\hypertarget{data__structures_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\-structures.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy_const.h}"}
00010 \textcolor{comment}{/* to use floats instead of doubles in pf\_fold() comment next line */}
00011 \textcolor{preprocessor}{#define LARGE\_PF}
00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef  LARGE\_PF}
00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL double}
00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL float}
00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00017 \textcolor{preprocessor}{}
00018 \textcolor{preprocessor}{#ifndef NBASES}
00019 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBASES 8}
00020 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00021 \textcolor{preprocessor}{}
00022 \textcolor{preprocessor}{#ifndef MAXALPHA}
00023 \textcolor{preprocessor}{}
\hypertarget{data__structures_8h_source_l00026}{}\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{00026} \textcolor{preprocessor}{#define MAXALPHA              20}
00027 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00028 \textcolor{preprocessor}{}
\hypertarget{data__structures_8h_source_l00032}{}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{00032} \textcolor{preprocessor}{#define MAXDOS                1000}
00033 \textcolor{preprocessor}{}
00034 \textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_STACK\_SIZE     7}
00035 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_STACK\_SIZE     2}
00036 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_LINKER\_LENGTH  15}
00037 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_LINKER\_LENGTH  1}
00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MIN\_BOX\_SIZE       ((4*VRNA\_GQUAD\_MIN\_STACK\_SIZE)+(3*VRNA\_GQ
      UAD\_MIN\_LINKER\_LENGTH))}
00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define   VRNA\_GQUAD\_MAX\_BOX\_SIZE       ((4*VRNA\_GQUAD\_MAX\_STACK\_SIZE)+(3*VRNA\_GQ
      UAD\_MAX\_LINKER\_LENGTH))}
00040 \textcolor{preprocessor}{}
00041 
00042 \textcolor{comment}{/*}
00043 \textcolor{comment}{* ############################################################}
00044 \textcolor{comment}{* Here are the type definitions of various datastructures}
00045 \textcolor{comment}{* shared among the Vienna RNA Package}
00046 \textcolor{comment}{* ############################################################}
00047 \textcolor{comment}{*/}
00048 
\hypertarget{data__structures_8h_source_l00052}{}\hyperlink{structplist}{00052} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structplist}{plist} \{
00053   \textcolor{keywordtype}{int} i;
00054   \textcolor{keywordtype}{int} j;
00055   \textcolor{keywordtype}{float} p;
00056   \textcolor{keywordtype}{int} type;
00057 \} \hyperlink{structplist}{plist};
00058 
\hypertarget{data__structures_8h_source_l00062}{}\hyperlink{structcpair}{00062} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcpair}{cpair} \{
00063   \textcolor{keywordtype}{int} i,j,mfe;
00064   \textcolor{keywordtype}{float} p, hue, sat;
00065 \} \hyperlink{structcpair}{cpair};
00066 
\hypertarget{data__structures_8h_source_l00071}{}\hyperlink{structCOORDINATE}{00071} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
00072   \textcolor{keywordtype}{float} X; \textcolor{comment}{/* X coords */}
00073   \textcolor{keywordtype}{float} Y; \textcolor{comment}{/* Y coords */}
00074 \} \hyperlink{structCOORDINATE}{COORDINATE};
00075 
\hypertarget{data__structures_8h_source_l00079}{}\hyperlink{structsect}{00079} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structsect}{sect} \{
00080   \textcolor{keywordtype}{int}  i;
00081   \textcolor{keywordtype}{int}  j;
00082   \textcolor{keywordtype}{int} ml;
00083 \} \hyperlink{structsect}{sect};
00084 
\hypertarget{data__structures_8h_source_l00088}{}\hyperlink{structbondT}{00088} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondT}{bondT} \{
00089    \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i;
00090    \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} j;
00091 \} \hyperlink{structbondT}{bondT};
00092 
\hypertarget{data__structures_8h_source_l00096}{}\hyperlink{structbondTEn}{00096} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondTEn}{bondTEn} \{
00097    \textcolor{keywordtype}{int} i;
00098    \textcolor{keywordtype}{int} j;
00099    \textcolor{keywordtype}{int} energy;
00100 \} \hyperlink{structbondTEn}{bondTEn};
00101 
\hypertarget{data__structures_8h_source_l00106}{}\hyperlink{structmodel__detailsT}{00106} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
\hypertarget{data__structures_8h_source_l00107}{}\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{00107}   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};      
\hypertarget{data__structures_8h_source_l00113}{}\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{00113}   \textcolor{keywordtype}{int}     special\_hp;   
\hypertarget{data__structures_8h_source_l00114}{}\hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{00114}   \textcolor{keywordtype}{int}     noLP;         
\hypertarget{data__structures_8h_source_l00115}{}\hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{00115}   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{noGU};         
\hypertarget{data__structures_8h_source_l00116}{}\hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{00116}   \textcolor{keywordtype}{int}     noGUclosure;  
\hypertarget{data__structures_8h_source_l00117}{}\hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{00117}   \textcolor{keywordtype}{int}     \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML};        
