Add missing doc files
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / refman.aux
diff --git a/binaries/src/ViennaRNA/doc/latex/refman.aux b/binaries/src/ViennaRNA/doc/latex/refman.aux
new file mode 100644 (file)
index 0000000..50bf3d0
--- /dev/null
@@ -0,0 +1,1025 @@
+\relax 
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\citation{lorenz:2011}
+\citation{hofacker:1994}
+\@writefile{toc}{\contentsline {chapter}{\numberline {1}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A Package core -\/ R\discretionary {-}{}{}N\discretionary {-}{}{}Alib}{1}{chapter.1}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{index}{{1}{1}{Vienna\-R\-N\-A Package core -\/ R\-N\-Alib\relax }{chapter.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {1.1}Introduction}{1}{section.1.1}}
+\newlabel{index_mp_intro}{{1.1}{1}{Introduction\relax }{section.1.1}{}}
+\@writefile{brf}{\backcite{lorenz:2011}{{1}{1.1}{section.1.1}}}
+\@writefile{brf}{\backcite{hofacker:1994}{{1}{1.1}{section.1.1}}}
+\citation{fontana:1993b}
+\citation{shapiro:1988}
+\@writefile{toc}{\contentsline {chapter}{\numberline {2}Parsing and Comparing -\/ Functions to Manipulate Structures}{3}{chapter.2}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{mp_parse}{{2}{3}{Parsing and Comparing -\/ Functions to Manipulate Structures\relax }{chapter.2}{}}
+\@writefile{brf}{\backcite{fontana:1993b}{{3}{2}{section*.4}}}
+\@writefile{brf}{\backcite{shapiro:1988}{{3}{2}{section*.4}}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}Utilities -\/ Odds and Ends}{5}{chapter.3}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{mp_utils}{{3}{5}{Utilities -\/ Odds and Ends\relax }{chapter.3}{}}
+\newlabel{mp_utils_toc}{{3}{5}{Utilities -\/ Odds and Ends\relax }{chapter.3}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {3.1}Producing secondary structure graphs}{5}{section.3.1}}
+\newlabel{mp_utils_utils_ss}{{3.1}{5}{Producing secondary structure graphs\relax }{section.3.1}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}Example -\/ A Small Example Program}{7}{chapter.4}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{mp_example}{{4}{7}{Example -\/ A Small Example Program\relax }{chapter.4}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {5}Deprecated List}{9}{chapter.5}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{deprecated}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000008}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000012}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000007}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000005}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000006}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000015}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000014}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000016}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000003}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000010}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000017}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000011}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000001}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000004}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000002}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000018}{{5}{9}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000013}{{5}{10}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000009}{{5}{10}{Deprecated List\relax }{chapter.5}{}}
+\newlabel{deprecated__deprecated000019}{{5}{10}{Deprecated List\relax }{chapter.5}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {6}Module Index}{11}{chapter.6}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {6.1}Modules}{11}{section.6.1}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {7}Data Structure Index}{13}{chapter.7}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {7.1}Data Structures}{13}{section.7.1}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {8}File Index}{15}{chapter.8}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {8.1}File List}{15}{section.8.1}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {9}Module Documentation}{19}{chapter.9}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {9.1}R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding}{19}{section.9.1}}
+\newlabel{group__folding__routines}{{9.1}{19}{R\-N\-A Secondary Structure Folding\relax }{section.9.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {9.1.1}Detailed Description}{21}{subsection.9.1.1}}
+\@input{group__mfe__fold.aux}
+\@input{group__pf__fold.aux}
+\@input{group__mea__fold.aux}
+\@input{group__centroid__fold.aux}
+\@input{group__subopt__fold.aux}
+\@input{group__subopt__zuker.aux}
+\@input{group__subopt__wuchty.aux}
+\@input{group__subopt__stochbt.aux}
+\@input{group__cofold.aux}
+\@input{group__mfe__cofold.aux}
+\@input{group__pf__cofold.aux}
+\@input{group__up__cofold.aux}
+\@input{group__consensus__fold.aux}
+\@input{group__consensus__mfe__fold.aux}
+\@input{group__consensus__pf__fold.aux}
+\@input{group__consensus__stochbt.aux}
+\@input{group__local__fold.aux}
+\@input{group__local__mfe__fold.aux}
+\@input{group__local__pf__fold.aux}
+\@input{group__local__consensus__fold.aux}
+\@input{group__energy__parameters.aux}
+\@input{group__energy__parameters__rw.aux}
+\@input{group__energy__parameters__convert.aux}
+\@input{group__eval.aux}
+\@input{group__inverse__fold.aux}
+\@input{group__class__fold.aux}
+\@input{group__kl__neighborhood.aux}
+\@input{group__kl__neighborhood__mfe.aux}
+\@input{group__kl__neighborhood__pf.aux}
+\@input{group__kl__neighborhood__stochbt.aux}
+\@input{group__dos.aux}
+\@input{group__parse.aux}
+\@writefile{toc}{\contentsline {chapter}{\numberline {10}Data Structure Documentation}{91}{chapter.10}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {10.1}bond\discretionary {-}{}{}T Struct Reference}{91}{section.10.1}}
+\newlabel{structbondT}{{10.1}{91}{bond\-T Struct Reference\relax }{section.10.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.1.1}Detailed Description}{91}{subsection.10.1.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.2}bond\discretionary {-}{}{}T\discretionary {-}{}{}En Struct Reference}{91}{section.10.2}}
+\newlabel{structbondTEn}{{10.2}{91}{bond\-T\-En Struct Reference\relax }{section.10.2}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.2.1}Detailed Description}{91}{subsection.10.2.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.3}cofold\discretionary {-}{}{}F Struct Reference}{91}{section.10.3}}
+\newlabel{structcofoldF}{{10.3}{91}{cofold\-F Struct Reference\relax }{section.10.3}{}}
+\newlabel{structcofoldF_af6c496438321eb8bb907a21de1915c23}{{10.3}{91}{Data Fields\relax }{section*.65}{}}
+\newlabel{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{{10.3}{91}{Data Fields\relax }{section*.65}{}}
+\newlabel{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{{10.3}{91}{Data Fields\relax }{section*.65}{}}
+\newlabel{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{{10.3}{92}{Data Fields\relax }{section*.65}{}}
+\newlabel{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{{10.3}{92}{Data Fields\relax }{section*.65}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.4}Conc\discretionary {-}{}{}Ent Struct Reference}{92}{section.10.4}}
+\newlabel{structConcEnt}{{10.4}{92}{Conc\-Ent Struct Reference\relax }{section.10.4}{}}
+\newlabel{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{{10.4}{92}{Data Fields\relax }{section*.66}{}}
+\newlabel{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{{10.4}{92}{Data Fields\relax }{section*.66}{}}
+\newlabel{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{{10.4}{92}{Data Fields\relax }{section*.66}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.5}constrain Struct Reference}{92}{section.10.5}}
+\newlabel{structconstrain}{{10.5}{92}{constrain Struct Reference\relax }{section.10.5}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.5.1}Detailed Description}{92}{subsection.10.5.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.6}C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E Struct Reference}{92}{section.10.6}}
+\newlabel{structCOORDINATE}{{10.6}{92}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E Struct Reference\relax }{section.10.6}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.6.1}Detailed Description}{92}{subsection.10.6.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.7}cpair Struct Reference}{93}{section.10.7}}
+\newlabel{structcpair}{{10.7}{93}{cpair Struct Reference\relax }{section.10.7}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.7.1}Detailed Description}{93}{subsection.10.7.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.8}duplex\discretionary {-}{}{}T Struct Reference}{93}{section.10.8}}
+\newlabel{structduplexT}{{10.8}{93}{duplex\-T Struct Reference\relax }{section.10.8}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.9}dup\discretionary {-}{}{}Var Struct Reference}{93}{section.10.9}}
+\newlabel{structdupVar}{{10.9}{93}{dup\-Var Struct Reference\relax }{section.10.9}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.10}folden Struct Reference}{93}{section.10.10}}
+\newlabel{structfolden}{{10.10}{93}{folden Struct Reference\relax }{section.10.10}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.11}interact Struct Reference}{93}{section.10.11}}
+\newlabel{structinteract}{{10.11}{93}{interact Struct Reference\relax }{section.10.11}{}}
+\newlabel{structinteract_a1fc8b3860c083f164daa9712690a3a56}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_ad58303190f9e085c3ab59890cbf61223}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_a41793812abae560805414761fec398fe}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_ab6d031a21388be8763b75ea74c937f17}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{{10.11}{93}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_a7555cb6363d1479341eb72b9c087aa34}{{10.11}{94}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_a030ab45056342e12cb3955e4defd3904}{{10.11}{94}{Data Fields\relax }{section*.67}{}}
+\newlabel{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{{10.11}{94}{Data Fields\relax }{section*.67}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.12}intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{94}{section.10.12}}
+\newlabel{structintermediate__t}{{10.12}{94}{intermediate\-\_\-t Struct Reference\relax }{section.10.12}{}}
+\newlabel{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{{10.12}{94}{Data Fields\relax }{section*.68}{}}
+\newlabel{structintermediate__t_ac44e091915da58927978d54ef59234c7}{{10.12}{94}{Data Fields\relax }{section*.68}{}}
+\newlabel{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{{10.12}{94}{Data Fields\relax }{section*.68}{}}
+\newlabel{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{{10.12}{94}{Data Fields\relax }{section*.68}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.13}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L Struct Reference}{94}{section.10.13}}
+\newlabel{structINTERVAL}{{10.13}{94}{I\-N\-T\-E\-R\-V\-A\-L Struct Reference\relax }{section.10.13}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.13.1}Detailed Description}{95}{subsection.10.13.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.14}L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T Struct Reference}{95}{section.10.14}}
+\newlabel{structLIST}{{10.14}{95}{L\-I\-S\-T Struct Reference\relax }{section.10.14}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.15}L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T Struct Reference}{95}{section.10.15}}
