\subsection{Class List}
Here are the classes, structs, unions and interfaces with brief descriptions:\begin{DoxyCompactList}
\item\contentsline{section}{\hyperlink{classAdvancedDialog}{AdvancedDialog} (Control panel which basically presents the .cfg file in a large edit box along with additional necessary things (frame range and pixel size) )}{\pageref{classAdvancedDialog}}{}
\item\contentsline{section}{\hyperlink{classClassicGlow}{ClassicGlow} (Plugin implementing the classic glow/hot LUT which seems to be missing from ImageJ )}{\pageref{classClassicGlow}}{}
\item\contentsline{section}{\hyperlink{classCloseButtonListener}{CloseButtonListener} (Close button issues a window close event )}{\pageref{classCloseButtonListener}}{}
\item\contentsline{section}{\hyperlink{structConjugateGradientOnly}{ConjugateGradientOnly$<$ Size, Precision $>$} (Class for performing optimization with Conjugate Gradient, where only the derivatives are available )}{\pageref{structConjugateGradientOnly}}{}
\item\contentsline{section}{\hyperlink{classDataForMCMC}{DataForMCMC} (Closure hoding the data required do use GibbsSampler2 See \hyperlink{classFitSpots}{FitSpots} for naming of variables )}{\pageref{classDataForMCMC}}{}
\item\contentsline{section}{\hyperlink{classEControlPanel}{EControlPanel} (Control panel for running 3B plugin and providing interactive update )}{\pageref{classEControlPanel}}{}
\item\contentsline{section}{\hyperlink{classExportButtonListener}{ExportButtonListener} (Listener for the export button )}{\pageref{classExportButtonListener}}{}
\item\contentsline{section}{\hyperlink{classFitSpots}{FitSpots} (Mega class which actually does the meat of the spot fitting )}{\pageref{classFitSpots}}{}
\item\contentsline{section}{\hyperlink{classFitSpotsGraphics}{FitSpotsGraphics} (Graphics class for FittingSpots )}{\pageref{classFitSpotsGraphics}}{}
\item\contentsline{section}{\hyperlink{classFloatSliderWithBox}{FloatSliderWithBox} (This class makes a floating point slider bar with an edit box next to it for more precision )}{\pageref{classFloatSliderWithBox}}{}
\item\contentsline{section}{\hyperlink{classFreeEnergyHessian}{FreeEnergyHessian} (Class for computing the Hessian of the negative free energy )}{\pageref{classFreeEnergyHessian}}{}
\item\contentsline{section}{\hyperlink{classSampledMultispot_1_1GibbsSampler}{SampledMultispot::GibbsSampler} (Draw samples from the spot states given the spots positions and some data )}{\pageref{classSampledMultispot_1_1GibbsSampler}}{}
\item\contentsline{section}{\hyperlink{classSampledMultispot_1_1GibbsSampler2}{SampledMultispot::GibbsSampler2} (Gibbs sampling class which masks spots to reduce computation )}{\pageref{classSampledMultispot_1_1GibbsSampler2}}{}
\item\contentsline{section}{\hyperlink{structIndexLexicographicPosition}{IndexLexicographicPosition$<$ Cmp, First $>$} (Class for sorting a list of indexes to an array of spots lexicographically according to the 2D positions of the spots )}{\pageref{structIndexLexicographicPosition}}{}
\item\contentsline{section}{\hyperlink{classJNIUserInterface}{JNIUserInterface} (3B User interface for the Java plugin )}{\pageref{classJNIUserInterface}}{}
\item\contentsline{section}{\hyperlink{classKahan}{Kahan} (Class implementing the \hyperlink{classKahan}{Kahan} summation algorithm to allow accurate summation of very large numbers of doubles )}{\pageref{classKahan}}{}
\item\contentsline{section}{\hyperlink{structLessSecond}{LessSecond} (Comparator functor for the first element of a std::pair )}{\pageref{structLessSecond}}{}
\item\contentsline{section}{\hyperlink{classLoadTestData}{LoadTestData} (Plugin class to load the standard test data from the JAR file )}{\pageref{classLoadTestData}}{}
\item\contentsline{section}{\hyperlink{structLogFileParseError}{LogFileParseError} (Null struct thrown if a parse error is encountered when trying to load a log file )}{\pageref{structLogFileParseError}}{}
\item\contentsline{section}{\hyperlink{structMT19937}{MT19937} (Useful wrapper for \hyperlink{structMT19937}{MT19937} random number generator class )}{\pageref{structMT19937}}{}
\item\contentsline{section}{\hyperlink{classNegativeFreeEnergy}{NegativeFreeEnergy} (Class for computing the negitve free energy using thermodynamic integration )}{\pageref{classNegativeFreeEnergy}}{}
\item\contentsline{section}{\hyperlink{classNullGraphics}{NullGraphics} (Graphics class which does absoloutely nothing )}{\pageref{classNullGraphics}}{}
\item\contentsline{section}{\hyperlink{classNullUICallback}{NullUICallback} (User interface callback class which does nothing )}{\pageref{classNullUICallback}}{}
\item\contentsline{section}{\hyperlink{structMT19937_1_1ParseError}{MT19937::ParseError} (Null struct thrown if attempting to load state from stream yields a parse error )}{\pageref{structMT19937_1_1ParseError}}{}
\item\contentsline{section}{\hyperlink{structSampledBackgroundData}{SampledBackgroundData} (Closure holding image data generated using samples drawn from the model )}{\pageref{structSampledBackgroundData}}{}
\item\contentsline{section}{\hyperlink{classFloatSliderWithBox_1_1SliderChanged}{FloatSliderWithBox::SliderChanged} }{\pageref{classFloatSliderWithBox_1_1SliderChanged}}{}
\item\contentsline{section}{\hyperlink{classSomethingChanges}{SomethingChanges} (Listener class which triggers a complete redraw )}{\pageref{classSomethingChanges}}{}
\item\contentsline{section}{\hyperlink{classSPair}{SPair} (Utility class to hold a pair of strings )}{\pageref{classSPair}}{}
\item\contentsline{section}{\hyperlink{classSpot}{Spot} (Basic spot class, simply contains coordinates )}{\pageref{classSpot}}{}
\item\contentsline{section}{\hyperlink{structSpotNegProbabilityDiffWithSampledBackground}{SpotNegProbabilityDiffWithSampledBackground} (Compute the derivative of the negative log probability with respect to the parameters of one spot, given some samples of the other spots )}{\pageref{structSpotNegProbabilityDiffWithSampledBackground}}{}
\item\contentsline{section}{\hyperlink{structSampledMultispot_1_1SpotWithBackgroundMasked}{SampledMultispot::SpotWithBackgroundMasked} (This class compute the log-\/diff-\/hess probability of a spot, given an image patch and background due to existing spots )}{\pageref{structSampledMultispot_1_1SpotWithBackgroundMasked}}{}
\item\contentsline{section}{\hyperlink{structStateParameters}{StateParameters} (Internal state (excluding fixed settings) which represents the entire internal state of spot fitting )}{\pageref{structStateParameters}}{}
\item\contentsline{section}{\hyperlink{classStopButtonListener}{StopButtonListener} (Stop 3B thread )}{\pageref{classStopButtonListener}}{}
\item\contentsline{section}{\hyperlink{classFloatSliderWithBox_1_1TextChanged}{FloatSliderWithBox::TextChanged} }{\pageref{classFloatSliderWithBox_1_1TextChanged}}{}
\item\contentsline{section}{\hyperlink{classthree__B}{three\_\-B} (ImageJ plugin class )}{\pageref{classthree__B}}{}
\item\contentsline{section}{\hyperlink{classThreeBDialog}{ThreeBDialog} (Dialog box for starting 3B The dialog highlights bad things in red )}{\pageref{classThreeBDialog}}{}
\item\contentsline{section}{\hyperlink{classThreeBGlobalConstants}{ThreeBGlobalConstants} }{\pageref{classThreeBGlobalConstants}}{}
\item\contentsline{section}{\hyperlink{classThreeBHelp}{ThreeBHelp} (3B plugin cclass to bring up a basic help window )}{\pageref{classThreeBHelp}}{}
\item\contentsline{section}{\hyperlink{classThreeBLoader}{ThreeBLoader} (Plugin class to load up an old 3B run )}{\pageref{classThreeBLoader}}{}
\item\contentsline{section}{\hyperlink{classThreeBRunner}{ThreeBRunner} (This class deals with running the actual 3B code It should be run in a separate thread It will make calls back to a viewer, and accepts termination calls as well )}{\pageref{classThreeBRunner}}{}
\item\contentsline{section}{\hyperlink{classUserInterfaceCallback}{UserInterfaceCallback} (Callback class used by \hyperlink{classFitSpots}{FitSpots} to provide enough hooks for a user interface )}{\pageref{classUserInterfaceCallback}}{}
\item\contentsline{section}{\hyperlink{structUserInterfaceCallback_1_1UserIssuedStop}{UserInterfaceCallback::UserIssuedStop} }{\pageref{structUserInterfaceCallback_1_1UserIssuedStop}}{}
\item\contentsline{section}{\hyperlink{classUtil}{Util} (Utility calss to hold a number of handy static functions )}{\pageref{classUtil}}{}
\end{DoxyCompactList}