\hypertarget{data__structures_8h_source_l00118}{}\hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{00118}   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};         
\hypertarget{data__structures_8h_source_l00119}{}\hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{00119}   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad};        
00120 \} \hyperlink{structmodel__detailsT}{model_detailsT};
00121 
\hypertarget{data__structures_8h_source_l00125}{}\hyperlink{structparamT}{00125} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00126   \textcolor{keywordtype}{int} id;
00127   \textcolor{keywordtype}{int} stack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
00128   \textcolor{keywordtype}{int} hairpin[31];
00129   \textcolor{keywordtype}{int} bulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
00130   \textcolor{keywordtype}{int} internal\_loop[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
00131   \textcolor{keywordtype}{int} mismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00132   \textcolor{keywordtype}{int} mismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00133   \textcolor{keywordtype}{int} mismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00134   \textcolor{keywordtype}{int} mismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00135   \textcolor{keywordtype}{int} mismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00136   \textcolor{keywordtype}{int} mismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00137   \textcolor{keywordtype}{int} dangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
00138   \textcolor{keywordtype}{int} dangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
00139   \textcolor{keywordtype}{int} int11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00140   \textcolor{keywordtype}{int} int21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
00141   \textcolor{keywordtype}{int} int22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
00142   \textcolor{keywordtype}{int} ninio[5];
00143   \textcolor{keywordtype}{double}  lxc;
00144   \textcolor{keywordtype}{int}     MLbase;
00145   \textcolor{keywordtype}{int}     MLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
00146   \textcolor{keywordtype}{int}     MLclosing;
00147   \textcolor{keywordtype}{int}     TerminalAU;
00148   \textcolor{keywordtype}{int}     DuplexInit;
00149   \textcolor{keywordtype}{int}     Tetraloop\_E[200];
00150   \textcolor{keywordtype}{char}    Tetraloops[1401];
00151   \textcolor{keywordtype}{int}     Triloop\_E[40];
00152   \textcolor{keywordtype}{char}    Triloops[241];
00153   \textcolor{keywordtype}{int}     Hexaloop\_E[40];
00154   \textcolor{keywordtype}{char}    Hexaloops[1801];
00155   \textcolor{keywordtype}{int}     TripleC;
00156   \textcolor{keywordtype}{int}     MultipleCA;
00157   \textcolor{keywordtype}{int}     MultipleCB;
00158   \textcolor{keywordtype}{int}     \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad} [VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
00159                 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
00160 
\hypertarget{data__structures_8h_source_l00161}{}\hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{00161}   \textcolor{keywordtype}{double}  \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};            
\hypertarget{data__structures_8h_source_l00163}{}\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{00163}   \hyperlink{structmodel__detailsT}{model_detailsT} model\_details;   
00165 \}  \hyperlink{structparamT}{paramT};
00166 
\hypertarget{data__structures_8h_source_l00170}{}\hyperlink{structpf__paramT}{00170} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00171   \textcolor{keywordtype}{int}     id;
00172   \textcolor{keywordtype}{double}  expstack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
00173   \textcolor{keywordtype}{double}  exphairpin[31];
00174   \textcolor{keywordtype}{double}  expbulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
00175   \textcolor{keywordtype}{double}  expinternal[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
00176   \textcolor{keywordtype}{double}  expmismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00177   \textcolor{keywordtype}{double}  expmismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00178   \textcolor{keywordtype}{double}  expmismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00179   \textcolor{keywordtype}{double}  expmismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00180   \textcolor{keywordtype}{double}  expmismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00181   \textcolor{keywordtype}{double}  expmismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00182   \textcolor{keywordtype}{double}  expdangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
00183   \textcolor{keywordtype}{double}  expdangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
00184   \textcolor{keywordtype}{double}  expint11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00185   \textcolor{keywordtype}{double}  expint21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
00186   \textcolor{keywordtype}{double}  expint22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
00187   \textcolor{keywordtype}{double}  expninio[5][\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1];
00188   \textcolor{keywordtype}{double}  lxc;
00189   \textcolor{keywordtype}{double}  expMLbase;
00190   \textcolor{keywordtype}{double}  expMLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
00191   \textcolor{keywordtype}{double}  expMLclosing;
00192   \textcolor{keywordtype}{double}  expTermAU;
00193   \textcolor{keywordtype}{double}  expDuplexInit;
00194   \textcolor{keywordtype}{double}  exptetra[40];
00195   \textcolor{keywordtype}{double}  exptri[40];
00196   \textcolor{keywordtype}{double}  exphex[40];
00197   \textcolor{keywordtype}{char}    Tetraloops[1401];
00198   \textcolor{keywordtype}{double}  expTriloop[40];
00199   \textcolor{keywordtype}{char}    Triloops[241];
00200   \textcolor{keywordtype}{char}    Hexaloops[1801];
00201   \textcolor{keywordtype}{double}  expTripleC;
00202   \textcolor{keywordtype}{double}  expMultipleCA;
00203   \textcolor{keywordtype}{double}  expMultipleCB;
00204   \textcolor{keywordtype}{double}  expgquad[VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1]
00205                   [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1];
00206 
00207   \textcolor{keywordtype}{double}  kT;
\hypertarget{data__structures_8h_source_l00208}{}\hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{00208}   \textcolor{keywordtype}{double}  \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf_scale};     
\hypertarget{data__structures_8h_source_l00210}{}\hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{00210}   \textcolor{keywordtype}{double}  \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};  
\hypertarget{data__structures_8h_source_l00211}{}\hyperlink{structpf__paramT_a3d2af9040acfa08295efb50f0219149d}{00211}   \textcolor{keywordtype}{double}  alpha;        
\hypertarget{data__structures_8h_source_l00218}{}\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{00218}   \hyperlink{structmodel__detailsT}{model_detailsT} model\_details; 
00220 \}  \hyperlink{structpf__paramT}{pf_paramT};
00221 
00222 
00223 
00224 \textcolor{comment}{/*}
00225 \textcolor{comment}{* ############################################################}
00226 \textcolor{comment}{* SUBOPT data structures}
00227 \textcolor{comment}{* ############################################################}
00228 \textcolor{comment}{*/}
00229 
00230 
\hypertarget{data__structures_8h_source_l00234}{}\hyperlink{structPAIR}{00234} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
00235   \textcolor{keywordtype}{int} i;
00236   \textcolor{keywordtype}{int} j;
00237 \} \hyperlink{structPAIR}{PAIR};
00238 
\hypertarget{data__structures_8h_source_l00242}{}\hyperlink{structINTERVAL}{00242} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
00243     \textcolor{keywordtype}{int} i;
00244     \textcolor{keywordtype}{int} j;
00245     \textcolor{keywordtype}{int} array\_flag;
00246 \} \hyperlink{structINTERVAL}{INTERVAL};
00247 
\hypertarget{data__structures_8h_source_l00251}{}\hyperlink{structSOLUTION}{00251} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
\hypertarget{data__structures_8h_source_l00252}{}\hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{00252}   \textcolor{keywordtype}{float} energy;       
\hypertarget{data__structures_8h_source_l00253}{}\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{00253}   \textcolor{keywordtype}{char} *structure;    
00254 \} \hyperlink{structSOLUTION}{SOLUTION};
00255 
00256 \textcolor{comment}{/*}
00257 \textcolor{comment}{* ############################################################}
00258 \textcolor{comment}{* COFOLD data structures}
00259 \textcolor{comment}{* ############################################################}
00260 \textcolor{comment}{*/}
00261 
\hypertarget{data__structures_8h_source_l00265}{}\hyperlink{structcofoldF}{00265} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcofoldF}{cofoldF} \{
00266   \textcolor{comment}{/* free energies for: */}
\hypertarget{data__structures_8h_source_l00267}{}\hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{00267}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{F0AB};  
\hypertarget{data__structures_8h_source_l00268}{}\hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{00268}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{FAB};   
\hypertarget{data__structures_8h_source_l00269}{}\hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{00269}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{FcAB};  
\hypertarget{data__structures_8h_source_l00270}{}\hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{00270}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{FA};    
\hypertarget{data__structures_8h_source_l00271}{}\hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{00271}   \textcolor{keywordtype}{double} \hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{FB};    
00272 \} \hyperlink{structcofoldF}{cofoldF};
00273 
\hypertarget{data__structures_8h_source_l00277}{}\hyperlink{structConcEnt}{00277} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structConcEnt}{ConcEnt} \{
\hypertarget{data__structures_8h_source_l00278}{}\hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{00278}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{A0};    
\hypertarget{data__structures_8h_source_l00279}{}\hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{00279}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{B0};    
\hypertarget{data__structures_8h_source_l00280}{}\hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{00280}   \textcolor{keywordtype}{double} \hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{ABc};   
00281   \textcolor{keywordtype}{double} AAc;
00282   \textcolor{keywordtype}{double} BBc;
00283   \textcolor{keywordtype}{double} Ac;
00284   \textcolor{keywordtype}{double} Bc;
00285 \} \hyperlink{structConcEnt}{ConcEnt};
00286 
\hypertarget{data__structures_8h_source_l00290}{}\hyperlink{structpairpro}{00290} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpairpro}{pairpro}\{
00291   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AB;
00292   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AA;
00293   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *A;
00294   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *B;
00295   \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *BB;
00296 \}\hyperlink{structpairpro}{pairpro};
00297 
\hypertarget{data__structures_8h_source_l00308}{}\hyperlink{structpair__info}{00308} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
\hypertarget{data__structures_8h_source_l00309}{}\hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{00309}    \textcolor{keywordtype}{unsigned} i;    
\hypertarget{data__structures_8h_source_l00310}{}\hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{00310}    \textcolor{keywordtype}{unsigned} j;    
\hypertarget{data__structures_8h_source_l00311}{}\hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{00311}    \textcolor{keywordtype}{float} p;       
\hypertarget{data__structures_8h_source_l00312}{}\hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{00312}    \textcolor{keywordtype}{float} ent;     
\hypertarget{data__structures_8h_source_l00313}{}\hyperlink{structpair__info_a23fc316453d179474bed7f6ed2489723}{00313}    \textcolor{keywordtype}{short} bp[8];   
\hypertarget{data__structures_8h_source_l00314}{}\hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{00314}    \textcolor{keywordtype}{char} comp;     
00315 \} \hyperlink{structpair__info}{pair_info};
00316 
00317 
00318 \textcolor{comment}{/*}
00319 \textcolor{comment}{* ############################################################}
00320 \textcolor{comment}{* FINDPATH data structures}
00321 \textcolor{comment}{* ############################################################}
00322 \textcolor{comment}{*/}
00323 
\hypertarget{data__structures_8h_source_l00327}{}\hyperlink{structmove__t}{00327} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }move \{
00328   \textcolor{keywordtype}{int} i;  \textcolor{comment}{/* i,j>0 insert; i,j<0 delete */}
00329   \textcolor{keywordtype}{int} j;
00330   \textcolor{keywordtype}{int} when;  \textcolor{comment}{/* 0 if still available, else resulting distance from start */}
00331   \textcolor{keywordtype}{int} E;
00332 \} \hyperlink{structmove__t}{move_t};
00333 
\hypertarget{data__structures_8h_source_l00337}{}\hyperlink{structintermediate__t}{00337} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }intermediate \{
\hypertarget{data__structures_8h_source_l00338}{}\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{00338}   \textcolor{keywordtype}{short} *pt;      
\hypertarget{data__structures_8h_source_l00339}{}\hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{00339}   \textcolor{keywordtype}{int} Sen;        
\hypertarget{data__structures_8h_source_l00340}{}\hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{00340}   \textcolor{keywordtype}{int} curr\_en;    
\hypertarget{data__structures_8h_source_l00341}{}\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{00341}   \hyperlink{structmove__t}{move_t} *moves;  
00342 \} \hyperlink{structintermediate__t}{intermediate_t};
00343 
\hypertarget{data__structures_8h_source_l00347}{}\hyperlink{structpath__t}{00347} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }path \{
00348   \textcolor{keywordtype}{double} en;
00349   \textcolor{keywordtype}{char} *s;
00350 \} \hyperlink{structpath__t}{path_t};
00351 
00352 \textcolor{comment}{/*}
00353 \textcolor{comment}{* ############################################################}
00354 \textcolor{comment}{* RNAup data structures}
00355 \textcolor{comment}{* ############################################################}
00356 \textcolor{comment}{*/}
00357 
\hypertarget{data__structures_8h_source_l00361}{}\hyperlink{structpu__contrib}{00361} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__contrib}{pu_contrib} \{
\hypertarget{data__structures_8h_source_l00362}{}\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{00362}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{H}; 
\hypertarget{data__structures_8h_source_l00363}{}\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{00363}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{I}; 
\hypertarget{data__structures_8h_source_l00364}{}\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{00364}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{M}; 
\hypertarget{data__structures_8h_source_l00365}{}\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{00365}   \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{E}; 
\hypertarget{data__structures_8h_source_l00366}{}\hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{00366}   \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{length}; 
\hypertarget{data__structures_8h_source_l00367}{}\hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{00367}   \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{w};      
00368 \} \hyperlink{structpu__contrib}{pu_contrib};
00369 
\hypertarget{data__structures_8h_source_l00373}{}\hyperlink{structinteract}{00373} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structinteract}{interact} \{
\hypertarget{data__structures_8h_source_l00374}{}\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{00374}   \textcolor{keywordtype}{double} *\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{Pi};       
\hypertarget{data__structures_8h_source_l00375}{}\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{00375}   \textcolor{keywordtype}{double} *\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{Gi};       
\hypertarget{data__structures_8h_source_l00376}{}\hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{00376}   \textcolor{keywordtype}{double} \hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{Gikjl};     
\hypertarget{data__structures_8h_source_l00378}{}\hyperlink{structinteract_a41793812abae560805414761fec398fe}{00378}   \textcolor{keywordtype}{double} \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl_wo};  
\hypertarget{data__structures_8h_source_l00379}{}\hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{00379}   \textcolor{keywordtype}{int} \hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{i};            
\hypertarget{data__structures_8h_source_l00380}{}\hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{00380}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{k};            
\hypertarget{data__structures_8h_source_l00381}{}\hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{00381}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{j};            
\hypertarget{data__structures_8h_source_l00382}{}\hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{00382}   \textcolor{keywordtype}{int} \hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{l};            
\hypertarget{data__structures_8h_source_l00383}{}\hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{00383}   \textcolor{keywordtype}{int} \hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{length};       
00384 \} \hyperlink{structinteract}{interact};
00385 
\hypertarget{data__structures_8h_source_l00389}{}\hyperlink{structpu__out}{00389} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__out}{pu_out} \{
\hypertarget{data__structures_8h_source_l00390}{}\hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{00390}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{len};            
\hypertarget{data__structures_8h_source_l00391}{}\hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{00391}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u_vals};         
\hypertarget{data__structures_8h_source_l00392}{}\hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{00392}   \textcolor{keywordtype}{int} \hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{contribs};       
\hypertarget{data__structures_8h_source_l00393}{}\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{00393}   \textcolor{keywordtype}{char} **\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{header};      
\hypertarget{data__structures_8h_source_l00394}{}\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{00394}   \textcolor{keywordtype}{double} **\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u_values};  
00395 \} \hyperlink{structpu__out}{pu_out};
00396 
\hypertarget{data__structures_8h_source_l00400}{}\hyperlink{structconstrain}{00400} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structconstrain}{constrain}\{
00401   \textcolor{keywordtype}{int} *indx;
00402   \textcolor{keywordtype}{char} *ptype;
00403 \} \hyperlink{structconstrain}{constrain};
00404 
00405 \textcolor{comment}{/*}
00406 \textcolor{comment}{* ############################################################}
00407 \textcolor{comment}{* RNAduplex data structures}
00408 \textcolor{comment}{* ############################################################}
00409 \textcolor{comment}{*/}
00410 
\hypertarget{data__structures_8h_source_l00414}{}\hyperlink{structduplexT}{00414} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
00415   \textcolor{keywordtype}{int} i;
00416   \textcolor{keywordtype}{int} j;
00417   \textcolor{keywordtype}{int} end;
00418   \textcolor{keywordtype}{char} *structure;
00419   \textcolor{keywordtype}{double} energy;
00420   \textcolor{keywordtype}{double} energy\_backtrack;
00421   \textcolor{keywordtype}{double} opening\_backtrack\_x;
00422   \textcolor{keywordtype}{double} opening\_backtrack\_y;
00423   \textcolor{keywordtype}{int} offset;
00424   \textcolor{keywordtype}{double} dG1;
00425   \textcolor{keywordtype}{double} dG2;
00426   \textcolor{keywordtype}{double} ddG;
00427   \textcolor{keywordtype}{int} tb;
00428   \textcolor{keywordtype}{int} te;
00429   \textcolor{keywordtype}{int} qb;
00430   \textcolor{keywordtype}{int} qe;
00431 \} \hyperlink{structduplexT}{duplexT};
00432 
00433 \textcolor{comment}{/*}
00434 \textcolor{comment}{* ############################################################}
00435 \textcolor{comment}{* RNAsnoop data structures}
00436 \textcolor{comment}{* ############################################################}
00437 \textcolor{comment}{*/}
00438 
\hypertarget{data__structures_8h_source_l00442}{}\hyperlink{structfolden}{00442} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }node \{
00443   \textcolor{keywordtype}{int} k;
00444   \textcolor{keywordtype}{int} energy;
00445   \textcolor{keyword}{struct }node *next;
00446 \} \hyperlink{structfolden}{folden};
00447 
\hypertarget{data__structures_8h_source_l00451}{}\hyperlink{structsnoopT}{00451} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{
00452   \textcolor{keywordtype}{int} i;
00453   \textcolor{keywordtype}{int} j;
00454   \textcolor{keywordtype}{int} u;
00455   \textcolor{keywordtype}{char} *structure;
00456   \textcolor{keywordtype}{float} energy;
00457   \textcolor{keywordtype}{float} Duplex\_El;
00458   \textcolor{keywordtype}{float} Duplex\_Er;
00459   \textcolor{keywordtype}{float} Loop\_E;
00460   \textcolor{keywordtype}{float} Loop\_D;
00461   \textcolor{keywordtype}{float} pscd;
00462   \textcolor{keywordtype}{float} psct;
00463   \textcolor{keywordtype}{float} pscg;
00464   \textcolor{keywordtype}{float} Duplex\_Ol;
00465   \textcolor{keywordtype}{float} Duplex\_Or;
00466   \textcolor{keywordtype}{float} Duplex\_Ot;
00467   \textcolor{keywordtype}{float} fullStemEnergy;
00468 \} \hyperlink{structsnoopT}{snoopT};
00469 
00470 
00471 
00472 
00473 
00474 
00475 
00476 \textcolor{comment}{/*}
00477 \textcolor{comment}{* ############################################################}
00478 \textcolor{comment}{* PKplex data structures}
00479 \textcolor{comment}{* ############################################################}