+\newlabel{structLST__BUCKET}{{10.15}{95}{L\-S\-T\-\_\-\-B\-U\-C\-K\-E\-T Struct Reference\relax }{section.10.15}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.16}model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T Struct Reference}{96}{section.10.16}}
+\newlabel{structmodel__detailsT}{{10.16}{96}{model\-\_\-details\-T Struct Reference\relax }{section.10.16}{}}
+\newlabel{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\newlabel{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{{10.16}{96}{Data Fields\relax }{section*.69}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.16.1}Detailed Description}{96}{subsection.10.16.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.16.2}Field Documentation}{96}{subsection.10.16.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {10.16.2.1}dangles}{96}{subsubsection.10.16.2.1}}
+\newlabel{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{{10.16.2.1}{96}{dangles\relax }{subsubsection.10.16.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.17}move\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{96}{section.10.17}}
+\newlabel{structmove__t}{{10.17}{96}{move\-\_\-t Struct Reference\relax }{section.10.17}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.18}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R Struct Reference}{97}{section.10.18}}
+\newlabel{structPAIR}{{10.18}{97}{P\-A\-I\-R Struct Reference\relax }{section.10.18}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.18.1}Detailed Description}{97}{subsection.10.18.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.19}pair\discretionary {-}{}{}\_\discretionary {-}{}{}info Struct Reference}{97}{section.10.19}}
+\newlabel{structpair__info}{{10.19}{97}{pair\-\_\-info Struct Reference\relax }{section.10.19}{}}
+\newlabel{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\newlabel{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\newlabel{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\newlabel{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\newlabel{structpair__info_a23fc316453d179474bed7f6ed2489723}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\newlabel{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{{10.19}{97}{Data Fields\relax }{section*.70}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.19.1}Detailed Description}{97}{subsection.10.19.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.20}pairpro Struct Reference}{98}{section.10.20}}
+\newlabel{structpairpro}{{10.20}{98}{pairpro Struct Reference\relax }{section.10.20}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.21}param\discretionary {-}{}{}T Struct Reference}{98}{section.10.21}}
+\newlabel{structparamT}{{10.21}{98}{param\-T Struct Reference\relax }{section.10.21}{}}
+\newlabel{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{{10.21}{98}{Data Fields\relax }{section*.71}{}}
+\newlabel{structparamT_aeb912822ef912705bc202b14f9d71ad9}{{10.21}{99}{Data Fields\relax }{section*.71}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.21.1}Detailed Description}{99}{subsection.10.21.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.22}path\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{99}{section.10.22}}
+\newlabel{structpath__t}{{10.22}{99}{path\-\_\-t Struct Reference\relax }{section.10.22}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.23}pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T Struct Reference}{99}{section.10.23}}
+\newlabel{structpf__paramT}{{10.23}{99}{pf\-\_\-param\-T Struct Reference\relax }{section.10.23}{}}
+\newlabel{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{{10.23}{99}{Data Fields\relax }{section*.72}{}}
+\newlabel{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{{10.23}{99}{Data Fields\relax }{section*.72}{}}
+\newlabel{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{{10.23}{99}{Data Fields\relax }{section*.72}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.23.1}Detailed Description}{100}{subsection.10.23.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.23.2}Field Documentation}{100}{subsection.10.23.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {10.23.2.1}alpha}{100}{subsubsection.10.23.2.1}}
+\newlabel{structpf__paramT_a3d2af9040acfa08295efb50f0219149d}{{10.23.2.1}{100}{alpha\relax }{subsubsection.10.23.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.24}plist Struct Reference}{100}{section.10.24}}
+\newlabel{structplist}{{10.24}{100}{plist Struct Reference\relax }{section.10.24}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.24.1}Detailed Description}{100}{subsection.10.24.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.25}Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list Struct Reference}{100}{section.10.25}}
+\newlabel{structPostorder__list}{{10.25}{100}{Postorder\-\_\-list Struct Reference\relax }{section.10.25}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.26}pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib Struct Reference}{100}{section.10.26}}
+\newlabel{structpu__contrib}{{10.26}{100}{pu\-\_\-contrib Struct Reference\relax }{section.10.26}{}}
+\newlabel{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{{10.26}{100}{Data Fields\relax }{section*.73}{}}
+\newlabel{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{{10.26}{100}{Data Fields\relax }{section*.73}{}}
+\newlabel{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{{10.26}{100}{Data Fields\relax }{section*.73}{}}
+\newlabel{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{{10.26}{100}{Data Fields\relax }{section*.73}{}}
+\newlabel{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{{10.26}{101}{Data Fields\relax }{section*.73}{}}
+\newlabel{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{{10.26}{101}{Data Fields\relax }{section*.73}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.26.1}Detailed Description}{101}{subsection.10.26.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.27}pu\discretionary {-}{}{}\_\discretionary {-}{}{}out Struct Reference}{101}{section.10.27}}
+\newlabel{structpu__out}{{10.27}{101}{pu\-\_\-out Struct Reference\relax }{section.10.27}{}}
+\newlabel{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{{10.27}{101}{Data Fields\relax }{section*.74}{}}
+\newlabel{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{{10.27}{101}{Data Fields\relax }{section*.74}{}}
+\newlabel{structpu__out_a638b0de1837cfd441871d005d3ab2938}{{10.27}{101}{Data Fields\relax }{section*.74}{}}
+\newlabel{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{{10.27}{101}{Data Fields\relax }{section*.74}{}}
+\newlabel{structpu__out_a366edbc4170d5c177908e178ff340828}{{10.27}{101}{Data Fields\relax }{section*.74}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.27.1}Detailed Description}{101}{subsection.10.27.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.28}sect Struct Reference}{101}{section.10.28}}
+\newlabel{structsect}{{10.28}{101}{sect Struct Reference\relax }{section.10.28}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.28.1}Detailed Description}{101}{subsection.10.28.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.29}snoop\discretionary {-}{}{}T Struct Reference}{102}{section.10.29}}
+\newlabel{structsnoopT}{{10.29}{102}{snoop\-T Struct Reference\relax }{section.10.29}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.30}S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N Struct Reference}{102}{section.10.30}}
+\newlabel{structSOLUTION}{{10.30}{102}{S\-O\-L\-U\-T\-I\-O\-N Struct Reference\relax }{section.10.30}{}}
+\newlabel{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{{10.30}{102}{Data Fields\relax }{section*.75}{}}
+\newlabel{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{{10.30}{102}{Data Fields\relax }{section*.75}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.30.1}Detailed Description}{102}{subsection.10.30.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.31}struct\discretionary {-}{}{}\_\discretionary {-}{}{}en Struct Reference}{102}{section.10.31}}
+\newlabel{structstruct__en}{{10.31}{102}{struct\-\_\-en Struct Reference\relax }{section.10.31}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.32}svm\discretionary {-}{}{}\_\discretionary {-}{}{}model Struct Reference}{102}{section.10.32}}
+\newlabel{structsvm__model}{{10.32}{102}{svm\-\_\-model Struct Reference\relax }{section.10.32}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.33}sw\discretionary {-}{}{}String Struct Reference}{102}{section.10.33}}
+\newlabel{structswString}{{10.33}{102}{sw\-String Struct Reference\relax }{section.10.33}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.34}Tree Struct Reference}{103}{section.10.34}}
+\newlabel{structTree}{{10.34}{103}{Tree Struct Reference\relax }{section.10.34}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.35}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution Struct Reference}{103}{section.10.35}}
+\newlabel{structTwoDfold__solution}{{10.35}{103}{Two\-Dfold\-\_\-solution Struct Reference\relax }{section.10.35}{}}
+\newlabel{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{{10.35}{103}{Data Fields\relax }{section*.76}{}}
+\newlabel{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{{10.35}{103}{Data Fields\relax }{section*.76}{}}
+\newlabel{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{{10.35}{103}{Data Fields\relax }{section*.76}{}}
+\newlabel{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{{10.35}{103}{Data Fields\relax }{section*.76}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.35.1}Detailed Description}{103}{subsection.10.35.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.36}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars Struct Reference}{104}{section.10.36}}
+\newlabel{structTwoDfold__vars}{{10.36}{104}{Two\-Dfold\-\_\-vars Struct Reference\relax }{section.10.36}{}}
+\newlabel{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{{10.36}{104}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{{10.36}{105}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{{10.36}{105}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{{10.36}{105}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{{10.36}{105}{Data Fields\relax }{section*.77}{}}
+\newlabel{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{{10.36}{105}{Data Fields\relax }{section*.77}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.36.1}Detailed Description}{105}{subsection.10.36.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.37}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution Struct Reference}{105}{section.10.37}}
+\newlabel{structTwoDpfold__solution}{{10.37}{105}{Two\-Dpfold\-\_\-solution Struct Reference\relax }{section.10.37}{}}
+\newlabel{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{{10.37}{105}{Data Fields\relax }{section*.78}{}}
+\newlabel{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{{10.37}{105}{Data Fields\relax }{section*.78}{}}
+\newlabel{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{{10.37}{105}{Data Fields\relax }{section*.78}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.37.1}Detailed Description}{105}{subsection.10.37.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.38}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars Struct Reference}{106}{section.10.38}}
+\newlabel{structTwoDpfold__vars}{{10.38}{106}{Two\-Dpfold\-\_\-vars Struct Reference\relax }{section.10.38}{}}
