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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 / 1_88_84__epars_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex
index f3b9b55..75cda7e 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex
@@ -1,8 +1,9 @@
-\hypertarget{1_88_84__epars_8h}{\section{1.8.4\-\_\-epars.h}
-\label{1_88_84__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h}}
+\hypertarget{1_88_84__epars_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\-epars.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_}
 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_}
 00003 \textcolor{preprocessor}{}
@@ -12,18 +13,18 @@
 00041 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
 00042 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define INF       1000000}
 00043 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBPAIRS   7}
-00044 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NST       0     }\textcolor{comment}{/* Energy for nonstandard stacked pairs */}\textcolor{preprocessor}{}
-00045 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEF       -50   }\textcolor{comment}{/* Default terminal mismatch, used for I */}\textcolor{preprocessor}{}
-00046 \textcolor{preprocessor}{}                        \textcolor{comment}{/* and any non\_pairing bases */}
-00047 \textcolor{preprocessor}{#define NSM       0     }\textcolor{comment}{/* terminal mismatch for non standard pairs */}\textcolor{preprocessor}{}
-00048 \textcolor{preprocessor}{}
+00044 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NST       0     }\textcolor{comment}{/* Energy for nonstandard stacked pairs */}
+00045 \textcolor{preprocessor}{#define DEF       -50   }\textcolor{comment}{/* Default terminal mismatch, used for I */}
+00046                         \textcolor{comment}{/* and any non\_pairing bases */}
+00047 \textcolor{preprocessor}{#define NSM       0     }\textcolor{comment}{/* terminal mismatch for non standard pairs */}
+00048 
 00049 PRIVATE \textcolor{keywordtype}{double} Tmeasure\_184 = 37 + \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0};  \textcolor{comment}{/* temperature of param measurements */}
 00050 PRIVATE \textcolor{keywordtype}{double} lxc37\_184    = 107.856;  \textcolor{comment}{/* parameter for logarithmic loop}
 00051 \textcolor{comment}{                                           energy extrapolation */}
 00052 
 00053 PRIVATE \textcolor{keywordtype}{int} stack37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] =
 00054 \textcolor{comment}{/*          CG     GC     GU     UG     AU     UA  */}
-00055 \{ \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\},
+00055 \{ \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   INF,   INF,   INF,   INF,   INF, INF\},
 00056   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -240,  -330,  -210,  -140,  -210,  -210, NST\},
 00057   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -330,  -340,  -250,  -150,  -220,  -240, NST\},
 00058   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -210,  -250,   130,   -50,  -140,  -130, NST\},
@@ -36,7 +37,7 @@
 00065 \textcolor{comment}{/* different from mfold-2.3, which uses values from mfold-2.2 */}
 00066 PRIVATE \textcolor{keywordtype}{int} enthalpies\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] =
 00067 \textcolor{comment}{/*          CG     GC     GU     UG     AU     UA  */}
-00068 \{ \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\},
+00068 \{ \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   INF,   INF,   INF,   INF,   INF, INF\},
 00069   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1060, -1340, -1210,  -560, -1050, -1040, NST\},
 00070   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1340, -1490, -1260,  -830, -1140, -1240, NST\},
 00071   \{  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1210, -1260, -1460, -1350,  -880, -1280, NST\},
@@ -48,12 +49,12 @@
 00077 
 00078 \textcolor{comment}{/* old values are here just for comparison */}
 00079 PRIVATE \textcolor{keywordtype}{int} oldhairpin37\_184[31] = \{ \textcolor{comment}{/* from ViennaRNA 1.3 */}
-00080   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 490, 440, 470, 500, 510, 520, 531,
+00080   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF, 410, 490, 440, 470, 500, 510, 520, 531,
 00081        542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
 00082        611, 616, 621, 626, 630, 634, 638, 642, 646, 650\};
 00083 
 00084 PRIVATE \textcolor{keywordtype}{int} hairpin37\_184[31] = \{
-00085   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 570, 560, 560, 540, 590, 560, 640, 650,
+00085   \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF, 570, 560, 560, 540, 590, 560, 640, 650,
 00086        660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
 00087        730, 735, 740, 744, 749, 753, 757, 761, 765, 769\};
 00088 
@@ -220,7 +221,7 @@
 00249 \textcolor{comment}{/* 5' dangling ends (unpaird base stacks on first paired base) */}
 00250 PRIVATE \textcolor{keywordtype}{int} dangle5\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]=
 00251 \{\textcolor{comment}{/*   @     A     C     G     U   */}
-00252    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF\}, \textcolor{comment}{/* no pair */}
+00252    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF,  INF,  INF\}, \textcolor{comment}{/* no pair */}
 00253    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -50,  -30,  -20,  -10\}, \textcolor{comment}{/* CG  (stacks on C) */}
 00254    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -20,  -30,   -0,   -0\}, \textcolor{comment}{/* GC  (stacks on G) */}
 00255    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -30,  -30,  -40,  -20\}, \textcolor{comment}{/* GU */}
@@ -233,7 +234,7 @@
 00262 \textcolor{comment}{/* 3' dangling ends (unpaired base stacks on second paired base */}
 00263 PRIVATE \textcolor{keywordtype}{int} dangle3\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]=
 00264 \{\textcolor{comment}{/*   @     A     C     G     U   */}
-00265    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF\},  \textcolor{comment}{/* no pair */}
+00265    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF,  INF,  INF\},  \textcolor{comment}{/* no pair */}
 00266    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -110,  -40, -130,  -60\},  \textcolor{comment}{/* CG  (stacks on G) */}
 00267    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -170,  -80, -170, -120\},  \textcolor{comment}{/* GC */}
 00268    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  -70,  -10,  -70,  -10\},  \textcolor{comment}{/* GU */}
@@ -246,7 +247,7 @@
 00275 \textcolor{comment}{/* enthalpies for temperature scaling */}
 00276 PRIVATE \textcolor{keywordtype}{int} dangle3\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] =
 00277 \{\textcolor{comment}{/*   @     A     C     G     U   */}
-00278    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF\},  \textcolor{comment}{/* no pair */}
+00278    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF,  INF,  INF\},  \textcolor{comment}{/* no pair */}
 00279    \{   0, -740, -280, -640, -360\},
 00280    \{   0, -900, -410, -860, -750\},
 00281    \{   0, -740, -240, -720, -490\},
@@ -258,7 +259,7 @@
 00287 
 00288 PRIVATE \textcolor{keywordtype}{int} dangle5\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] =
 00289 \{\textcolor{comment}{/*   @     A     C     G     U   */}
-00290    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF\},  \textcolor{comment}{/* no pair */}
+00290    \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},  INF,  INF,  INF\},  \textcolor{comment}{/* no pair */}
 00291    \{   0, -240,  330,   80, -140\},
 00292    \{   0, -160,   70, -460,  -40\},
 00293    \{   0,  160,  220,   70,  310\},
@@ -335,4 +336,4 @@
 00364 PRIVATE \textcolor{keywordtype}{int} DuplexInit\_184 = 410;
 00365 
 00366 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}