doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@354 636b058d-ea47-450e-bf9e-a15bfbe3eedb

9 files changed, 185 insertions, 143 deletions

diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index eec8c14f..b02929ab 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -228,6 +228,42 @@ language={English},
 }
 
 %------------------------------------------------------------------
+@article{blockers2012,
+  author    = {Dominique Attali and
+               Andr{\'e} Lieutier and
+               David Salinas},
+  title     = {Efficient Data Structure for Representing and Simplifying
+               Simplicial complexes in High Dimensions},
+  journal   = {Int. J. Comput. Geometry Appl.},
+  volume    = {22},
+  number    = {4},
+  year      = {2012},
+  pages     = {279-304},
+  ee        = {http://dx.doi.org/10.1142/S0218195912600060},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+%------------------------------------------------------------------
+@article{rips2012,
+    hal_id = {hal-00785072},
+    url = {http://hal.archives-ouvertes.fr/hal-00785072},
+    title = {{Vietoris-Rips Complexes also Provide Topologically Correct Reconstructions of Sampled Shapes}},
+    author = {Attali, Dominique and Lieutier, Andr{\'e} and Salinas, David},
+    keywords = {Shape reconstruction \sep Rips complexes \sep clique complexes \sep \v Cech complexes ; homotopy equivalence ; collapses ; high dimensions},
+    language = {Anglais},
+    affiliation = {Grenoble Images Parole Signal Automatique - GIPSA-lab , Laboratoire Jean Kuntzmann - LJK},
+    pages = {448-465},
+    journal = {Computational Geometry},
+    volume = {46},
+    number = {4, special issue },
+    audience = {internationale },
+    doi = {10.1016/j.comgeo.2012.02.009 },
+    year = {2012},
+    pdf = {http://hal.archives-ouvertes.fr/hal-00785072/PDF/2012-cgta-Rips.pdf},
+}
+
+
+%------------------------------------------------------------------
 @article{DBLP:journals/corr/abs-1210-1429,
   author    = {Pawel Dlotko and
                Hubert Wagner},
@@ -373,6 +409,37 @@ proceedings{DBLP:conf/issac/1996,
   bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
+
+proceedings{DBLP:conf/issac/1996,
+  editor    = {Erwin Engeler and
+               B. F. Caviness and
+               Yagati N. Lakshman},
+  title     = {Proceedings of the 1996 International Symposium on Symbolic
+               and Algebraic Computation, ISSAC '96, Zurich, Switzerland,
+               July 24-26, 1996},
+  booktitle = {ISSAC},
+  publisher = {ACM},
+  year      = {1996},
+  isbn      = {0-89791-796-0},
+  ee        = {http://dl.acm.org/citation.cfm?id=236869},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+@inproceedings{socg_blockers_2011,
+ author = {Attali, Dominique and Lieutier, Andr{\'e} and Salinas, David},
+ title = {Efficient data structure for representing and simplifying simplicial complexes in high dimensions},
+ booktitle = {Proceedings of the 27th annual ACM symposium on Computational geometry},
+ series = {SoCG '11},
+ year = {2011},
+ location = {Paris, France},
+ pages = {501--509},
+ numpages = {9},
+ keywords = {clique complexes, data structure, edge contraction, flag complexes, high dimensions, homotopy equivalence, shape reconstruction, shape simplification, simplicial complexes, vietoris-rips complexes},
+} 
+
+
+
 %------------------------------------------------------------------
 
 %MISC
@@ -565,8 +632,7 @@ inproceedings{DBLP:conf/soda/1997,
 
 
 
-
-inproceedings{attali-rips_approx,
+@inproceedings{attali-rips_approx,
   author    = {Dominique Attali and
                Andr{\'e} Lieutier and
                David Salinas},
@@ -582,6 +648,8 @@ inproceedings{attali-rips_approx,
 
 
 