+\newlabel{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\newlabel{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{{10.38}{106}{Data Fields\relax }{section*.79}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {10.38.1}Detailed Description}{107}{subsection.10.38.1}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {11}File Documentation}{109}{chapter.11}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{toc}{\contentsline {section}{\numberline {11.1}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.h File Reference}{109}{section.11.1}}
+\newlabel{2Dfold_8h}{{11.1}{109}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.h File Reference\relax }{section.11.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.2}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.h File Reference}{110}{section.11.2}}
+\newlabel{2Dpfold_8h}{{11.2}{110}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.h File Reference\relax }{section.11.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.3}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.h File Reference}{111}{section.11.3}}
+\newlabel{alifold_8h}{{11.3}{111}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.h File Reference\relax }{section.11.3}{}}
+\newlabel{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{{11.3}{111}{Functions\relax }{section*.82}{}}
+\newlabel{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{{11.3}{111}{Functions\relax }{section*.82}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.3.1}Detailed Description}{112}{subsection.11.3.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.3.2}Function Documentation}{112}{subsection.11.3.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.3.2.1}update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}{112}{subsubsection.11.3.2.1}}
+\newlabel{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{{11.3.2.1}{112}{update\-\_\-alifold\-\_\-params\relax }{subsubsection.11.3.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.4}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.h File Reference}{113}{section.11.4}}
+\newlabel{cofold_8h}{{11.4}{113}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.h File Reference\relax }{section.11.4}{}}
+\newlabel{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{{11.4}{113}{Functions\relax }{section*.84}{}}
+\newlabel{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{{11.4}{113}{Functions\relax }{section*.84}{}}
+\newlabel{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{{11.4}{113}{Functions\relax }{section*.84}{}}
+\newlabel{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{{11.4}{113}{Functions\relax }{section*.84}{}}
+\gdef \LT@lxxii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.4.1}Detailed Description}{114}{subsection.11.4.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.4.2}Function Documentation}{114}{subsection.11.4.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.4.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}{114}{subsubsection.11.4.2.1}}
+\newlabel{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{{11.4.2.1}{114}{get\-\_\-monomere\-\_\-mfes\relax }{subsubsection.11.4.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.4.2.2}initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}{114}{subsubsection.11.4.2.2}}
+\newlabel{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{{11.4.2.2}{114}{initialize\-\_\-cofold\relax }{subsubsection.11.4.2.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.5}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{114}{section.11.5}}
+\newlabel{convert__epars_8h}{{11.5}{114}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.h File Reference\relax }{section.11.5}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.5.1}Detailed Description}{115}{subsection.11.5.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.6}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/data\discretionary {-}{}{}\_\discretionary {-}{}{}structures.h File Reference}{115}{section.11.6}}
+\newlabel{data__structures_8h}{{11.6}{115}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.h File Reference\relax }{section.11.6}{}}
+\newlabel{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{{11.6}{117}{Macros\relax }{section*.88}{}}
+\newlabel{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{{11.6}{117}{Macros\relax }{section*.88}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.6.1}Detailed Description}{117}{subsection.11.6.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.7}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.h File Reference}{117}{section.11.7}}
+\newlabel{dist__vars_8h}{{11.7}{117}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.h File Reference\relax }{section.11.7}{}}
+\newlabel{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{{11.7}{117}{Variables\relax }{section*.90}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.7.1}Detailed Description}{118}{subsection.11.7.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.7.2}Variable Documentation}{118}{subsection.11.7.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.7.2.1}edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}{118}{subsubsection.11.7.2.1}}
+\newlabel{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{{11.7.2.1}{118}{edit\-\_\-backtrack\relax }{subsubsection.11.7.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.7.2.2}cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}{118}{subsubsection.11.7.2.2}}
+\newlabel{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{{11.7.2.2}{118}{cost\-\_\-matrix\relax }{subsubsection.11.7.2.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.8}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/duplex.h File Reference}{118}{section.11.8}}
+\newlabel{duplex_8h}{{11.8}{118}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/duplex.h File Reference\relax }{section.11.8}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.8.1}Detailed Description}{119}{subsection.11.8.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.9}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/edit\discretionary {-}{}{}\_\discretionary {-}{}{}cost.h File Reference}{119}{section.11.9}}
+\newlabel{edit__cost_8h}{{11.9}{119}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.h File Reference\relax }{section.11.9}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.9.1}Detailed Description}{119}{subsection.11.9.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.10}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.h File Reference}{119}{section.11.10}}
+\newlabel{energy__const_8h}{{11.10}{119}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.h File Reference\relax }{section.11.10}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.10.1}Detailed Description}{120}{subsection.11.10.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.10.2}Macro Definition Documentation}{120}{subsection.11.10.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.1}G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T}{120}{subsubsection.11.10.2.1}}
+\newlabel{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{{11.10.2.1}{120}{G\-A\-S\-C\-O\-N\-S\-T\relax }{subsubsection.11.10.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.2}K0}{120}{subsubsection.11.10.2.2}}
+\newlabel{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{{11.10.2.2}{120}{K0\relax }{subsubsection.11.10.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.3}I\discretionary {-}{}{}N\discretionary {-}{}{}F}{120}{subsubsection.11.10.2.3}}
+\newlabel{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{{11.10.2.3}{120}{I\-N\-F\relax }{subsubsection.11.10.2.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.4}F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N}{120}{subsubsection.11.10.2.4}}
+\newlabel{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{{11.10.2.4}{120}{F\-O\-R\-B\-I\-D\-D\-E\-N\relax }{subsubsection.11.10.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.5}B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S}{120}{subsubsection.11.10.2.5}}
+\newlabel{energy__const_8h_a96a9822fa134450197dd454b1478a193}{{11.10.2.5}{120}{B\-O\-N\-U\-S\relax }{subsubsection.11.10.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.6}N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S}{120}{subsubsection.11.10.2.6}}
+\newlabel{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{{11.10.2.6}{120}{N\-B\-P\-A\-I\-R\-S\relax }{subsubsection.11.10.2.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.7}T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N}{120}{subsubsection.11.10.2.7}}
+\newlabel{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{{11.10.2.7}{120}{T\-U\-R\-N\relax }{subsubsection.11.10.2.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.10.2.8}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P}{120}{subsubsection.11.10.2.8}}
+\newlabel{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{{11.10.2.8}{120}{M\-A\-X\-L\-O\-O\-P\relax }{subsubsection.11.10.2.8}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.11}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/findpath.h File Reference}{120}{section.11.11}}
+\newlabel{findpath_8h}{{11.11}{120}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.h File Reference\relax }{section.11.11}{}}
+\gdef \LT@lxxiii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.11.1}Detailed Description}{121}{subsection.11.11.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.11.2}Function Documentation}{121}{subsection.11.11.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.11.2.1}find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle}{121}{subsubsection.11.11.2.1}}
+\newlabel{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{{11.11.2.1}{121}{find\-\_\-saddle\relax }{subsubsection.11.11.2.1}{}}
+\gdef \LT@lxxiv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@lxxv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.11.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}path}{122}{subsubsection.11.11.2.2}}
+\newlabel{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{{11.11.2.2}{122}{get\-\_\-path\relax }{subsubsection.11.11.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.11.2.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}path}{122}{subsubsection.11.11.2.3}}
+\newlabel{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{{11.11.2.3}{122}{free\-\_\-path\relax }{subsubsection.11.11.2.3}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.12}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold.h File Reference}{122}{section.11.12}}
+\newlabel{fold_8h}{{11.12}{122}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.h File Reference\relax }{section.11.12}{}}
+\newlabel{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{{11.12}{123}{Functions\relax }{section*.93}{}}
+\newlabel{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{{11.12}{124}{Functions\relax }{section*.93}{}}
+\newlabel{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{{11.12}{124}{Variables\relax }{section*.94}{}}
+\newlabel{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{{11.12}{124}{Variables\relax }{section*.94}{}}
+\newlabel{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{{11.12}{124}{Variables\relax }{section*.94}{}}
+\newlabel{group__eval_ga567530678f6260a1a649a5beca5da4c5}{{11.12}{124}{Variables\relax }{section*.94}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.12.1}Detailed Description}{124}{subsection.11.12.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.12.2}Function Documentation}{124}{subsection.11.12.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.1}parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{124}{subsubsection.11.12.2.1}}
