# HG changeset patch
# User Dmitriy Morozov <morozov@cs.duke.edu>
# Date 1203423961 18000
# Node ID f905b57dd7abdb8c34bbb211eb05c90b68b045bd
# Parent bb79215d1f932b0bcdee904b88e32faed52f9d68
Added class groups to Doxygen documentation
diff -r bb79215d1f93 -r f905b57dd7ab include/dionysus.h
--- a/include/dionysus.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/dionysus.h Tue Feb 19 07:26:01 2008 -0500
@@ -1,6 +1,6 @@
/*
* Author: Dmitriy Morozov
- * Department of Computer Science, Duke University, 2006
+ * Department of Computer Science, Duke University, 2006--2008
*
* For now file exists only to store the main page of the documentation
*/
@@ -9,3 +9,16 @@
* Detailed description of Dionysus with references to all the classes,
* and code samples goes here.
*/
+
+/**
+ * \defgroup topology Topology Classes
+ */
+
+/**
+ * \defgroup geometry Geometry Classes
+ */
+
+/**
+ * \defgroup kinetic Kinetic Data Structures Classes
+ * \ingroup geometry
+ */
diff -r bb79215d1f93 -r f905b57dd7ab include/geometry/euclidean.h
--- a/include/geometry/euclidean.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/euclidean.h Tue Feb 19 07:26:01 2008 -0500
@@ -14,6 +14,10 @@
#include "number-traits.h"
+/**
+ * Geometric Kernel. Defines operations on geometric primitives.
+ * \ingroup geometry
+ */
template<class NumberType_ = double>
class Kernel
{
@@ -56,7 +60,10 @@
};
-/* Point */
+/**
+ * Point class.
+ * \ingroup geometry
+ */
template<class NumberType_>
class Kernel<NumberType_>::Point: public VectorType
{
@@ -77,7 +84,10 @@
};
-/* Sphere */
+/**
+ * Sphere class.
+ * \ingroup geometry
+ */
template<class NumberType_>
class Kernel<NumberType_>::Sphere
{
diff -r bb79215d1f93 -r f905b57dd7ab include/geometry/kinetic-sort.h
--- a/include/geometry/kinetic-sort.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/kinetic-sort.h Tue Feb 19 07:26:01 2008 -0500
@@ -16,6 +16,8 @@
* \arg Simulator_ the Simulator type, e.g. Simulator. Note that KineticSort does not store
* a pointer to the Simulator (so a pointer is passed in each relevant operation)
* \arg Swap_ is called with an ElementIterator_ when a swap needs to be performed
+ *
+ * \ingroup kinetic
*/
template<class ElementIterator_, class TrajectoryExtractor_,
class Simulator_, class Swap_ = boost::function<void(ElementIterator_ pos, Simulator_* simulator)> >
diff -r bb79215d1f93 -r f905b57dd7ab include/geometry/simulator.h
--- a/include/geometry/simulator.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/geometry/simulator.h Tue Feb 19 07:26:01 2008 -0500
@@ -12,6 +12,8 @@
* Event addition, and processes events one by one. Degeneracies are handled by
* assuming that the RationalFunction responsible for the event must be positive
* before the Event occurs.
+ *
+ * \ingroup kinetic
*/
template<class PolyKernel_, template<class Event> class EventComparison_ = std::less>
class Simulator
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/cycle.h
--- a/include/topology/cycle.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/cycle.h Tue Feb 19 07:26:01 2008 -0500
@@ -16,6 +16,8 @@
* The actual order of the elements is defined by OrderCmp. Instances of those
* classes are not stored in Cycle for efficiency, and are passed as arguments to those methods
* that require them.
+ *
+ * \ingroup topology
*/
template <class Itm, class OrderCmp, class ConsistencyCmp = OrderCmp>
class Cycle: public List<Itm>
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/filtration.h
--- a/include/topology/filtration.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtration.h Tue Feb 19 07:26:01 2008 -0500
@@ -22,6 +22,8 @@
* and provides pair_simplices() method that computes the RU-decomposition
* for the simplex order stored in the filtration. Iterators remain valid
* through all the operations.
+ *
+ * \ingroup topology
*/
template<class Smplx, class FltrSmplx = FiltrationSimplex<Smplx>, class Vnrd = Vineyard<FltrSmplx> >
class Filtration: public FltrSmplx::Container
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/filtrationcontainer.h
--- a/include/topology/filtrationcontainer.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtrationcontainer.h Tue Feb 19 07:26:01 2008 -0500
@@ -13,6 +13,8 @@
* FiltrationContainer class. Serves as a parent of Filtration that
* describes the container functionality. Used by FiltrationSimplex
* to get Cycle representation.
+ *
+ * \ingroup topology
*/
template<class FltrSmplx>
class FiltrationContainer: public ConsistencyList<FltrSmplx>
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/filtrationsimplex.h
--- a/include/topology/filtrationsimplex.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/filtrationsimplex.h Tue Feb 19 07:26:01 2008 -0500
@@ -21,6 +21,8 @@
/**
* Evaluator is a base class for the structures that are able to return a value
* given a simplex.
+ *
+ * \ingroup topology
*/
template<class Smplx>
class Evaluator
@@ -37,6 +39,8 @@
/**
* FiltrationSimplex stores information needed for the RU-decomposition:
* cycle (column of R), trail (row of U), and pair.
+ *
+ * \ingroup topology
*/
template<class Smplx>
class FiltrationSimplex: public Smplx
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/simplex.h
--- a/include/topology/simplex.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/simplex.h Tue Feb 19 07:26:01 2008 -0500
@@ -20,6 +20,8 @@
* SimplexWithVertices is a basic simplex class. It stores vertices of a given type,
* and knows how to compute its own boundary. It should probably be used as a base
* class for any explicit simplex representation.
+ *
+ * \ingroup topology
*/
template<class V>
class SimplexWithVertices
@@ -83,6 +85,8 @@
/**
* SimplexWithValue explicitly adds a RealType value to the SimplexWithVertices.
+ *
+ * \ingroup topology
*/
template<class Vert>
class SimplexWithValue: public SimplexWithVertices<Vert>
@@ -130,6 +134,8 @@
/**
* SimplexWithAttachment stores the vertex to which the simplex is attached (meant for lower-star filtrations)
+ *
+ * \ingroup topology
*/
template<typename V>
class SimplexWithAttachment: public SimplexWithVertices<V>
diff -r bb79215d1f93 -r f905b57dd7ab include/topology/vineyard.h
--- a/include/topology/vineyard.h Tue Feb 19 06:56:49 2008 -0500
+++ b/include/topology/vineyard.h Tue Feb 19 07:26:01 2008 -0500
@@ -23,6 +23,8 @@
/**
* Vineyard class. Keeps track of vines and knees. switched() is the key function called
* by filtration when pairing switches after a Filtration::transpose().
+ *
+ * \ingroup topology
*/
template<class FltrSmplx>
class Vineyard
@@ -65,6 +67,8 @@
/**
* Knee class stores the knee in R^3 as well as the cycle that is associated with the Simplex starting from the Knee.
+ *
+ * \ingroup topology
*/
template<class S>
class Knee