+
+
 @article{Carlsson:2008:LBS:1325290.1325300,
  author = {Carlsson, Gunnar and Ishkhanov, Tigran and Silva, Vin and Zomorodian, Afra},
  title = {On the Local Behavior of Spaces of Natural Images},
diff --git a/src/Doxyfile b/src/Doxyfile
index 7dbf9a06..420824f4 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -1896,7 +1896,7 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
@@ -1904,7 +1904,7 @@ MACRO_EXPANSION        = NO
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES the includes files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -1936,7 +1936,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = protected=private
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The
@@ -2019,7 +2019,7 @@ PERL_PATH              = /usr/bin/perl
 # powerful graphs.
 # The default value is: YES.
 
-CLASS_DIAGRAMS         = YES
+CLASS_DIAGRAMS         = NO
 
 # You can define message sequence charts within doxygen comments using the \msc
 # command. Doxygen will then run the mscgen tool (see:
@@ -2092,7 +2092,7 @@ DOT_FONTPATH           =
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CLASS_GRAPH            = YES
+CLASS_GRAPH            = NO
 
 # If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
 # graph for each documented class showing the direct and indirect implementation
@@ -2101,7 +2101,7 @@ CLASS_GRAPH            = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-COLLABORATION_GRAPH    = YES
+COLLABORATION_GRAPH    = NO
 
 # If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
 # groups, showing the direct groups dependencies.
@@ -2166,7 +2166,7 @@ INCLUDED_BY_GRAPH      = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALL_GRAPH             = YES
+CALL_GRAPH             = NO
 
 # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
 # dependency graph for every global function or class method.
@@ -2177,7 +2177,7 @@ CALL_GRAPH             = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = YES
+CALLER_GRAPH           = NO
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 70173462..2b3efc28 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -33,9 +33,9 @@
 
 namespace Gudhi{
 
-/** \defgroup persistent_cohomology Persistent Cohomology Package
+/** \defgroup persistent_cohomology Persistent Cohomology
   *
-  
+
   Computation of persistent cohomology using the algorithm of 
    \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 
    and the Compressed Annotation Matrix 
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 5caa5e25..44f7a0d6 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -34,7 +34,7 @@
 
 namespace Gudhi{
 
-/** \defgroup simplex_tree Filtered Complexes Package
+/** \defgroup simplex_tree Filtered Complexes 
   * 
   * A simplicial complex \f$\mathbf{K}\f$
   * on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of simplices 
diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
index 1fa9dc06..5cd3a22c 100644
--- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
+++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
@@ -23,10 +23,6 @@ namespace skbl {
 struct SkeletonBlockerDS
 {
 	/**
-	 * @todo faire un default value pour les vertex_handle
-	 */
-
-	/**
 	 * @brief index that allows to find the vertex in the boost graph
 	 */
 	typedef int boost_vertex_handle;
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 00e1935b..d05bdc19 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -35,13 +35,13 @@
 
 
 
-/** \defgroup skbl Skeleton-Blocker Package
+/** \defgroup skbl Skeleton-Blocker 
 
 \author David Salinas
 
 \section Introduction
 The Skeleton-Blocker data-structure had been introduced in the two papers 
-[\cite skbl_socg2011,\cite skbl_ijcga2012]. 
+\cite socg_blockers_2011,\cite blockers2012\cite blockers2012. 
 It proposes a light encoding for simplicial complexes by storing only an *implicit* representation of its
 simplices.
 Intuitively, it just stores the 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that
@@ -53,7 +53,7 @@ This data-structure handles all  simplicial complexes operations such as
 
 \section Definitions
 
-We recall briefly classical definitions of simplicial complexes  [\cite Munkres].
+We recall briefly classical definitions of simplicial complexes   \cite Munkres-elementsalgtop1984.
 An abstract simplex is a finite non-empty set and its dimension is its number of elements minus 1.
 Whenever \f$\tau \subset \sigma\f$ and \f$\tau \neq \emptyset \f$, \f$ \tau \f$ is called a face of 
 \f$ \sigma\f$  and \f$ \sigma\f$ is called a coface of \f$ \tau \f$ . Furthermore,
@@ -102,8 +102,6 @@ of the parent complex
 The two last classes are derived classes from the <Code>Skeleton_blocker_complex</Code> class. The class <Code>Skeleton_blocker_link_complex</Code> inheritates from a template passed parameter
 that may be either <Code>Skeleton_blocker_complex</Code> or <Code>Skeleton_blocker_geometric_complex</Code> (a link may store points coordinates or not).
 
-\todo{include links}
-
 \subsection Visitor
 
 The class <Code>Skeleton_blocker_complex</Code> has a visitor that is called when usual operations such as adding an edge or remove a vertex are called.
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index 24f95ddd..97cadfc9 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -158,13 +158,13 @@ public:
 	 * Constructs the restricted complex of 'parent_complex' to
 	 * vertices of 'simplex'.
 	 */
-	friend void make_restricted_complex(const ComplexType & parent_complex, const Simplex_handle& simplex, Skeleton_blocker_sub_complex & result){
-		result.clear();
+	void make_restricted_complex(const ComplexType & parent_complex, const Simplex_handle& simplex){
+		this->clear();
 		// add vertices to the sub complex
 		for (auto x : simplex){
 			assert(parent_complex.contains_vertex(x));
-			auto x_local = result.add_vertex(parent_complex[x].get_id());
-			result[x_local] = parent_complex[x];
+			auto x_local = this->add_vertex(parent_complex[x].get_id());
+			(*this)[x_local] = parent_complex[x];
 		}
 
 		// add edges to the sub complex
@@ -174,7 +174,7 @@ public:
 			parent_complex.add_neighbours(x, x_neigh, true);
 			x_neigh.intersection(simplex);
 			for (auto y : x_neigh){
-				result.add_edge(parent_complex[x].get_id(), parent_complex[y].get_id());
+				this->add_edge(parent_complex[x].get_id(), parent_complex[y].get_id());
 			}
 		}
 
@@ -183,8 +183,8 @@ public:
 			// check if it is the first time we encounter the blocker
 			if (simplex.contains(*blocker)){
 				Root_simplex_handle blocker_root(parent_complex.get_id(*(blocker)));
-				Simplex_handle blocker_restr(*result.get_simplex_address(blocker_root));
-				result.add_blocker(new Simplex_handle(blocker_restr));
+				Simplex_handle blocker_restr(*(this->get_simplex_address(blocker_root)));
+				this->add_blocker(new Simplex_handle(blocker_restr));
 			}
 		}
 	}
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 61ee8684..c0a0a2eb 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -1,24 +1,24 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
 #ifndef GUDHI_SKELETON_BLOCKER_COMPLEX_H
 #define GUDHI_SKELETON_BLOCKER_COMPLEX_H
@@ -150,7 +150,6 @@ protected:
 
 
 	//todo remove!!!
-public:
 
 	/** Each vertex can access to the blockers passing through it. */
 	BlockerMap blocker_map_;
@@ -164,7 +163,7 @@ public:
 
 
 	/////////////////////////////////////////////////////////////////////////////
-	/** @name Constructors / Destructors / Initialization
+	/** @name Constructors, Destructors
 	 */
 	//@{
 	Skeleton_blocker_complex(int num_vertices_ = 0,Visitor* visitor_=NULL):visitor(visitor_){
@@ -281,7 +280,7 @@ public:
 	 * @brief Constructor with a list of simplices
 	 * @details The list of simplices must be the list
 	 * of simplices of a simplicial complex.
-	 *todo rewrite as iterators
+	 *
 	 */
 	Skeleton_blocker_complex(std::list<Simplex_handle>& simplices,Visitor* visitor_=NULL):
 		num_vertices_(0),num_blockers_(0),
@@ -316,7 +315,6 @@ public:
 	}
 
 
-
 	// We cannot use the default copy constructor since we need
 	// to make a copy of each of the blockers
 	Skeleton_blocker_complex(const Skeleton_blocker_complex& copy){
@@ -355,7 +353,7 @@ public:
 	}
 
 	/**
-	 * Clears the simplicial complex. After a call to this function,
+	 * @details Clears the simplicial complex. After a call to this function,
 	 * blockers are destroyed. The 1-skeleton and the set of blockers
 	 * are both empty.
 	 */
@@ -398,11 +396,19 @@ public:
 		return *local;
 	}
 
+	/**
+	 * @brief Return the vertex node associated to local Vertex_handle.
+	 * @remark Assume that the vertex is present in the complex.
+	 */
 	Graph_vertex& operator[](Vertex_handle address){
 		assert(0<=address.vertex && address.vertex< boost::num_vertices(skeleton));
 		return skeleton[address.vertex];
 	}
 
+	/**
+	 * @brief Return the vertex node associated to local Vertex_handle.
+	 * @remark Assume that the vertex is present in the complex.
+	 */
 	const Graph_vertex& operator[](Vertex_handle address) const{
 		assert(0<=address.vertex && address.vertex< boost::num_vertices(skeleton));
 		return skeleton[address.vertex];
@@ -426,7 +432,8 @@ public:
 
 	/**
 	 * @brief Remove a vertex from the simplicial complex
-	 * @remark In fact, it just deactivates the vertex.
+	 * @remark It just deactivates the vertex with a boolean flag but does not
+	 * remove it from vertices from complexity issues.
 	 */
 	void remove_vertex(Vertex_handle address){
 		assert(contains_vertex(address));
@@ -438,17 +445,11 @@ public:
 		if (visitor) visitor->on_remove_vertex(address);
 	}
 
-	/**
-	 * @return true iff the simplicial complex contains the vertex u
-	 */
 	bool contains_vertex(Vertex_handle u) const{
 		if (u.vertex<0 || u.vertex>=boost::num_vertices(skeleton)) return false;
 		return (*this)[u].is_active();
 	}
 
-	/**
-	 * @return true iff the simplicial complex contains the vertex u
-	 */
 	bool contains_vertex(Root_vertex_handle u) const{
 		boost::optional<Vertex_handle> address = get_address(u);
 		return address &&  (*this)[*address].is_active();
@@ -466,9 +467,8 @@ public:
 	}
 
 	/**
-	 * Given an Id return the address of the vertex having this Id in the complex.
-	 * For a simplicial complex, the address is the id but it may not be the case for a SubComplex.
-	 *
+	 * @brief Given an Id return the address of the vertex having this Id in the complex.
+	 * @remark For a simplicial complex, the address is the id but it may not be the case for a SubComplex.
 	 */
 	virtual boost::optional<Vertex_handle> get_address(Root_vertex_handle id) const{
 		boost::optional<Vertex_handle> res;
@@ -488,10 +488,14 @@ public:
 
 
 	/**
+	 * @brief Convert an address of a vertex of a complex to the address in
+	 * the current complex.
+	 * @details
 	 * If the current complex is a sub (or sup) complex of 'other', it converts
 	 * the address of a vertex v expressed in 'other' to the address of the vertex
 	 * v in the current one.
-	 * @remark this methods uses Root_vertex_handle to identify the vertex
+	 * @remark this methods uses Root_vertex_handle to identify the vertex and
+	 * assumes the vertex is present in the current complex.
 	 */
 	Vertex_handle convert_handle_from_another_complex(
 			const Skeleton_blocker_complex& other,Vertex_handle vh_in_other) const{
@@ -500,7 +504,9 @@ public:
 		return *vh_in_current_complex;
 	}
 
-
+	/**
+	 * @brief return the graph degree of a vertex.
+	 */
 	int degree(Vertex_handle local) const{
 		assert(0<=local.vertex && local.vertex< boost::num_vertices(skeleton));
 		return degree_[local.vertex];
@@ -527,24 +533,40 @@ public:
 		return res;
 	}
 
+	/**
+	 * @brief returns the stored node associated to an edge
+	 */
 	Graph_edge& operator[](Edge_handle edge_handle){
 		return skeleton[edge_handle];
 	}
 
+	/**
+	 * @brief returns the stored node associated to an edge
+	 */
 	const Graph_edge& operator[](Edge_handle edge_handle) const{
 		return skeleton[edge_handle];
 	}
 
+	/**
+	 * @brief returns the first vertex of an edge
+	 * @details it assumes that the edge is present in the complex
+	 */
 	Vertex_handle first_vertex(Edge_handle edge_handle) const{
 		return source(edge_handle,skeleton);
 	}
 
+	/**
+	 * @brief returns the first vertex of an edge
+	 * @details it assumes that the edge is present in the complex
+	 */
 	Vertex_handle second_vertex(Edge_handle edge_handle) const{
 		return target(edge_handle,skeleton);
 	}
 
 	/**
 	 * @brief returns the simplex made with the two vertices of the edge
+	 * @details it assumes that the edge is present in the complex
+
 	 */
 	Simplex_handle get_vertices(Edge_handle edge_handle) const{
 		auto edge((*this)[edge_handle]);
@@ -574,7 +596,7 @@ public:
 	}
 
 	/**
-	 * @brief Adds all edges of simplex sigma to the simplicial complex.
+	 * @brief Adds all edges and their cofaces of a simplex to the simplicial complex.
 	 */
 	void add_edges(const Simplex_handle & sigma){
 		Simplex_handle_iterator i, j;
@@ -584,7 +606,8 @@ public:
 	}
 
 	/**
-	 * @brief Removes edge ab from the simplicial complex and all its cofaces.
+	 * @brief Removes an edge from the simplicial complex and all its cofaces.
+	 * @details returns the former Edge_handle representing the edge
 	 */
 	virtual Edge_handle remove_edge(Vertex_handle a, Vertex_handle b){
 		bool found;
@@ -661,23 +684,10 @@ public:
 	/** @name Blockers operations
 	 */
 	//@{
-	/**
-	 * Adds the 2-blocker abc
-	 */
-	void add_blocker(Vertex_handle a, Vertex_handle b, Vertex_handle c){
-		add_blocker(Simplex_handle(a,b,c));
-	}
 
 	/**
-	 * Adds the 3-blocker abcd
-	 */
-	void add_blocker(Vertex_handle a, Vertex_handle b, Vertex_handle c, Vertex_handle d){
-		add_blocker(Simplex_handle(a,b,c,d));
-	}
-
-	/**
-	 * Adds the simplex blocker_pt to the set of blockers and
-	 * returns a Blocker_handle toward it if was not present before.
+	 * @brief Adds the simplex to the set of blockers and
+	 * returns a Blocker_handle toward it if was not present before and 0 otherwise.
 	 */
 	Blocker_handle add_blocker(const Simplex_handle& blocker){
 		if (contains_blocker(blocker))
@@ -701,7 +711,7 @@ public:
 
 protected:
 	/**
-	 * Adds the simplex s to the set of blockers
+	 * @brief Adds the simplex to the set of blockers
 	 */
 	void add_blocker(Blocker_handle blocker){
 		if (contains_blocker(*blocker))
@@ -745,8 +755,8 @@ protected:
 
 public:
 	/**
-	 * Removes the simplex sigma from the set of blockers.
-	 * sigma has to belongs to the set of blockers
+	 * @brief Removes the simplex from the set of blockers.
+	 * @remark sigma has to belongs to the set of blockers
 	 */
 	void remove_blocker(const Blocker_handle sigma){
 		for (auto vertex : *sigma){
@@ -759,7 +769,7 @@ public:
 
 
 	/**
-	 * Remove all blockers, in other words, it expand the simplicial
+	 * @brief Remove all blockers, in other words, it expand the simplicial
 	 * complex to the smallest flag complex that contains it.
 	 */
 	void remove_blockers(){
@@ -851,17 +861,9 @@ private:
 
 
 
-
-	/////////////////////////////////////////////////////////////////////////////
-	/** @name Neighbourhood access
-	 */
-	//@{
-
-public:
+protected:
 	/**
-	 * @brief Adds to simplex n the neighbours of v:
-	 * \f$ n \leftarrow n \cup N(v) \f$.
-	 *
+	 * @details Adds to simplex the neighbours of v e.g. \f$ n \leftarrow n \cup N(v) \f$.
 	 * If keep_only_superior is true then only vertices that are greater than v are added.
 	 */
 	virtual void add_neighbours(Vertex_handle v, Simplex_handle & n,bool keep_only_superior=false) const{
@@ -877,34 +879,25 @@ public:
 	}
 
 	/**
-	 * @brief Add to simplex res all vertices which are
+	 * @details Add to simplex res all vertices which are
 	 * neighbours of alpha: ie \f$ res \leftarrow res \cup N(alpha) \f$.
 	 *
 	 * If 'keep_only_superior' is true then only vertices that are greater than alpha are added.
-	 *
 	 * todo revoir
 	 *
 	 */
 	virtual void add_neighbours(const Simplex_handle &alpha, Simplex_handle & res,bool keep_only_superior=false) const{
 		res.clear();
-		// ----------------------------
-		// Compute vertices in the link
-		// we compute the intersection of N(alpha_i) and store it in n
-		// ----------------------------
 		auto alpha_vertex = alpha.begin();
 		add_neighbours(*alpha_vertex,res,keep_only_superior);
 		for (alpha_vertex = (alpha.begin())++ ; alpha_vertex != alpha.end() ; ++alpha_vertex)
-		{
 			keep_neighbours(*alpha_vertex,res,keep_only_superior);
-		}
 	}
 
 	/**
-	 * @brief Eliminates from simplex n all vertices which are
-	 * not neighbours of v: \f$ res \leftarrow res \cap N(v) \f$.
-	 *
+	 * @details Remove from simplex n all vertices which are
+	 * not neighbours of v e.g. \f$ res \leftarrow res \cap N(v) \f$.
 	 * If 'keep_only_superior' is true then only vertices that are greater than v are keeped.
-	 *
 	 */
 	virtual void keep_neighbours(Vertex_handle v, Simplex_handle& res,bool keep_only_superior=false) const{
 		Simplex_handle nv;
@@ -913,24 +906,17 @@ public:
 	}
 
 	/**
-	 * @brief Eliminates from simplex n all vertices which are
-	 * neighbours of v: \f$ res \leftarrow res \setminus N(v) \f$.
-	 *
+	 * @details Remove from simplex all vertices which are
+	 * neighbours of v eg \f$ res \leftarrow res \setminus N(v) \f$.
 	 * If 'keep_only_superior' is true then only vertices that are greater than v are added.
-	 *
 	 */
 	virtual void remove_neighbours(Vertex_handle v, Simplex_handle & res,bool keep_only_superior=false) const{
 		Simplex_handle nv;
 		add_neighbours(v,nv,keep_only_superior);
 		res.difference(nv);
 	}
-	//@}
 
 
-	/////////////////////////////////////////////////////////////////////////////
-	/** @name Operations on the simplicial complex
-	 */
-	//@{
 public:
 
 	/**
@@ -1003,8 +989,9 @@ public:
 
 	/*
 	 * @brief returns the number of edges in the complex.
-	 * todo in O(n), cache the value
+	 * @details currently in O(n)
 	 */
+	//	todo cache the value
 	int num_edges() const{
 		return boost::num_edges(skeleton);
 	}
@@ -1032,22 +1019,6 @@ public:
 		return boost::connected_components(this->skeleton,&component[0]) - num_vert_collapsed;
 	}
 
-
-	//todo remove
-	// do
-	void keep_only_largest_cc(){
-		std::vector<unsigned> component(skeleton.vertex_set().size());
-		boost::connected_components(this->skeleton,&component[0]);
-		auto maxCC = min_element(component.begin(),component.end());
-		for (unsigned i = 0; i != component.size(); ++i){
-			if(component[i]!=*maxCC){
-				if(this->contains_vertex(Vertex_handle(i)))
-					this->remove_vertex(Vertex_handle(i));
-			}
-		}
-	}
-
-
 	/**
 	 * @brief %Test if the complex is a cone.
 	 * @details Runs in O(n) where n is the number of vertices.
@@ -1223,6 +1194,9 @@ public:
 
 	typedef boost::iterator_range     < Complex_simplex_iterator > Complex_simplex_range;
 
+	/**
+	 * @brief Returns a Complex_simplex_range over all the simplices of the complex
+	 */
 	Complex_simplex_range simplex_range() const
 	{
 		Complex_simplex_iterator end(this,true);
@@ -1265,7 +1239,9 @@ private:
 public:
 
 
-
+	/**
+	 * @brief Returns a range of the blockers of the complex passing through a vertex
+	 */
 	Complex_blocker_around_vertex_range blocker_range(Vertex_handle v)
 	{
 		auto begin = Complex_blocker_around_vertex_iterator(blocker_map_.lower_bound(v));
@@ -1274,7 +1250,7 @@ public:
 	}
 
 	/**
-	 * @brief Returns a Complex_blocker_around_vertex_range over all blockers of the complex adjacent to the vertex v.
+	 * @brief Returns a range of the blockers of the complex passing through a vertex
 	 */
 	Const_complex_blocker_around_vertex_range const_blocker_range(Vertex_handle v) const
 	{
@@ -1310,7 +1286,9 @@ private:
 
 public:
 
-
+	/**
+	 * @brief Returns a range of the blockers of the complex
+	 */
 	Complex_blocker_range blocker_range()
 	{
 		auto begin = Complex_blocker_iterator(blocker_map_.begin(), blocker_map_.end() );
@@ -1318,7 +1296,9 @@ public:
 		return Complex_blocker_range(begin,end);
 	}
 
-
+	/**
+	 * @brief Returns a range of the blockers of the complex
+	 */
 	Const_complex_blocker_range const_blocker_range() const
 	{
 		auto begin = Const_complex_blocker_iterator(blocker_map_.begin(), blocker_map_.end() );
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index f81f5a94..11b990c0 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -10,7 +10,7 @@ state-of-the-art algorithms and data structures for computational topology.
 
 The current release of the library allows to use several data-structures for simplicial complexes :
 simplex tree, Hasse diagram or skeleton-blocker. Several  operations can then be done on top of these
-representations persistent homology computation, or simplification. 
+representations such a spersistent homology computation or simplification. 
 
 All data-structures are generic and several of their aspects (such as stored elements, policies) 
 can be parametrized via template classes.
@@ -30,7 +30,7 @@ Some packages require additional libraries :
 The procedure to install these packages according to your operating system is 
 detailled here http://doc.cgal.org/latest/Manual/installation.html
 
-The library compiles in Linux, Mac OSX and visual studio 2013.
+The library compiles in Linux, Mac OSX and Visual Studio 2013.
 
 \section d Demos and Examples
 
@@ -51,6 +51,6 @@ make
 \details 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: Clément Maria,     clement.maria@inria.fr \endverbatim
+\verbatim  Contact: gudhi-devel@lists.gforge.inria.fr \endverbatim
 
 */
\ No newline at end of file