00480 \textcolor{comment}{*/}
00481 
\hypertarget{data__structures_8h_source_l00485}{}\hyperlink{structdupVar}{00485} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structdupVar}{dupVar}\{
00486   \textcolor{keywordtype}{int} i;
00487   \textcolor{keywordtype}{int} j;
00488   \textcolor{keywordtype}{int} end;
00489   \textcolor{keywordtype}{char} *pk\_helix;
00490   \textcolor{keywordtype}{char} *structure;
00491   \textcolor{keywordtype}{double} energy;
00492   \textcolor{keywordtype}{int} offset;
00493   \textcolor{keywordtype}{double} dG1;
00494   \textcolor{keywordtype}{double} dG2;
00495   \textcolor{keywordtype}{double} ddG;
00496   \textcolor{keywordtype}{int} tb;
00497   \textcolor{keywordtype}{int} te;
00498   \textcolor{keywordtype}{int} qb;
00499   \textcolor{keywordtype}{int} qe;
00500   \textcolor{keywordtype}{int} inactive;
00501   \textcolor{keywordtype}{int} processed;
00502 \} \hyperlink{structdupVar}{dupVar};
00503 
00504 
00505 
00506 \textcolor{comment}{/*}
00507 \textcolor{comment}{* ############################################################}
00508 \textcolor{comment}{* 2Dfold data structures}
00509 \textcolor{comment}{* ############################################################}
00510 \textcolor{comment}{*/}
00511 
\hypertarget{data__structures_8h_source_l00526}{}\hyperlink{structTwoDfold__solution}{00526} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
\hypertarget{data__structures_8h_source_l00527}{}\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{00527}   \textcolor{keywordtype}{int} k;          
\hypertarget{data__structures_8h_source_l00528}{}\hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{00528}   \textcolor{keywordtype}{int} l;          
\hypertarget{data__structures_8h_source_l00529}{}\hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{00529}   \textcolor{keywordtype}{float} en;       
\hypertarget{data__structures_8h_source_l00530}{}\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{00530}   \textcolor{keywordtype}{char} *s;        
00531 \} \hyperlink{structTwoDfold__solution}{TwoDfold_solution};
00532 
\hypertarget{data__structures_8h_source_l00538}{}\hyperlink{structTwoDfold__vars}{00538} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
\hypertarget{data__structures_8h_source_l00539}{}\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{00539}   \hyperlink{structparamT}{paramT}          *P;             
\hypertarget{data__structures_8h_source_l00540}{}\hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{00540}   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do_backtrack};   
\hypertarget{data__structures_8h_source_l00541}{}\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{00541}   \textcolor{keywordtype}{char}            *ptype;         
\hypertarget{data__structures_8h_source_l00542}{}\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{00542}   \textcolor{keywordtype}{char}            *sequence;      
\hypertarget{data__structures_8h_source_l00543}{}\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{00543}   \textcolor{keywordtype}{short}           *S, *S1;        
\hypertarget{data__structures_8h_source_l00544}{}\hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{00544}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    maxD1;          
\hypertarget{data__structures_8h_source_l00545}{}\hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{00545}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    maxD2;          
\hypertarget{data__structures_8h_source_l00548}{}\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{00548}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *mm1;           
\hypertarget{data__structures_8h_source_l00549}{}\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{00549}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *mm2;           
\hypertarget{data__structures_8h_source_l00551}{}\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{00551}   \textcolor{keywordtype}{int}             *my\_iindx;      
00553   \textcolor{keywordtype}{double}          \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};
00554 
\hypertarget{data__structures_8h_source_l00555}{}\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{00555}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *referenceBPs1; 
\hypertarget{data__structures_8h_source_l00556}{}\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{00556}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *referenceBPs2; 
\hypertarget{data__structures_8h_source_l00557}{}\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{00557}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *bpdist;        
00559   \textcolor{keywordtype}{short}           *reference\_pt1;
00560   \textcolor{keywordtype}{short}           *reference\_pt2;
00561   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
00562   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
00563   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    seq\_length;
00564 
00565   \textcolor{keywordtype}{int}             ***E\_F5;
00566   \textcolor{keywordtype}{int}             ***E\_F3;
00567   \textcolor{keywordtype}{int}             ***E\_C;
00568   \textcolor{keywordtype}{int}             ***E\_M;
00569   \textcolor{keywordtype}{int}             ***E\_M1;
00570   \textcolor{keywordtype}{int}             ***E\_M2;
00571 
00572   \textcolor{keywordtype}{int}             **E\_Fc;
00573   \textcolor{keywordtype}{int}             **E\_FcH;
00574   \textcolor{keywordtype}{int}             **E\_FcI;
00575   \textcolor{keywordtype}{int}             **E\_FcM;
00576 
00577   \textcolor{keywordtype}{int}             **l\_min\_values;
00578   \textcolor{keywordtype}{int}             **l\_max\_values;
00579   \textcolor{keywordtype}{int}             *k\_min\_values;
00580   \textcolor{keywordtype}{int}             *k\_max\_values;
00581 
00582   \textcolor{keywordtype}{int}             **l\_min\_values\_m;
00583   \textcolor{keywordtype}{int}             **l\_max\_values\_m;
00584   \textcolor{keywordtype}{int}             *k\_min\_values\_m;
00585   \textcolor{keywordtype}{int}             *k\_max\_values\_m;
00586 
00587   \textcolor{keywordtype}{int}             **l\_min\_values\_m1;
00588   \textcolor{keywordtype}{int}             **l\_max\_values\_m1;
00589   \textcolor{keywordtype}{int}             *k\_min\_values\_m1;
00590   \textcolor{keywordtype}{int}             *k\_max\_values\_m1;
00591 
00592   \textcolor{keywordtype}{int}             **l\_min\_values\_f;
00593   \textcolor{keywordtype}{int}             **l\_max\_values\_f;
00594   \textcolor{keywordtype}{int}             *k\_min\_values\_f;
00595   \textcolor{keywordtype}{int}             *k\_max\_values\_f;
00596 
00597   \textcolor{keywordtype}{int}             **l\_min\_values\_f3;
00598   \textcolor{keywordtype}{int}             **l\_max\_values\_f3;
00599   \textcolor{keywordtype}{int}             *k\_min\_values\_f3;
00600   \textcolor{keywordtype}{int}             *k\_max\_values\_f3;
00601 
00602   \textcolor{keywordtype}{int}             **l\_min\_values\_m2;
00603   \textcolor{keywordtype}{int}             **l\_max\_values\_m2;
00604   \textcolor{keywordtype}{int}             *k\_min\_values\_m2;
00605   \textcolor{keywordtype}{int}             *k\_max\_values\_m2;
00606 
00607   \textcolor{keywordtype}{int}             *l\_min\_values\_fc;
00608   \textcolor{keywordtype}{int}             *l\_max\_values\_fc;
00609   \textcolor{keywordtype}{int}             k\_min\_values\_fc;
00610   \textcolor{keywordtype}{int}             k\_max\_values\_fc;
00611 
00612   \textcolor{keywordtype}{int}             *l\_min\_values\_fcH;
00613   \textcolor{keywordtype}{int}             *l\_max\_values\_fcH;
00614   \textcolor{keywordtype}{int}             k\_min\_values\_fcH;
00615   \textcolor{keywordtype}{int}             k\_max\_values\_fcH;
00616 
00617   \textcolor{keywordtype}{int}             *l\_min\_values\_fcI;
00618   \textcolor{keywordtype}{int}             *l\_max\_values\_fcI;
00619   \textcolor{keywordtype}{int}             k\_min\_values\_fcI;
00620   \textcolor{keywordtype}{int}             k\_max\_values\_fcI;
00621 
00622   \textcolor{keywordtype}{int}             *l\_min\_values\_fcM;
00623   \textcolor{keywordtype}{int}             *l\_max\_values\_fcM;
00624   \textcolor{keywordtype}{int}             k\_min\_values\_fcM;
00625   \textcolor{keywordtype}{int}             k\_max\_values\_fcM;
00626 
00627   \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) 
      */}
00628   \textcolor{keywordtype}{int}             *E\_F5\_rem;
00629   \textcolor{keywordtype}{int}             *E\_F3\_rem;
00630   \textcolor{keywordtype}{int}             *E\_C\_rem;
00631   \textcolor{keywordtype}{int}             *E\_M\_rem;
00632   \textcolor{keywordtype}{int}             *E\_M1\_rem;
00633   \textcolor{keywordtype}{int}             *E\_M2\_rem;
00634 
00635   \textcolor{keywordtype}{int}             E\_Fc\_rem;
00636   \textcolor{keywordtype}{int}             E\_FcH\_rem;
00637   \textcolor{keywordtype}{int}             E\_FcI\_rem;
00638   \textcolor{keywordtype}{int}             E\_FcM\_rem;
00639 
00640 \textcolor{preprocessor}{#ifdef COUNT\_STATES}
00641 \textcolor{preprocessor}{}  \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_F5;
00642   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_C;
00643   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_M;
00644   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long}             ***N\_M1;
00645 \textcolor{preprocessor}{#endif}
00646 \textcolor{preprocessor}{}\} \hyperlink{structTwoDfold__vars}{TwoDfold_vars};
00647 
\hypertarget{data__structures_8h_source_l00660}{}\hyperlink{structTwoDpfold__solution}{00660} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
\hypertarget{data__structures_8h_source_l00661}{}\hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{00661}   \textcolor{keywordtype}{int} k;          
\hypertarget{data__structures_8h_source_l00662}{}\hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{00662}   \textcolor{keywordtype}{int} l;          
\hypertarget{data__structures_8h_source_l00663}{}\hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{00663}   FLT\_OR\_DBL  q;  
00664 \} \hyperlink{structTwoDpfold__solution}{TwoDpfold_solution};
00665 
\hypertarget{data__structures_8h_source_l00672}{}\hyperlink{structTwoDpfold__vars}{00672} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{
00673 
00674   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    alloc;
\hypertarget{data__structures_8h_source_l00675}{}\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{00675}   \textcolor{keywordtype}{char}            *ptype;         
\hypertarget{data__structures_8h_source_l00676}{}\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{00676}   \textcolor{keywordtype}{char}            *sequence;      
\hypertarget{data__structures_8h_source_l00677}{}\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{00677}   \textcolor{keywordtype}{short}           *S, *S1;        
\hypertarget{data__structures_8h_source_l00678}{}\hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{00678}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    maxD1;          
\hypertarget{data__structures_8h_source_l00679}{}\hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{00679}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    maxD2;          
00681   \textcolor{keywordtype}{double}          \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature};    \textcolor{comment}{/* temperature in last call to scale\_pf\_params 
      */}
00682   \textcolor{keywordtype}{double}          init\_temp;      \textcolor{comment}{/* temperature in last call to scale\_pf\_params 
      */}
00683   FLT\_OR\_DBL      *scale;
00684   FLT\_OR\_DBL      \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf_scale};
00685   \hyperlink{structpf__paramT}{pf_paramT}       *pf\_params;     \textcolor{comment}{/* holds all [unscaled] pf parameters */}
00686 
\hypertarget{data__structures_8h_source_l00687}{}\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{00687}   \textcolor{keywordtype}{int}             *my\_iindx;      
\hypertarget{data__structures_8h_source_l00688}{}\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{00688}   \textcolor{keywordtype}{int}             *jindx;         
00690   \textcolor{keywordtype}{short}           *reference\_pt1;
00691   \textcolor{keywordtype}{short}           *reference\_pt2;
00692 
\hypertarget{data__structures_8h_source_l00693}{}\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{00693}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *referenceBPs1; 
\hypertarget{data__structures_8h_source_l00694}{}\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{00694}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *referenceBPs2; 
\hypertarget{data__structures_8h_source_l00695}{}\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{00695}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *bpdist;        
\hypertarget{data__structures_8h_source_l00697}{}\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{00697}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *mm1;           
\hypertarget{data__structures_8h_source_l00698}{}\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{00698}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    *mm2;           
00700   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ};
00701   \textcolor{keywordtype}{int}             \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles};
00702   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}    seq\_length;
00703 
00704   FLT\_OR\_DBL      ***Q;
00705   FLT\_OR\_DBL      ***Q\_B;
00706   FLT\_OR\_DBL      ***Q\_M;
00707   FLT\_OR\_DBL      ***Q\_M1;
00708   FLT\_OR\_DBL      ***Q\_M2;
00709 
00710   FLT\_OR\_DBL      **Q\_c;
00711   FLT\_OR\_DBL      **Q\_cH;
00712   FLT\_OR\_DBL      **Q\_cI;
00713   FLT\_OR\_DBL      **Q\_cM;
00714 
00715   \textcolor{keywordtype}{int}             **l\_min\_values;
00716   \textcolor{keywordtype}{int}             **l\_max\_values;
00717   \textcolor{keywordtype}{int}             *k\_min\_values;
00718   \textcolor{keywordtype}{int}             *k\_max\_values;
00719 
00720   \textcolor{keywordtype}{int}             **l\_min\_values\_b;
00721   \textcolor{keywordtype}{int}             **l\_max\_values\_b;
00722   \textcolor{keywordtype}{int}             *k\_min\_values\_b;
00723   \textcolor{keywordtype}{int}             *k\_max\_values\_b;
00724 
00725   \textcolor{keywordtype}{int}             **l\_min\_values\_m;
00726   \textcolor{keywordtype}{int}             **l\_max\_values\_m;
00727   \textcolor{keywordtype}{int}             *k\_min\_values\_m;
00728   \textcolor{keywordtype}{int}             *k\_max\_values\_m;
00729 
00730   \textcolor{keywordtype}{int}             **l\_min\_values\_m1;
00731   \textcolor{keywordtype}{int}             **l\_max\_values\_m1;
00732   \textcolor{keywordtype}{int}             *k\_min\_values\_m1;
00733   \textcolor{keywordtype}{int}             *k\_max\_values\_m1;
00734 
00735   \textcolor{keywordtype}{int}             **l\_min\_values\_m2;
00736   \textcolor{keywordtype}{int}             **l\_max\_values\_m2;
00737   \textcolor{keywordtype}{int}             *k\_min\_values\_m2;
00738   \textcolor{keywordtype}{int}             *k\_max\_values\_m2;
00739 
00740   \textcolor{keywordtype}{int}             *l\_min\_values\_qc;
00741   \textcolor{keywordtype}{int}             *l\_max\_values\_qc;
00742   \textcolor{keywordtype}{int}             k\_min\_values\_qc;
00743   \textcolor{keywordtype}{int}             k\_max\_values\_qc;
00744 
00745   \textcolor{keywordtype}{int}             *l\_min\_values\_qcH;
00746   \textcolor{keywordtype}{int}             *l\_max\_values\_qcH;
00747   \textcolor{keywordtype}{int}             k\_min\_values\_qcH;
00748   \textcolor{keywordtype}{int}             k\_max\_values\_qcH;
00749 
00750   \textcolor{keywordtype}{int}             *l\_min\_values\_qcI;
00751   \textcolor{keywordtype}{int}             *l\_max\_values\_qcI;
00752   \textcolor{keywordtype}{int}             k\_min\_values\_qcI;
00753   \textcolor{keywordtype}{int}             k\_max\_values\_qcI;
00754 
00755   \textcolor{keywordtype}{int}             *l\_min\_values\_qcM;
00756   \textcolor{keywordtype}{int}             *l\_max\_values\_qcM;
00757   \textcolor{keywordtype}{int}             k\_min\_values\_qcM;
00758   \textcolor{keywordtype}{int}             k\_max\_values\_qcM;
00759 
00760   \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) 
      */}
00761   FLT\_OR\_DBL      *Q\_rem;
00762   FLT\_OR\_DBL      *Q\_B\_rem;
00763   FLT\_OR\_DBL      *Q\_M\_rem;
00764   FLT\_OR\_DBL      *Q\_M1\_rem;
00765   FLT\_OR\_DBL      *Q\_M2\_rem;
00766 
00767   FLT\_OR\_DBL      Q\_c\_rem;
00768   FLT\_OR\_DBL      Q\_cH\_rem;
00769   FLT\_OR\_DBL      Q\_cI\_rem;
00770   FLT\_OR\_DBL      Q\_cM\_rem;
00771 
00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold_vars};
00773 
00774 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
