\documentclass[a4paper]{article}
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\makeindex
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\begin{document}
\hypersetup{pageanchor=false}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large ThreeB \\[1ex]\large 1.1 }\\
\vspace*{1cm}
{\large Generated by Doxygen 1.7.4}\\
\vspace*{0.5cm}
{\small Wed Nov 28 2012 16:07:16}\\
\end{center}
\end{titlepage}
\pagenumbering{roman}
\tableofcontents
\pagenumbering{arabic}
\hypersetup{pageanchor=true}
\section{3B Microscopy Analysis}
\label{index}\hypertarget{index}{}\input{index}
\section{Compiling the programs}
\label{sComp}
\hypertarget{sComp}{}
\input{sComp}
\section{Module Index}
\input{modules}
\section{Namespace Index}
\input{namespaces}
\section{Class Index}
\input{hierarchy}
\section{Class Index}
\input{annotated}
\section{File Index}
\input{files}
\section{Module Documentation}
\input{group__gDebug}
\input{group__gUtility}
\input{group__gHMM}
\input{group__gPlugin}
\input{group__gStorm}
\input{group__gStormImages}
\input{group__gMultiSpot}
\section{Namespace Documentation}
\input{namespaceSampledMultispot}
\section{Class Documentation}
\input{classAdvancedDialog}
\input{classClassicGlow}
\input{classCloseButtonListener}
\input{structConjugateGradientOnly}
\input{classDataForMCMC}
\input{classEControlPanel}
\input{classExportButtonListener}
\input{classFitSpots}
\input{classFitSpotsGraphics}
\input{classFloatSliderWithBox}
\input{classFreeEnergyHessian}
\input{classSampledMultispot_1_1GibbsSampler}
\input{classSampledMultispot_1_1GibbsSampler2}
\input{structIndexLexicographicPosition}
\input{classJNIUserInterface}
\input{classKahan}
\input{structLessSecond}
\input{classLoadTestData}
\input{structLogFileParseError}
\input{structMT19937}
\input{classNegativeFreeEnergy}
\input{classNullGraphics}
\input{classNullUICallback}
\input{structMT19937_1_1ParseError}
\input{structSampledBackgroundData}
\input{classFloatSliderWithBox_1_1SliderChanged}
\input{classSomethingChanges}
\input{classSPair}
\input{classSpot}
\input{structSpotNegProbabilityDiffWithSampledBackground}
\input{structSampledMultispot_1_1SpotWithBackgroundMasked}
\input{structStateParameters}
\input{classStopButtonListener}
\input{classFloatSliderWithBox_1_1TextChanged}
\input{classthree__B}
\input{classThreeBDialog}
\input{classThreeBGlobalConstants}
\input{classThreeBHelp}
\input{classThreeBLoader}
\input{classThreeBRunner}
\input{classUserInterfaceCallback}
\input{structUserInterfaceCallback_1_1UserIssuedStop}
\input{classUtil}
\section{File Documentation}
\input{ClassicGlow_8java}
\input{conjugate__gradient__only_8h}
\input{debug_8h}
\input{documentation_8h}
\input{forward__algorithm_8h}
\input{LoadTestData_8java}
\input{mersenne_8cpp}
\input{mt19937_8h}
\input{multispot5_8cc}
\input{multispot5_8h}
\input{multispot5__headless_8cc}
\input{multispot5__jni_8cc}
\input{randomc_8h}
\input{sampled__multispot_8h}
\input{storm_8h}
\input{storm__imagery_8cc}
\input{storm__imagery_8h}
\input{three__B_8java}
\input{ThreeBHelp_8java}
\input{ThreeBLoader_8java}
\input{utility_8cc}
\input{utility_8h}
\printindex
\end{document}