+\newlabel{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{{11.12.2.1}{124}{parenthesis\-\_\-structure\relax }{subsubsection.11.12.2.1}{}}
+\gdef \LT@lxxvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@lxxvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.2}parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker}{125}{subsubsection.11.12.2.2}}
+\newlabel{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{{11.12.2.2}{125}{parenthesis\-\_\-zuker\relax }{subsubsection.11.12.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.3}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move}{125}{subsubsection.11.12.2.3}}
+\newlabel{fold_8h_a539ecaed89730f7644c202f304d7529b}{{11.12.2.3}{125}{energy\-\_\-of\-\_\-move\relax }{subsubsection.11.12.2.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.4}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{125}{subsubsection.11.12.2.4}}
+\newlabel{fold_8h_a49e0ee561be69faf0568213546f6a53f}{{11.12.2.4}{125}{energy\-\_\-of\-\_\-move\-\_\-pt\relax }{subsubsection.11.12.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.5}loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy}{125}{subsubsection.11.12.2.5}}
+\newlabel{fold_8h_a507d4fd93f4b398d793ba2402731388d}{{11.12.2.5}{125}{loop\-\_\-energy\relax }{subsubsection.11.12.2.5}{}}
+\gdef \LT@lxxviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@lxxix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.6}assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db}{126}{subsubsection.11.12.2.6}}
+\newlabel{fold_8h_adaa59b81664e2e36cb9932e891558fae}{{11.12.2.6}{126}{assign\-\_\-plist\-\_\-from\-\_\-db\relax }{subsubsection.11.12.2.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.7}Loop\discretionary {-}{}{}Energy}{126}{subsubsection.11.12.2.7}}
+\newlabel{fold_8h_a2163034a25c6115d894b199e97e03f6c}{{11.12.2.7}{126}{Loop\-Energy\relax }{subsubsection.11.12.2.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.8}Hairpin\discretionary {-}{}{}E}{126}{subsubsection.11.12.2.8}}
+\newlabel{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{{11.12.2.8}{126}{Hairpin\-E\relax }{subsubsection.11.12.2.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.9}initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{126}{subsubsection.11.12.2.9}}
+\newlabel{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{{11.12.2.9}{126}{initialize\-\_\-fold\relax }{subsubsection.11.12.2.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.10}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct}{126}{subsubsection.11.12.2.10}}
+\newlabel{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{{11.12.2.10}{126}{energy\-\_\-of\-\_\-struct\relax }{subsubsection.11.12.2.10}{}}
+\gdef \LT@lxxx {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@lxxxi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.11}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{127}{subsubsection.11.12.2.11}}
+\newlabel{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{{11.12.2.11}{127}{energy\-\_\-of\-\_\-struct\-\_\-pt\relax }{subsubsection.11.12.2.11}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.12.2.12}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct}{127}{subsubsection.11.12.2.12}}
+\newlabel{fold_8h_a657222e2758c46bf13b416ef3032e417}{{11.12.2.12}{127}{energy\-\_\-of\-\_\-circ\-\_\-struct\relax }{subsubsection.11.12.2.12}{}}
+\gdef \LT@lxxxii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.13}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.h File Reference}{128}{section.11.13}}
+\newlabel{fold__vars_8h}{{11.13}{128}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.h File Reference\relax }{section.11.13}{}}
+\newlabel{fold__vars_8h_a0afc287c2464866d94858c39175154af}{{11.13}{129}{Variables\relax }{section*.96}{}}
+\newlabel{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{{11.13}{129}{Variables\relax }{section*.96}{}}
+\newlabel{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{{11.13}{129}{Variables\relax }{section*.96}{}}
+\newlabel{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{{11.13}{129}{Variables\relax }{section*.96}{}}
+\newlabel{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{{11.13}{129}{Variables\relax }{section*.96}{}}
+\gdef \LT@lxxxiii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\newlabel{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{{11.13}{130}{Variables\relax }{section*.96}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.13.1}Detailed Description}{130}{subsection.11.13.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.13.2}Function Documentation}{130}{subsection.11.13.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.2.1}set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details}{130}{subsubsection.11.13.2.1}}
+\newlabel{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{{11.13.2.1}{130}{set\-\_\-model\-\_\-details\relax }{subsubsection.11.13.2.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.13.3}Variable Documentation}{130}{subsection.11.13.3}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.1}no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs}{130}{subsubsection.11.13.3.1}}
+\newlabel{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{{11.13.3.1}{130}{no\-Lonely\-Pairs\relax }{subsubsection.11.13.3.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.2}dangles}{130}{subsubsection.11.13.3.2}}
+\newlabel{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{{11.13.3.2}{130}{dangles\relax }{subsubsection.11.13.3.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.3}tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop}{131}{subsubsection.11.13.3.3}}
+\newlabel{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{{11.13.3.3}{131}{tetra\-\_\-loop\relax }{subsubsection.11.13.3.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.4}energy\discretionary {-}{}{}\_\discretionary {-}{}{}set}{131}{subsubsection.11.13.3.4}}
+\newlabel{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{{11.13.3.4}{131}{energy\-\_\-set\relax }{subsubsection.11.13.3.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.5}old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}{131}{subsubsection.11.13.3.5}}
+\newlabel{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{{11.13.3.5}{131}{old\-Ali\-En\relax }{subsubsection.11.13.3.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.6}ribo}{131}{subsubsection.11.13.3.6}}
+\newlabel{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{{11.13.3.6}{131}{ribo\relax }{subsubsection.11.13.3.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.7}Ribosum\discretionary {-}{}{}File}{131}{subsubsection.11.13.3.7}}
+\newlabel{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{{11.13.3.7}{131}{Ribosum\-File\relax }{subsubsection.11.13.3.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.8}nonstandards}{131}{subsubsection.11.13.3.8}}
+\newlabel{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{{11.13.3.8}{131}{nonstandards\relax }{subsubsection.11.13.3.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.9}temperature}{131}{subsubsection.11.13.3.9}}
+\newlabel{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{{11.13.3.9}{131}{temperature\relax }{subsubsection.11.13.3.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.10}james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}{131}{subsubsection.11.13.3.10}}
+\newlabel{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{{11.13.3.10}{131}{james\-\_\-rule\relax }{subsubsection.11.13.3.10}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.11}log\discretionary {-}{}{}M\discretionary {-}{}{}L}{132}{subsubsection.11.13.3.11}}
+\newlabel{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{{11.13.3.11}{132}{log\-M\-L\relax }{subsubsection.11.13.3.11}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.12}cut\discretionary {-}{}{}\_\discretionary {-}{}{}point}{132}{subsubsection.11.13.3.12}}
+\newlabel{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{{11.13.3.12}{132}{cut\-\_\-point\relax }{subsubsection.11.13.3.12}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.13}base\discretionary {-}{}{}\_\discretionary {-}{}{}pair}{132}{subsubsection.11.13.3.13}}
+\newlabel{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{{11.13.3.13}{132}{base\-\_\-pair\relax }{subsubsection.11.13.3.13}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.14}pr}{132}{subsubsection.11.13.3.14}}
+\newlabel{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{{11.13.3.14}{132}{pr\relax }{subsubsection.11.13.3.14}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.15}iindx}{132}{subsubsection.11.13.3.15}}
+\newlabel{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{{11.13.3.15}{132}{iindx\relax }{subsubsection.11.13.3.15}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.16}pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale}{132}{subsubsection.11.13.3.16}}
+\newlabel{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{{11.13.3.16}{132}{pf\-\_\-scale\relax }{subsubsection.11.13.3.16}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.17}do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}{132}{subsubsection.11.13.3.17}}
+\newlabel{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{{11.13.3.17}{132}{do\-\_\-backtrack\relax }{subsubsection.11.13.3.17}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.13.3.18}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type}{133}{subsubsection.11.13.3.18}}
+\newlabel{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{{11.13.3.18}{133}{backtrack\-\_\-type\relax }{subsubsection.11.13.3.18}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.14}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/gquad.h File Reference}{133}{section.11.14}}
+\newlabel{gquad_8h}{{11.14}{133}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.h File Reference\relax }{section.11.14}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.14.1}Detailed Description}{133}{subsection.11.14.1}}
+\gdef \LT@lxxxiv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@lxxxv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.14.2}Function Documentation}{134}{subsection.11.14.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.14.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}{134}{subsubsection.11.14.2.1}}
+\newlabel{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{{11.14.2.1}{134}{get\-\_\-gquad\-\_\-matrix\relax }{subsubsection.11.14.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.14.2.2}parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad}{134}{subsubsection.11.14.2.2}}
+\newlabel{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{{11.14.2.2}{134}{parse\-\_\-gquad\relax }{subsubsection.11.14.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.14.2.3}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{134}{subsubsection.11.14.2.3}}
+\newlabel{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{{11.14.2.3}{134}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\relax }{subsubsection.11.14.2.3}{}}
+\gdef \LT@lxxxvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.14.2.4}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L}{135}{subsubsection.11.14.2.4}}
