After doc review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@931 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 578da0e6fff453560e666e8f00147f9e10cb6de6

5 files changed, 54 insertions, 24 deletions

diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index cd6f5a4b..4f381892 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -1,8 +1,6 @@
 #include <iostream>
 #include <string>
 
-// to construct a Delaunay_triangulation from a OFF file
-#include <gudhi/Delaunay_triangulation_off_io.h>
 #include <gudhi/Alpha_complex.h>
 
 void usage(char * const progName) {
@@ -35,14 +33,12 @@ int main(int argc, char **argv) {
 
   std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    //if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) {
-      std::cout << "   ( ";
-      for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
-        std::cout << vertex << " ";
-      }
-      std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
-      std::cout << std::endl;
-    //}
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
   }
   return 0;
 }
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
index e460f177..62f594d1 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -6,34 +6,50 @@
 #include <string>
 #include <vector>
 
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_complex.h"
+#include <gudhi/Alpha_complex.h>
 
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel;
 typedef Kernel::Point_d Point;
 typedef std::vector<Point> Vector_of_points;
 
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " alpha_square_max_value" << std::endl;
+  std::cerr << "       i.e.: " << progName << " 32.0" << std::endl;
+  exit(-1); // ----- >>
+}
+
 int main(int argc, char **argv) {
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  double alpha_square_max_value = atof(argv[1]);
+  
   // ----------------------------------------------------------------------------
   // Init of a list of points
   // ----------------------------------------------------------------------------
   Vector_of_points points;
 
-  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+  std::vector<double> coords = { 1.0, 1.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 7.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 4.0, 6.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 9.0, 6.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 0.0, 0.0, 1.0, 0.0 };
+  coords = { 0.0, 14.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 0.0, 1.0, 0.0, 0.0 };
+  coords = { 2.0, 19.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 1.0, 0.0, 0.0, 0.0 };
+  coords = { 9.0, 17.0 };
   points.push_back(Point(coords.begin(), coords.end()));
 
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
   // ----------------------------------------------------------------------------
-  double max_alpha_square_value = 1e10;
-  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(points, max_alpha_square_value);
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(points, alpha_square_max_value);
 
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 10b87f04..33ff6805 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -27,10 +27,6 @@ if(CGAL_FOUND)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
       include( ${EIGEN3_USE_FILE} )
-      if (CMAKE_BUILD_TYPE MATCHES Debug)
-        # For programs to be more verbose
-        add_definitions(-DDEBUG_TRACES)
-      endif()
       
       add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
       target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
new file mode 100644
index 00000000..553431a9
--- /dev/null
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
@@ -0,0 +1,22 @@
+Alpha complex is of dimension 2 - 20 simplices - 7 vertices.
+Iterator on alpha complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 5 4 ) -> [6.25] 
+   ( 4 1 ) -> [20] 
+   ( 4 2 ) -> [8.5] 
+   ( 6 2 ) -> [9.25] 
+   ( 6 5 ) -> [10] 
+   ( 6 4 ) -> [11.25] 
+   ( 6 5 4 ) -> [12.5] 
+   ( 6 4 2 ) -> [12.9959] 
+   ( 3 0 ) -> [13.25] 
+   ( 4 1 ) -> [20] 
+   ( 1 0 ) -> [22.7367] 
+   ( 3 1 0 ) -> [22.7367] 
+   ( 5 0 ) -> [30.25] 
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt
index 71f29a00..71f29a00 100644
--- a/src/Alpha_complex/example/alphaoffreader_for_doc.txt
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt