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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / gquad_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/gquad_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/gquad_8h_source.tex
index 900cd28..b613673 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/gquad_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/gquad_8h_source.tex
@@ -1,12 +1,13 @@
-\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}}
+\hypertarget{gquad_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 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}"}
+00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
 00005 
 00006 \textcolor{preprocessor}{#ifndef INLINE}
 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
@@ -22,7 +23,7 @@
 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);
+00026                         \hyperlink{structpf__paramT}{pf_paramT} *pf);
 00027 
 00028 \textcolor{keywordtype}{int}         E\_gquad\_ali(\textcolor{keywordtype}{int} i,
 00029                         \textcolor{keywordtype}{int} L,
@@ -40,7 +41,7 @@
 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);
+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,
@@ -49,7 +50,7 @@
 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);
+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,
@@ -67,7 +68,7 @@
 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,
+00087                                   \hyperlink{structpf__paramT}{pf_paramT} *pf,
 00088                                   \textcolor{keywordtype}{int} *L,
 00089                                   \textcolor{keywordtype}{int} l[3]);
 00090 
@@ -77,7 +78,7 @@
 00094                                       FLT\_OR\_DBL *G,
 00095                                       FLT\_OR\_DBL *probs,
 00096                                       FLT\_OR\_DBL *scale,
-00097                                       \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+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,
@@ -86,16 +87,16 @@
 00103                                       FLT\_OR\_DBL *scale,
 00104                                       \textcolor{keywordtype}{int} *L,
 00105                                       \textcolor{keywordtype}{int} l[3],
-00106                                       \hyperlink{structpf__paramT}{pf\_paramT} *pf);
+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]);
+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,
+\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,
@@ -109,7 +110,7 @@
 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};
+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;
@@ -177,7 +178,7 @@
 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,
+\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,
@@ -191,7 +192,7 @@
 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};
+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;
@@ -273,7 +274,7 @@
 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};
+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;
@@ -407,7 +408,7 @@
 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};
+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;
@@ -479,7 +480,7 @@
 00539                     \textcolor{keywordtype}{short} *S,
 00540                     FLT\_OR\_DBL *G,
 00541                     \textcolor{keywordtype}{int} *index,
-00542                     \hyperlink{structpf__paramT}{pf\_paramT} *pf)\{
+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;
@@ -542,4 +543,4 @@
 00602 \}
 00603 
 00604 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}