+\newlabel{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{{11.14.2.4}{135}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L\relax }{subsubsection.11.14.2.4}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.15}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/inverse.h File Reference}{135}{section.11.15}}
+\newlabel{inverse_8h}{{11.15}{135}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/inverse.h File Reference\relax }{section.11.15}{}}
+\newlabel{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}{{11.15}{135}{Variables\relax }{section*.99}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.15.1}Detailed Description}{135}{subsection.11.15.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.16}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}Lfold.h File Reference}{135}{section.11.16}}
+\newlabel{Lfold_8h}{{11.16}{135}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-Lfold.h File Reference\relax }{section.11.16}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.16.1}Detailed Description}{136}{subsection.11.16.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.17}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.h File Reference}{136}{section.11.17}}
+\newlabel{loop__energies_8h}{{11.17}{136}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/loop\-\_\-energies.h File Reference\relax }{section.11.17}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.17.1}Detailed Description}{136}{subsection.11.17.1}}
+\gdef \LT@lxxxvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.17.2}Function Documentation}{137}{subsection.11.17.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.1}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{137}{subsubsection.11.17.2.1}}
+\newlabel{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{{11.17.2.1}{137}{E\-\_\-\-Int\-Loop\relax }{subsubsection.11.17.2.1}{}}
+\gdef \LT@lxxxviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.2}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}{138}{subsubsection.11.17.2.2}}
+\newlabel{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{{11.17.2.2}{138}{E\-\_\-\-Hairpin\relax }{subsubsection.11.17.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.3}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}{138}{subsubsection.11.17.2.3}}
+\newlabel{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{{11.17.2.3}{138}{E\-\_\-\-Stem\relax }{subsubsection.11.17.2.3}{}}
+\gdef \LT@lxxxix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.4}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}{139}{subsubsection.11.17.2.4}}
+\newlabel{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{{11.17.2.4}{139}{exp\-\_\-\-E\-\_\-\-Stem\relax }{subsubsection.11.17.2.4}{}}
+\gdef \LT@xc {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.5}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}{140}{subsubsection.11.17.2.5}}
+\newlabel{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{{11.17.2.5}{140}{exp\-\_\-\-E\-\_\-\-Hairpin\relax }{subsubsection.11.17.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.17.2.6}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{140}{subsubsection.11.17.2.6}}
+\newlabel{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{{11.17.2.6}{140}{exp\-\_\-\-E\-\_\-\-Int\-Loop\relax }{subsubsection.11.17.2.6}{}}
+\gdef \LT@xci {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.18}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}L\discretionary {-}{}{}Pfold.h File Reference}{141}{section.11.18}}
+\newlabel{LPfold_8h}{{11.18}{141}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.h File Reference\relax }{section.11.18}{}}
+\newlabel{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{{11.18}{142}{Functions\relax }{section*.108}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.18.1}Detailed Description}{142}{subsection.11.18.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.18.2}Function Documentation}{142}{subsection.11.18.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.18.2.1}init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P}{142}{subsubsection.11.18.2.1}}
+\newlabel{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{{11.18.2.1}{142}{init\-\_\-pf\-\_\-fold\-L\-P\relax }{subsubsection.11.18.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.19}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A.h File Reference}{142}{section.11.19}}
+\newlabel{MEA_8h}{{11.19}{142}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-M\-E\-A.h File Reference\relax }{section.11.19}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.19.1}Detailed Description}{143}{subsection.11.19.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.19.2}Function Documentation}{143}{subsection.11.19.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.19.2.1}M\discretionary {-}{}{}E\discretionary {-}{}{}A}{143}{subsubsection.11.19.2.1}}
+\newlabel{MEA_8h_a396ec6144c6a74fcbab4cea6b42d76c3}{{11.19.2.1}{143}{M\-E\-A\relax }{subsubsection.11.19.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.20}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/mm.h File Reference}{144}{section.11.20}}
+\newlabel{mm_8h}{{11.20}{144}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.h File Reference\relax }{section.11.20}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.20.1}Detailed Description}{144}{subsection.11.20.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.21}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/naview.h File Reference}{144}{section.11.21}}
+\newlabel{naview_8h}{{11.21}{144}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.h File Reference\relax }{section.11.21}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.22}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/params.h File Reference}{145}{section.11.22}}
+\newlabel{params_8h}{{11.22}{145}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.h File Reference\relax }{section.11.22}{}}
+\newlabel{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{{11.22}{146}{Functions\relax }{section*.110}{}}
+\newlabel{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{{11.22}{146}{Functions\relax }{section*.110}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.23}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func.h File Reference}{146}{section.11.23}}
+\newlabel{part__func_8h}{{11.23}{146}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.h File Reference\relax }{section.11.23}{}}
+\newlabel{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{{11.23}{147}{Functions\relax }{section*.111}{}}
+\newlabel{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{{11.23}{147}{Functions\relax }{section*.111}{}}
+\newlabel{part__func_8h_a1f562d463c14d4703d9656056200eb38}{{11.23}{147}{Functions\relax }{section*.111}{}}
+\newlabel{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{{11.23}{147}{Functions\relax }{section*.111}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.23.1}Detailed Description}{148}{subsection.11.23.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.23.2}Function Documentation}{148}{subsection.11.23.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.23.2.1}init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{148}{subsubsection.11.23.2.1}}
+\newlabel{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{{11.23.2.1}{148}{init\-\_\-pf\-\_\-fold\relax }{subsubsection.11.23.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.23.2.2}centroid}{148}{subsubsection.11.23.2.2}}
+\newlabel{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{{11.23.2.2}{148}{centroid\relax }{subsubsection.11.23.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.23.2.3}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist}{148}{subsubsection.11.23.2.3}}
+\newlabel{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{{11.23.2.3}{148}{mean\-\_\-bp\-\_\-dist\relax }{subsubsection.11.23.2.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.23.2.4}exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy}{148}{subsubsection.11.23.2.4}}
+\newlabel{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{{11.23.2.4}{148}{exp\-Loop\-Energy\relax }{subsubsection.11.23.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.23.2.5}exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy}{148}{subsubsection.11.23.2.5}}
+\newlabel{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{{11.23.2.5}{148}{exp\-Hairpin\-Energy\relax }{subsubsection.11.23.2.5}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.24}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.h File Reference}{148}{section.11.24}}
+\newlabel{part__func__co_8h}{{11.24}{148}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.h File Reference\relax }{section.11.24}{}}
+\newlabel{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{{11.24}{149}{Functions\relax }{section*.113}{}}
+\newlabel{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{{11.24}{150}{Variables\relax }{section*.114}{}}
+\newlabel{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{{11.24}{150}{Variables\relax }{section*.114}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.24.1}Detailed Description}{150}{subsection.11.24.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.24.2}Function Documentation}{150}{subsection.11.24.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.24.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}plist}{150}{subsubsection.11.24.2.1}}
+\newlabel{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{{11.24.2.1}{150}{get\-\_\-plist\relax }{subsubsection.11.24.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.24.2.2}init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{150}{subsubsection.11.24.2.2}}
+\newlabel{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{{11.24.2.2}{150}{init\-\_\-co\-\_\-pf\-\_\-fold\relax }{subsubsection.11.24.2.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.25}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}up.h File Reference}{150}{section.11.25}}
+\newlabel{part__func__up_8h}{{11.25}{150}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.h File Reference\relax }{section.11.25}{}}
+\newlabel{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}{{11.25}{151}{Functions\relax }{section*.115}{}}
+\newlabel{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}{{11.25}{151}{Functions\relax }{section*.115}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.25.1}Detailed Description}{151}{subsection.11.25.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.26}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.h File Reference}{152}{section.11.26}}
+\newlabel{plot__layouts_8h}{{11.26}{152}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/plot\-\_\-layouts.h File Reference\relax }{section.11.26}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.26.1}Detailed Description}{153}{subsection.11.26.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.26.2}Macro Definition Documentation}{153}{subsection.11.26.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}I\discretionary {-}{}{}M\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}E}{153}{subsubsection.11.26.2.1}}
+\newlabel{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{{11.26.2.1}{153}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E\relax }{subsubsection.11.26.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.2.2}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}V\discretionary {-}{}{}I\discretionary {-}{}{}E\discretionary {-}{}{}W}{153}{subsubsection.11.26.2.2}}
+\newlabel{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{{11.26.2.2}{153}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W\relax }{subsubsection.11.26.2.2}{}}
+\gdef \LT@xcii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@xciii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.2.3}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}C\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}R}{154}{subsubsection.11.26.2.3}}
+\newlabel{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{{11.26.2.3}{154}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R\relax }{subsubsection.11.26.2.3}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.26.3}Function Documentation}{154}{subsection.11.26.3}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.3.1}simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}{154}{subsubsection.11.26.3.1}}
+\newlabel{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{{11.26.3.1}{154}{simple\-\_\-xy\-\_\-coordinates\relax }{subsubsection.11.26.3.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.3.2}simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}{154}{subsubsection.11.26.3.2}}
+\newlabel{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{{11.26.3.2}{154}{simple\-\_\-circplot\-\_\-coordinates\relax }{subsubsection.11.26.3.2}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.26.4}Variable Documentation}{155}{subsection.11.26.4}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.26.4.1}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type}{155}{subsubsection.11.26.4.1}}
+\newlabel{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{{11.26.4.1}{155}{rna\-\_\-plot\-\_\-type\relax }{subsubsection.11.26.4.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.27}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/profiledist.h File Reference}{155}{section.11.27}}
+\newlabel{profiledist_8h}{{11.27}{155}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.h File Reference\relax }{section.11.27}{}}
+\gdef \LT@xciv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\newlabel{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{{11.27}{156}{Functions\relax }{section*.119}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.27.1}Function Documentation}{156}{subsection.11.27.1}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.27.1.1}profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{156}{subsubsection.11.27.1.1}}
+\newlabel{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{{11.27.1.1}{156}{profile\-\_\-edit\-\_\-distance\relax }{subsubsection.11.27.1.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.27.1.2}Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{156}{subsubsection.11.27.1.2}}
+\newlabel{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{{11.27.1.2}{156}{Make\-\_\-bp\-\_\-profile\-\_\-bppm\relax }{subsubsection.11.27.1.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.27.1.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}profile}{156}{subsubsection.11.27.1.3}}
+\newlabel{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{{11.27.1.3}{156}{free\-\_\-profile\relax }{subsubsection.11.27.1.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.27.1.4}Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile}{156}{subsubsection.11.27.1.4}}
+\newlabel{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{{11.27.1.4}{156}{Make\-\_\-bp\-\_\-profile\relax }{subsubsection.11.27.1.4}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.28}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.h File Reference}{157}{section.11.28}}
+\newlabel{PS__dot_8h}{{11.28}{157}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.h File Reference\relax }{section.11.28}{}}
+\gdef \LT@xcv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@xcvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.28.1}Detailed Description}{158}{subsection.11.28.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.28.2}Function Documentation}{158}{subsection.11.28.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.1}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{158}{subsubsection.11.28.2.1}}
+\newlabel{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{{11.28.2.1}{158}{P\-S\-\_\-rna\-\_\-plot\relax }{subsubsection.11.28.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.2}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a}{158}{subsubsection.11.28.2.2}}
+\newlabel{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{{11.28.2.2}{158}{P\-S\-\_\-rna\-\_\-plot\-\_\-a\relax }{subsubsection.11.28.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.3}gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}{158}{subsubsection.11.28.2.3}}
+\newlabel{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{{11.28.2.3}{158}{gml\-R\-N\-A\relax }{subsubsection.11.28.2.3}{}}
+\gdef \LT@xcvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@xcviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@xcix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@c {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.4}ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.4}}
+\newlabel{PS__dot_8h_add368528755f9a830727b680243541df}{{11.28.2.4}{159}{ssv\-\_\-rna\-\_\-plot\relax }{subsubsection.11.28.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.5}svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.5}}
+\newlabel{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{{11.28.2.5}{159}{svg\-\_\-rna\-\_\-plot\relax }{subsubsection.11.28.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.6}xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.6}}
+\newlabel{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{{11.28.2.6}{159}{xrna\-\_\-plot\relax }{subsubsection.11.28.2.6}{}}
+\gdef \LT@ci {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.7}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list}{160}{subsubsection.11.28.2.7}}
+\newlabel{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{{11.28.2.7}{160}{P\-S\-\_\-dot\-\_\-plot\-\_\-list\relax }{subsubsection.11.28.2.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.8}ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln}{160}{subsubsection.11.28.2.8}}
+\newlabel{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{{11.28.2.8}{160}{ali\-P\-S\-\_\-color\-\_\-aln\relax }{subsubsection.11.28.2.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.28.2.9}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{160}{subsubsection.11.28.2.9}}
+\newlabel{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{{11.28.2.9}{160}{P\-S\-\_\-dot\-\_\-plot\relax }{subsubsection.11.28.2.9}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.29}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/read\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{160}{section.11.29}}
+\newlabel{read__epars_8h}{{11.29}{160}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.h File Reference\relax }{section.11.29}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.30}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.h File Reference}{161}{section.11.30}}
+\newlabel{RNAstruct_8h}{{11.30}{161}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.h File Reference\relax }{section.11.30}{}}
+\newlabel{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\newlabel{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\newlabel{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\newlabel{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\newlabel{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\newlabel{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{{11.30}{161}{Variables\relax }{section*.123}{}}
+\gdef \LT@cii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@ciii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@civ {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.30.1}Detailed Description}{162}{subsection.11.30.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.30.2}Function Documentation}{162}{subsection.11.30.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.1}b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T}{162}{subsubsection.11.30.2.1}}
+\newlabel{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}{{11.30.2.1}{162}{b2\-H\-I\-T\relax }{subsubsection.11.30.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.2}b2\discretionary {-}{}{}C}{162}{subsubsection.11.30.2.2}}
+\newlabel{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{{11.30.2.2}{162}{b2\-C\relax }{subsubsection.11.30.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.3}b2\discretionary {-}{}{}Shapiro}{162}{subsubsection.11.30.2.3}}
+\newlabel{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{{11.30.2.3}{162}{b2\-Shapiro\relax }{subsubsection.11.30.2.3}{}}
+\gdef \LT@cv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.4}add\discretionary {-}{}{}\_\discretionary {-}{}{}root}{163}{subsubsection.11.30.2.4}}
+\newlabel{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{{11.30.2.4}{163}{add\-\_\-root\relax }{subsubsection.11.30.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.5}expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro}{163}{subsubsection.11.30.2.5}}
+\newlabel{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{{11.30.2.5}{163}{expand\-\_\-\-Shapiro\relax }{subsubsection.11.30.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.6}expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}{163}{subsubsection.11.30.2.6}}
+\newlabel{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{{11.30.2.6}{163}{expand\-\_\-\-Full\relax }{subsubsection.11.30.2.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.7}unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}{163}{subsubsection.11.30.2.7}}
+\newlabel{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{{11.30.2.7}{163}{unexpand\-\_\-\-Full\relax }{subsubsection.11.30.2.7}{}}
+\gdef \LT@cix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cx {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.8}unweight}{164}{subsubsection.11.30.2.8}}
+\newlabel{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{{11.30.2.8}{164}{unweight\relax }{subsubsection.11.30.2.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.9}unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F}{164}{subsubsection.11.30.2.9}}
+\newlabel{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{{11.30.2.9}{164}{unexpand\-\_\-aligned\-\_\-\-F\relax }{subsubsection.11.30.2.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.30.2.10}parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{164}{subsubsection.11.30.2.10}}
+\newlabel{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{{11.30.2.10}{164}{parse\-\_\-structure\relax }{subsubsection.11.30.2.10}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.31}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/stringdist.h File Reference}{164}{section.11.31}}
+\newlabel{stringdist_8h}{{11.31}{164}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.h File Reference\relax }{section.11.31}{}}
+\gdef \LT@cxii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxiii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.31.1}Detailed Description}{165}{subsection.11.31.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.31.2}Function Documentation}{165}{subsection.11.31.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.31.2.1}Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String}{165}{subsubsection.11.31.2.1}}
+\newlabel{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{{11.31.2.1}{165}{Make\-\_\-sw\-String\relax }{subsubsection.11.31.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.31.2.2}string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{165}{subsubsection.11.31.2.2}}
+\newlabel{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{{11.31.2.2}{165}{string\-\_\-edit\-\_\-distance\relax }{subsubsection.11.31.2.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.32}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/subopt.h File Reference}{166}{section.11.32}}
+\newlabel{subopt_8h}{{11.32}{166}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.h File Reference\relax }{section.11.32}{}}
+\newlabel{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{{11.32}{166}{Functions\relax }{section*.125}{}}
+\newlabel{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{{11.32}{166}{Variables\relax }{section*.126}{}}
+\newlabel{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{{11.32}{166}{Variables\relax }{section*.126}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.32.1}Detailed Description}{167}{subsection.11.32.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.33}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/treedist.h File Reference}{167}{section.11.33}}
+\newlabel{treedist_8h}{{11.33}{167}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.h File Reference\relax }{section.11.33}{}}
+\newlabel{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{{11.33}{167}{Functions\relax }{section*.127}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.33.1}Detailed Description}{167}{subsection.11.33.1}}
+\gdef \LT@cxiv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.33.2}Function Documentation}{168}{subsection.11.33.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.33.2.1}make\discretionary {-}{}{}\_\discretionary {-}{}{}tree}{168}{subsubsection.11.33.2.1}}
+\newlabel{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{{11.33.2.1}{168}{make\-\_\-tree\relax }{subsubsection.11.33.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.33.2.2}tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{168}{subsubsection.11.33.2.2}}
+\newlabel{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{{11.33.2.2}{168}{tree\-\_\-edit\-\_\-distance\relax }{subsubsection.11.33.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.33.2.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}tree}{168}{subsubsection.11.33.2.3}}
+\newlabel{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{{11.33.2.3}{168}{free\-\_\-tree\relax }{subsubsection.11.33.2.3}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.34}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/utils.h File Reference}{168}{section.11.34}}
+\newlabel{utils_8h}{{11.34}{168}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.h File Reference\relax }{section.11.34}{}}
+\newlabel{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{{11.34}{170}{Functions\relax }{section*.129}{}}
+\newlabel{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{{11.34}{170}{Functions\relax }{section*.129}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.34.1}Detailed Description}{171}{subsection.11.34.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.34.2}Macro Definition Documentation}{171}{subsection.11.34.2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R}{171}{subsubsection.11.34.2.1}}
+\newlabel{utils_8h_ad403c9ea58f1836689404c2931419c8c}{{11.34.2.1}{171}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R\relax }{subsubsection.11.34.2.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.2}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}I\discretionary {-}{}{}T}{171}{subsubsection.11.34.2.2}}
+\newlabel{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{{11.34.2.2}{171}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T\relax }{subsubsection.11.34.2.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.3}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}{171}{subsubsection.11.34.2.3}}
+\newlabel{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{{11.34.2.3}{171}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C\relax }{subsubsection.11.34.2.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.4}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}E\discretionary {-}{}{}A\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}R}{171}{subsubsection.11.34.2.4}}
+\newlabel{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{{11.34.2.4}{171}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R\relax }{subsubsection.11.34.2.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.5}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}E\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}E}{171}{subsubsection.11.34.2.5}}
+\newlabel{utils_8h_a8566d6787972100e68b5a2a159b4cf45}{{11.34.2.5}{171}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E\relax }{subsubsection.11.34.2.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.6}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{172}{subsubsection.11.34.2.6}}
+\newlabel{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}{{11.34.2.6}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\relax }{subsubsection.11.34.2.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.7}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}U\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N}{172}{subsubsection.11.34.2.7}}
+\newlabel{utils_8h_a086742158293217a46ae2f71bb296937}{{11.34.2.7}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N\relax }{subsubsection.11.34.2.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.8}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}E\discretionary {-}{}{}S\discretionary {-}{}{}T}{172}{subsubsection.11.34.2.8}}
+\newlabel{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{{11.34.2.8}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T\relax }{subsubsection.11.34.2.8}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.9}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}N}{172}{subsubsection.11.34.2.9}}
+\newlabel{utils_8h_a0de536599b881c787b0943a2671da476}{{11.34.2.9}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N\relax }{subsubsection.11.34.2.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.10}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}S\discretionary {-}{}{}K\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}K\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E\discretionary {-}{}{}S}{172}{subsubsection.11.34.2.10}}
+\newlabel{utils_8h_ab4db885222b3b69608310d7c7e63e286}{{11.34.2.10}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S\relax }{subsubsection.11.34.2.10}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.11}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}K\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{172}{subsubsection.11.34.2.11}}
+\newlabel{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}{{11.34.2.11}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\relax }{subsubsection.11.34.2.11}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.12}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}S\discretionary {-}{}{}K\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}S}{172}{subsubsection.11.34.2.12}}
+\newlabel{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{{11.34.2.12}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S\relax }{subsubsection.11.34.2.12}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.13}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T}{172}{subsubsection.11.34.2.13}}
+\newlabel{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}{{11.34.2.13}{172}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T\relax }{subsubsection.11.34.2.13}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.14}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}E}{172}{subsubsection.11.34.2.14}}
+\newlabel{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{{11.34.2.14}{172}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E\relax }{subsubsection.11.34.2.14}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.15}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}O\discretionary {-}{}{}T}{172}{subsubsection.11.34.2.15}}
+\newlabel{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{{11.34.2.15}{172}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T\relax }{subsubsection.11.34.2.15}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.16}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}X}{172}{subsubsection.11.34.2.16}}
+\newlabel{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{{11.34.2.16}{172}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X\relax }{subsubsection.11.34.2.16}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.17}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{172}{subsubsection.11.34.2.17}}
+\newlabel{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{{11.34.2.17}{172}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K\relax }{subsubsection.11.34.2.17}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.18}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{173}{subsubsection.11.34.2.18}}
+\newlabel{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{{11.34.2.18}{173}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K\relax }{subsubsection.11.34.2.18}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.19}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{173}{subsubsection.11.34.2.19}}
+\newlabel{utils_8h_a7d725ef525b29891abef3f1ed42599a4}{{11.34.2.19}{173}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E\relax }{subsubsection.11.34.2.19}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.20}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}E\discretionary {-}{}{}A\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}R}{173}{subsubsection.11.34.2.20}}
+\newlabel{utils_8h_a08d12a9a846ea593b7171d277c9f033f}{{11.34.2.20}{173}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R\relax }{subsubsection.11.34.2.20}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.21}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}{173}{subsubsection.11.34.2.21}}
+\newlabel{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}{{11.34.2.21}{173}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L\relax }{subsubsection.11.34.2.21}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.22}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G}{173}{subsubsection.11.34.2.22}}
+\newlabel{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}{{11.34.2.22}{173}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G\relax }{subsubsection.11.34.2.22}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.23}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}P\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{173}{subsubsection.11.34.2.23}}
+\newlabel{utils_8h_abec89c09874528c6cb73140a4c3d86d7}{{11.34.2.23}{173}{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E\relax }{subsubsection.11.34.2.23}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.24}M\discretionary {-}{}{}I\discretionary {-}{}{}N2}{173}{subsubsection.11.34.2.24}}
+\newlabel{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{{11.34.2.24}{173}{M\-I\-N2\relax }{subsubsection.11.34.2.24}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.25}M\discretionary {-}{}{}A\discretionary {-}{}{}X2}{173}{subsubsection.11.34.2.25}}
+\newlabel{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{{11.34.2.25}{173}{M\-A\-X2\relax }{subsubsection.11.34.2.25}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.26}M\discretionary {-}{}{}I\discretionary {-}{}{}N3}{173}{subsubsection.11.34.2.26}}
