013 \textcolor{preprocessor}{}
+00020 \textcolor{keywordtype}{int} E\_gquad(\textcolor{keywordtype}{int} L,
+00021 \textcolor{keywordtype}{int} l[3],
+00022 \hyperlink{structparamT}{paramT} *P);
+00023
+00024 FLT\_OR\_DBL exp\_E\_gquad( \textcolor{keywordtype}{int} L,
+00025 \textcolor{keywordtype}{int} l[3],
+00026 \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+00027
+00028 \textcolor{keywordtype}{int} E\_gquad\_ali(\textcolor{keywordtype}{int} i,
+00029 \textcolor{keywordtype}{int} L,
+00030 \textcolor{keywordtype}{int} l[3],
+00031 \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S,
+00032 \textcolor{keywordtype}{int} n\_seq,
+00033 \hyperlink{structparamT}{paramT} *P);
+00034
+00035
+00036 \textcolor{keywordtype}{void} E\_gquad\_ali\_en( \textcolor{keywordtype}{int} i,
+00037 \textcolor{keywordtype}{int} L,
+00038 \textcolor{keywordtype}{int} l[3],
+00039 \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S,
+00040 \textcolor{keywordtype}{int} n\_seq,
+00041 \textcolor{keywordtype}{int} en[2],
+00042 \hyperlink{structparamT}{paramT} *P);
+00043
+00060 \textcolor{keywordtype}{int} *\hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\_gquad\_matrix}(\textcolor{keywordtype}{short} *S, \hyperlink{structparamT}{paramT} *P);
+00061
+00062 \textcolor{keywordtype}{int} *get\_gquad\_ali\_matrix(\textcolor{keywordtype}{short} *S\_cons,
+00063 \textcolor{keywordtype}{short} **S,
+00064 \textcolor{keywordtype}{int} n\_seq,
+00065 \hyperlink{structparamT}{paramT} *P);
+00066
+00067 FLT\_OR\_DBL *get\_gquad\_pf\_matrix( \textcolor{keywordtype}{short} *S,
+00068 FLT\_OR\_DBL *scale,
+00069 \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+00070
+00071 \textcolor{keywordtype}{int} **get\_gquad\_L\_matrix( \textcolor{keywordtype}{short} *S,
+00072 \textcolor{keywordtype}{int} start,
+00073 \textcolor{keywordtype}{int} maxdist,
+00074 \textcolor{keywordtype}{int} **g,
+00075 \hyperlink{structparamT}{paramT} *P);
+00076
+00077 \textcolor{keywordtype}{void} get\_gquad\_pattern\_mfe(\textcolor{keywordtype}{short} *S,
+00078 \textcolor{keywordtype}{int} i,
+00079 \textcolor{keywordtype}{int} j,
+00080 \hyperlink{structparamT}{paramT} *P,
+00081 \textcolor{keywordtype}{int} *L,
+00082 \textcolor{keywordtype}{int} l[3]);
+00083
+00084 \textcolor{keywordtype}{void} get\_gquad\_pattern\_pf( \textcolor{keywordtype}{short} *S,
+00085 \textcolor{keywordtype}{int} i,
+00086 \textcolor{keywordtype}{int} j,
+00087 \hyperlink{structpf__paramT}{pf\_paramT} *pf,
+00088 \textcolor{keywordtype}{int} *L,
+00089 \textcolor{keywordtype}{int} l[3]);
+00090
+00091 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_pr( \textcolor{keywordtype}{short} *S,
+00092 \textcolor{keywordtype}{int} gi,
+00093 \textcolor{keywordtype}{int} gj,
+00094 FLT\_OR\_DBL *G,
+00095 FLT\_OR\_DBL *probs,
+00096 FLT\_OR\_DBL *scale,
+00097 \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+00098 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_pr\_max(\textcolor{keywordtype}{short} *S,
+00099 \textcolor{keywordtype}{int} gi,
+00100 \textcolor{keywordtype}{int} gj,
+00101 FLT\_OR\_DBL *G,
+00102 FLT\_OR\_DBL *probs,
+00103 FLT\_OR\_DBL *scale,
+00104 \textcolor{keywordtype}{int} *L,
+00105 \textcolor{keywordtype}{int} l[3],
+00106 \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+00107
+00108 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_db( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
+00109 \textcolor{keywordtype}{float} pr);
+00110
+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]);
+00122
+00123
+00124
+\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,
+00143 \textcolor{keywordtype}{int} i,
+00144 \textcolor{keywordtype}{int} j,
+00145 \textcolor{keywordtype}{int} type,
+00146 \textcolor{keywordtype}{short} *S,
+00147 \textcolor{keywordtype}{int} *ggg,
+00148 \textcolor{keywordtype}{int} *index,
+00149 \textcolor{keywordtype}{int} *p,
+00150 \textcolor{keywordtype}{int} *q,
+00151 \hyperlink{structparamT}{paramT} *P)\{
+00152
+00153 \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1;
+00154 \textcolor{keywordtype}{short} si, sj;
+00155
+00156 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
+00157 si = S[i + 1];
+00158 sj = S[j - 1];
+00159 energy = 0;
+00160
+00161 \textcolor{keywordflow}{if}(dangles == 2)
+00162 energy += P->mismatchI[type][si][sj];
+00163
+00164 \textcolor{keywordflow}{if}(type > 2)
+00165 energy += P->TerminalAU;
+00166
+00167 k = i + 1;
+00168 \textcolor{keywordflow}{if}(S[k] == 3)\{
+00169 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00170 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
+00171 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00172 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
+00173 c0 = j - 3;
+00174 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00175 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
+00176 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00177 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00178 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[j - l - 1])\{
+00179 *p = k; *q = l;
+00180 \textcolor{keywordflow}{return} 1;
+00181 \}
+00182 \}
+00183 \}
+00184 \}
+00185
+00186 \textcolor{keywordflow}{for}(k = i + 2;
+00187 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00188 k++)\{
+00189 l1 = k - i - 1;
+00190 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
+00191 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00192 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
+00193 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00194 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
+00195 c0 = j - 1;
+00196 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00197 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
+00198 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00199 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00200 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1 + j - l - 1])\{
+00201 *p = k; *q = l;
+00202 \textcolor{keywordflow}{return} 1;
+00203 \}
+00204 \}
+00205 \}
+00206
+00207 l = j - 1;
+00208 \textcolor{keywordflow}{if}(S[l] == 3)
+00209 \textcolor{keywordflow}{for}(k = i + 4;
+00210 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00211 k++)\{
+00212 l1 = k - i - 1;
+00213 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
+00214 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00215 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1])\{
+00216 *p = k; *q = l;
+00217 \textcolor{keywordflow}{return} 1;
+00218 \}
+00219 \}
+00220
+00221 \textcolor{keywordflow}{return} 0;
+00222 \}
+00223
+\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,
+00241 \textcolor{keywordtype}{int} i,
+00242 \textcolor{keywordtype}{int} j,
+00243 \textcolor{keywordtype}{int} type,
+00244 \textcolor{keywordtype}{short} *S,
+00245 \textcolor{keywordtype}{int} **ggg,
+00246 \textcolor{keywordtype}{int} maxdist,
+00247 \textcolor{keywordtype}{int} *p,
+00248 \textcolor{keywordtype}{int} *q,
+00249 \hyperlink{structparamT}{paramT} *P)\{
+00250
+00251 \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1;
+00252 \textcolor{keywordtype}{short} si, sj;
+00253
+00254 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
+00255 si = S[i + 1];
+00256 sj = S[j - 1];
+00257 energy = 0;
+00258
+00259 \textcolor{keywordflow}{if}(dangles == 2)
+00260 energy += P->mismatchI[type][si][sj];
+00261
+00262 \textcolor{keywordflow}{if}(type > 2)
+00263 energy += P->TerminalAU;
+00264
+00265 k = i + 1;
+00266 \textcolor{keywordflow}{if}(S[k] == 3)\{
+00267 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00268 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
+00269 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00270 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
+00271 c0 = j - 3;
+00272 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00273 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
+00274 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00275 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00276 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[j - l - 1])\{
+00277 *p = k; *q = l;
+00278 \textcolor{keywordflow}{return} 1;
+00279 \}
+00280 \}
+00281 \}
+00282 \}
+00283
+00284 \textcolor{keywordflow}{for}(k = i + 2;
+00285 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00286 k++)\{
+00287 l1 = k - i - 1;
+00288 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
+00289 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00290 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
+00291 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00292 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl);
+00293 c0 = j - 1;
+00294 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00295 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl);
+00296 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00297 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00298 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1 + j - l - 1])\{
+00299 *p = k; *q = l;
+00300 \textcolor{keywordflow}{return} 1;
+00301 \}
+00302 \}
+00303 \}
+00304
+00305 l = j - 1;
+00306 \textcolor{keywordflow}{if}(S[l] == 3)
+00307 \textcolor{keywordflow}{for}(k = i + 4;
+00308 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00309 k++)\{
+00310 l1 = k - i - 1;
+00311 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break};
+00312 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00313 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1])\{
+00314 *p = k; *q = l;
+00315 \textcolor{keywordflow}{return} 1;
+00316 \}
+00317 \}
+00318
+00319 \textcolor{keywordflow}{return} 0;
+00320 \}
+00321
+00322 INLINE PRIVATE
+00323 \textcolor{keywordtype}{int}
+00324 E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i,
+00325 \textcolor{keywordtype}{int} j,
+00326 \textcolor{keywordtype}{int} type,
+00327 \textcolor{keywordtype}{short} *S,
+00328 \textcolor{keywordtype}{int} *ggg,
+00329 \textcolor{keywordtype}{int} *index,
+00330 \hyperlink{structparamT}{paramT} *P)\{
+00331
+00332 \textcolor{keywordtype}{int} energy, ge, en1, en2, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, p, q, l1, minq, maxq;
+00333 \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3;
+00334 \textcolor{keywordtype}{short} si, sj;
+00335
+00336 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
+00337 si = S[i + 1];
+00338 sj = S[j - 1];
+00339 energy = 0;
+00340
+00341 \textcolor{keywordflow}{if}(dangles == 2)
+00342 energy += P->mismatchI[type][si][sj];
+00343
+00344 \textcolor{keywordflow}{if}(type > 2)