+\newlabel{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{{11.34.2.26}{173}{M\-I\-N3\relax }{subsubsection.11.34.2.26}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.27}M\discretionary {-}{}{}A\discretionary {-}{}{}X3}{173}{subsubsection.11.34.2.27}}
+\newlabel{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{{11.34.2.27}{173}{M\-A\-X3\relax }{subsubsection.11.34.2.27}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.28}X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R}{173}{subsubsection.11.34.2.28}}
+\newlabel{utils_8h_a03943706e48069237cd57f2d35ca987e}{{11.34.2.28}{173}{X\-S\-T\-R\relax }{subsubsection.11.34.2.28}{}}
+\gdef \LT@cxvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.29}S\discretionary {-}{}{}T\discretionary {-}{}{}R}{174}{subsubsection.11.34.2.29}}
+\newlabel{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{{11.34.2.29}{174}{S\-T\-R\relax }{subsubsection.11.34.2.29}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.30}F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}{174}{subsubsection.11.34.2.30}}
+\newlabel{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{{11.34.2.30}{174}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H\relax }{subsubsection.11.34.2.30}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.2.31}F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}{174}{subsubsection.11.34.2.31}}
+\newlabel{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{{11.34.2.31}{174}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H\relax }{subsubsection.11.34.2.31}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.34.3}Function Documentation}{174}{subsection.11.34.3}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.1}space}{174}{subsubsection.11.34.3.1}}
+\newlabel{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{{11.34.3.1}{174}{space\relax }{subsubsection.11.34.3.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.2}xrealloc}{174}{subsubsection.11.34.3.2}}
+\newlabel{utils_8h_a9037ada838835b1b9db41581a021b0c8}{{11.34.3.2}{174}{xrealloc\relax }{subsubsection.11.34.3.2}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.3}nrerror}{174}{subsubsection.11.34.3.3}}
+\newlabel{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{{11.34.3.3}{174}{nrerror\relax }{subsubsection.11.34.3.3}{}}
+\gdef \LT@cxx {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.4}warn\discretionary {-}{}{}\_\discretionary {-}{}{}user}{175}{subsubsection.11.34.3.4}}
+\newlabel{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{{11.34.3.4}{175}{warn\-\_\-user\relax }{subsubsection.11.34.3.4}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.5}urn}{175}{subsubsection.11.34.3.5}}
+\newlabel{utils_8h_aaa328491c84996e445d027fde9800f2e}{{11.34.3.5}{175}{urn\relax }{subsubsection.11.34.3.5}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.6}int\discretionary {-}{}{}\_\discretionary {-}{}{}urn}{175}{subsubsection.11.34.3.6}}
+\newlabel{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{{11.34.3.6}{175}{int\-\_\-urn\relax }{subsubsection.11.34.3.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.7}time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp}{175}{subsubsection.11.34.3.7}}
+\newlabel{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{{11.34.3.7}{175}{time\-\_\-stamp\relax }{subsubsection.11.34.3.7}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.8}random\discretionary {-}{}{}\_\discretionary {-}{}{}string}{175}{subsubsection.11.34.3.8}}
+\newlabel{utils_8h_a1b95eac365a021572e1c37e5993a89be}{{11.34.3.8}{175}{random\-\_\-string\relax }{subsubsection.11.34.3.8}{}}
+\gdef \LT@cxxiii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxiv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.9}hamming}{176}{subsubsection.11.34.3.9}}
+\newlabel{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{{11.34.3.9}{176}{hamming\relax }{subsubsection.11.34.3.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.10}hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}{176}{subsubsection.11.34.3.10}}
+\newlabel{utils_8h_a96d3c36717d624514055ce201cab1542}{{11.34.3.10}{176}{hamming\-\_\-bound\relax }{subsubsection.11.34.3.10}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.11}get\discretionary {-}{}{}\_\discretionary {-}{}{}line}{176}{subsubsection.11.34.3.11}}
+\newlabel{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{{11.34.3.11}{176}{get\-\_\-line\relax }{subsubsection.11.34.3.11}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.12}get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line}{176}{subsubsection.11.34.3.12}}
+\newlabel{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{{11.34.3.12}{176}{get\-\_\-input\-\_\-line\relax }{subsubsection.11.34.3.12}{}}
+\gdef \LT@cxxvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.13}read\discretionary {-}{}{}\_\discretionary {-}{}{}record}{177}{subsubsection.11.34.3.13}}
+\newlabel{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{{11.34.3.13}{177}{read\-\_\-record\relax }{subsubsection.11.34.3.13}{}}
+\gdef \LT@cxxvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.14}pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{178}{subsubsection.11.34.3.14}}
+\newlabel{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{{11.34.3.14}{178}{pack\-\_\-structure\relax }{subsubsection.11.34.3.14}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.15}unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{178}{subsubsection.11.34.3.15}}
+\newlabel{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{{11.34.3.15}{178}{unpack\-\_\-structure\relax }{subsubsection.11.34.3.15}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.16}make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{178}{subsubsection.11.34.3.16}}
+\newlabel{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{{11.34.3.16}{178}{make\-\_\-pair\-\_\-table\relax }{subsubsection.11.34.3.16}{}}
+\gdef \LT@cxxx {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.17}copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{179}{subsubsection.11.34.3.17}}
+\newlabel{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{{11.34.3.17}{179}{copy\-\_\-pair\-\_\-table\relax }{subsubsection.11.34.3.17}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.18}alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{179}{subsubsection.11.34.3.18}}
+\newlabel{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{{11.34.3.18}{179}{alimake\-\_\-pair\-\_\-table\relax }{subsubsection.11.34.3.18}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.19}make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop}{179}{subsubsection.11.34.3.19}}
+\newlabel{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{{11.34.3.19}{179}{make\-\_\-pair\-\_\-table\-\_\-snoop\relax }{subsubsection.11.34.3.19}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.20}make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{179}{subsubsection.11.34.3.20}}
+\newlabel{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{{11.34.3.20}{179}{make\-\_\-loop\-\_\-index\-\_\-pt\relax }{subsubsection.11.34.3.20}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.21}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq}{179}{subsubsection.11.34.3.21}}
+\newlabel{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{{11.34.3.21}{179}{print\-\_\-tty\-\_\-input\-\_\-seq\relax }{subsubsection.11.34.3.21}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.22}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str}{179}{subsubsection.11.34.3.22}}
+\newlabel{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{{11.34.3.22}{179}{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str\relax }{subsubsection.11.34.3.22}{}}
+\gdef \LT@cxxxiii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxiv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxv {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxvi {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.23}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint}{180}{subsubsection.11.34.3.23}}
+\newlabel{utils_8h_a4d167deb70bb51723e44374dc981deb2}{{11.34.3.23}{180}{print\-\_\-tty\-\_\-constraint\relax }{subsubsection.11.34.3.23}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.24}str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}{180}{subsubsection.11.34.3.24}}
+\newlabel{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{{11.34.3.24}{180}{str\-\_\-\-D\-N\-A2\-R\-N\-A\relax }{subsubsection.11.34.3.24}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.25}str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase}{180}{subsubsection.11.34.3.25}}
+\newlabel{utils_8h_a17b796b806f96b70382077fb5bc519bb}{{11.34.3.25}{180}{str\-\_\-uppercase\relax }{subsubsection.11.34.3.25}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.26}get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx}{180}{subsubsection.11.34.3.26}}
+\newlabel{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{{11.34.3.26}{180}{get\-\_\-iindx\relax }{subsubsection.11.34.3.26}{}}
+\gdef \LT@cxxxvii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxviii {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\gdef \LT@cxxxix {\LT@entry 
+    {1}{78.18367pt}\LT@entry 
+    {1}{380.5249pt}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.27}get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}{181}{subsubsection.11.34.3.27}}
+\newlabel{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{{11.34.3.27}{181}{get\-\_\-indx\relax }{subsubsection.11.34.3.27}{}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.3.28}constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}{181}{subsubsection.11.34.3.28}}
+\newlabel{utils_8h_a36c3a6c3218b041f992052767bc74549}{{11.34.3.28}{181}{constrain\-\_\-ptypes\relax }{subsubsection.11.34.3.28}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.34.4}Variable Documentation}{182}{subsection.11.34.4}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {11.34.4.1}xsubi}{182}{subsubsection.11.34.4.1}}
+\newlabel{utils_8h_af9a866c8417afda7368bbac939ab3c47}{{11.34.4.1}{182}{xsubi\relax }{subsubsection.11.34.4.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.35}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{182}{section.11.35}}
+\newlabel{1_88_84__epars_8h}{{11.35}{182}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.8.4\-\_\-epars.h File Reference\relax }{section.11.35}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.35.1}Detailed Description}{182}{subsection.11.35.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {11.36}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.h File Reference}{182}{section.11.36}}
+\newlabel{1_88_84__intloops_8h}{{11.36}{182}{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.8.4\-\_\-intloops.h File Reference\relax }{section.11.36}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {11.36.1}Detailed Description}{182}{subsection.11.36.1}}
+\bibstyle{plain}
+\bibdata{viennarna}
+\bibcite{bernhart:2008}{{1}{}{{}}{{}}}
+\bibcite{bernhart:2006}{{2}{}{{}}{{}}}
+\bibcite{fontana:1993b}{{3}{}{{}}{{}}}
+\bibcite{hofacker:2002}{{4}{}{{}}{{}}}
+\bibcite{hofacker:1994}{{5}{}{{}}{{}}}
+\bibcite{hofacker:2006}{{6}{}{{}}{{}}}
+\bibcite{lorenz:2011}{{7}{}{{}}{{}}}
+\bibcite{lorenz:2009}{{8}{}{{}}{{}}}
+\bibcite{mathews:2004}{{9}{}{{}}{{}}}
+\bibcite{mccaskill:1990}{{10}{}{{}}{{}}}
+\bibcite{shapiro:1988}{{11}{}{{}}{{}}}
+\bibcite{turner:2010}{{12}{}{{}}{{}}}
+\bibcite{zuker:1981}{{13}{}{{}}{{}}}
+\@writefile{toc}{\contentsline {part}{Index}{183}{chapter*.131}}
+\providecommand\NAT@force@numbers{}\NAT@force@numbers