+00345 energy += P->TerminalAU;
+00346
+00347 ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
+00348
+00349 p = i + 1;
+00350 \textcolor{keywordflow}{if}(S[p] == 3)\{
+00351 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00352 minq = j - i + p - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2;
+00353 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00354 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00355 c0 = j - 3;
+00356 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00357 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00358 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00359 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00360 c0 = energy + ggg[index[q] + p] + P->internal\_loop[j - q - 1];
+00361 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00362 \}
+00363 \}
+00364 \}
+00365
+00366 \textcolor{keywordflow}{for}(p = i + 2;
+00367 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00368 p++)\{
+00369 l1 = p - i - 1;
+00370 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00371 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00372 minq = j - i + p - MAXLOOP - 2;
+00373 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00374 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00375 c0 = j - 1;
+00376 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00377 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00378 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00379 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00380 c0 = energy + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1];
+00381 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00382 \}
+00383 \}
+00384
+00385 q = j - 1;
+00386 \textcolor{keywordflow}{if}(S[q] == 3)
+00387 \textcolor{keywordflow}{for}(p = i + 4;
+00388 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00389 p++)\{
+00390 l1 = p - i - 1;
+00391 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00392 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00393 c0 = energy + ggg[index[q] + p] + P->internal\_loop[l1];
+00394 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00395 \}
+00396
+00397 \textcolor{preprocessor}{#if 0}
+00398 \textcolor{preprocessor}{} \textcolor{comment}{/* here comes the additional stuff for the odd dangle models */}
+00399 \textcolor{keywordflow}{if}(dangles % 1)\{
+00400 en1 = energy + P->dangle5[type][si];
+00401 en2 = energy + P->dangle5[type][sj];
+00402 en3 = energy + P->mismatchI[type][si][sj];
+00403
+00404 \textcolor{comment}{/* first case with 5' dangle (i.e. j-1) onto enclosing pair */}
+00405 p = i + 1;
+00406 \textcolor{keywordflow}{if}(S[p] == 3)\{
+00407 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00408 minq = j - i + p - MAXLOOP - 2;
+00409 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00410 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00411 c0 = j - 4;
+00412 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00413 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00414 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00415 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00416 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[j - q - 1];
+00417 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00418 \}
+00419 \}
+00420 \}
+00421
+00422 \textcolor{keywordflow}{for}(p = i + 2; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{
+00423 l1 = p - i - 1;
+00424 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00425 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00426 minq = j - i + p - MAXLOOP - 2;
+00427 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00428 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00429 c0 = j - 2;
+00430 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00431 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00432 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00433 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00434 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1];
+00435 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00436 \}
+00437 \}
+00438
+00439 q = j - 2;
+00440 \textcolor{keywordflow}{if}(S[q] == 3)
+00441 \textcolor{keywordflow}{for}(p = i + 4; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{
+00442 l1 = p - i - 1;
+00443 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00444 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00445 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + 1];
+00446 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00447 \}
+00448
+00449 \textcolor{comment}{/* second case with 3' dangle (i.e. i+1) onto enclosing pair */}
+00450
+00451 \}
+00452 \textcolor{preprocessor}{#endif}
+00453 \textcolor{preprocessor}{} \textcolor{keywordflow}{return} ge;
+00454 \}
+00455
+00456 INLINE PRIVATE
+00457 \textcolor{keywordtype}{int}
+00458 E\_GQuad\_IntLoop\_L(\textcolor{keywordtype}{int} i,
+00459 \textcolor{keywordtype}{int} j,
+00460 \textcolor{keywordtype}{int} type,
+00461 \textcolor{keywordtype}{short} *S,
+00462 \textcolor{keywordtype}{int} **ggg,
+00463 \textcolor{keywordtype}{int} maxdist,
+00464 \hyperlink{structparamT}{paramT} *P)\{
+00465
+00466 \textcolor{keywordtype}{int} energy, ge, en1, en2, dangles, p, q, l1, minq, maxq;
+00467 \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3;
+00468 \textcolor{keywordtype}{short} si, sj;
+00469
+00470 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles};
+00471 si = S[i + 1];
+00472 sj = S[j - 1];
+00473 energy = 0;
+00474
+00475 \textcolor{keywordflow}{if}(dangles == 2)
+00476 energy += P->mismatchI[type][si][sj];
+00477
+00478 \textcolor{keywordflow}{if}(type > 2)
+00479 energy += P->TerminalAU;
+00480
+00481 ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
+00482
+00483 p = i + 1;
+00484 \textcolor{keywordflow}{if}(S[p] == 3)\{
+00485 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00486 minq = j - i + p - MAXLOOP - 2;
+00487 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00488 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00489 c0 = j - 3;
+00490 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00491 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00492 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00493 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00494 c0 = energy + ggg[p][q-p] + P->internal\_loop[j - q - 1];
+00495 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00496 \}
+00497 \}
+00498 \}
+00499
+00500 \textcolor{keywordflow}{for}(p = i + 2;
+00501 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00502 p++)\{
+00503 l1 = p - i - 1;
+00504 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00505 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00506 minq = j - i + p - MAXLOOP - 2;
+00507 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00508 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq);
+00509 c0 = j - 1;
+00510 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00511 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq);
+00512 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{
+00513 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue};
+00514 c0 = energy + ggg[p][q - p] + P->internal\_loop[l1 + j - q - 1];
+00515 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00516 \}
+00517 \}
+00518
+00519 q = j - 1;
+00520 \textcolor{keywordflow}{if}(S[q] == 3)
+00521 \textcolor{keywordflow}{for}(p = i + 4;
+00522 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00523 p++)\{
+00524 l1 = p - i - 1;
+00525 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break};
+00526 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue};
+00527 c0 = energy + ggg[p][q - p] + P->internal\_loop[l1];
+00528 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0);
+00529 \}
+00530
+00531 \textcolor{keywordflow}{return} ge;
+00532 \}
+00533
+00534 INLINE PRIVATE
+00535 FLT\_OR\_DBL
+00536 exp\_E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i,
+00537 \textcolor{keywordtype}{int} j,
+00538 \textcolor{keywordtype}{int} type,
+00539 \textcolor{keywordtype}{short} *S,
+00540 FLT\_OR\_DBL *G,
+00541 \textcolor{keywordtype}{int} *index,
+00542 \hyperlink{structpf__paramT}{pf\_paramT} *pf)\{
+00543
+00544 \textcolor{keywordtype}{int} k, l, minl, maxl, u, r;
+00545 FLT\_OR\_DBL q, qe, *expintern;
+00546 \textcolor{keywordtype}{short} si, sj;
+00547
+00548 q = 0;
+00549 si = S[i + 1];
+00550 sj = S[j - 1];
+00551 qe = pf->expmismatchI[type][si][sj];
+00552 expintern = pf->expinternal;
+00553
+00554 \textcolor{keywordflow}{if}(type > 2)
+00555 qe *= pf->expTermAU;
+00556
+00557 k = i + 1;
+00558 \textcolor{keywordflow}{if}(S[k] == 3)\{
+00559 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{
+00560 minl = j - i + k - MAXLOOP - 2;
+00561 u = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00562 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(u, minl);
+00563 u = j - 3;
+00564 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00565 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(u, maxl);
+00566 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00567 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00568 q += qe * G[index[k]-l] * expintern[j - l - 1];
+00569 \}
+00570 \}
+00571 \}
+00572
+00573
+00574 \textcolor{keywordflow}{for}(k = i + 2;
+00575 k <= j - VRNA\_GQUAD\_MIN\_BOX\_SIZE;
+00576 k++)\{
+00577 u = k - i - 1;
+00578 \textcolor{keywordflow}{if}(u > MAXLOOP) \textcolor{keywordflow}{break};
+00579 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00580 minl = j - i + k - MAXLOOP - 2;
+00581 r = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1;
+00582 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(r, minl);
+00583 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1;
+00584 r = j - 1;
+00585 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(r, maxl);
+00586 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{
+00587 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue};
+00588 q += qe * G[index[k]-l] * expintern[u + j - l - 1];
+00589 \}
+00590 \}
+00591
+00592 l = j - 1;
+00593 \textcolor{keywordflow}{if}(S[l] == 3)
+00594 \textcolor{keywordflow}{for}(k = i + 4; k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; k++)\{
+00595 u = k - i - 1;
+00596 \textcolor{keywordflow}{if}(u>MAXLOOP) \textcolor{keywordflow}{break};
+00597 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue};
+00598 q += qe * G[index[k]-l] * expintern[u];
+00599 \}
+00600
+00601 \textcolor{keywordflow}{return} q;
+00602 \}
+00603
+00604 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff