Documentation updates

src/automaton.hh

@@ -8,8 +8,11 @@
  *  @section automata-description Description
  *  This part describes an automaton\<T\> : each @ref automaton<T> is mainly a represented by a set of @ref state<T>, each itself being represented by a set of @ref transition<T>.
  *
- *  - An automaton\<T\> can be deterministic or not.
- *  - It may bring probabilities (T = double, T = polynomial\<long long int\>), costs (T = cost\<int\>), counts (T = unsigned long long), or nothing (T = void).
+ *  @li An automaton\<T\> can be deterministic or not.
+ *  @li It may bring probabilities (T = double, T = polynomial\<long long int\>), costs (T = cost\<int\>), counts (T = unsigned long long), or nothing (T = void).
+ *
+ *  For an automaton, its set of states is stored in the @ref automaton::_states vector. For each state, its set of transitions is stored in the  @ref state::_next vector of vectors, the outer vector being of size @ref gv_align_alphabet_size, each state has an extra @ref state::_final integer to mark a possible final flag or final value. Each transition brings a destination state number  @ref transition::_state as an integer, and its transition probability / cost @ref transition::_prob as a templated \<T\> element
+
  *
  *  By default the automaton\<T\> constructor is almost empty (it creates only a final state 0 and the init state 1), but several methods are proposed to construct @ref seed-automaton, @ref probabilistic-automaton, @ref structural-automaton (@ref automaton-construction). Several methods are also proposed to manipulate theses automata (@ref automaton-manipulate), compute properties (@ref automaton-computed-properties), convert them into matrices (@ref automaton-matrix-conversion),
  *
@@ -38,7 +41,7 @@
  *          A coverage criterion for spaced seeds and its applications
  *                 to SVM string kernels and k-mer distances
  *
- *  Additional files are also provided at @rel https://bioinfo.lifl.fr/yass/iedera_coverage/index.html and at @ref https://bioinfo.lifl.fr/yass/iedera_coverage/index_additional.html
+ *  Additional files are also provided at @ref https://bioinfo.lifl.fr/yass/iedera_coverage/index.html and at @ref https://bioinfo.lifl.fr/yass/iedera_coverage/index_additional.html
  *
  *  @section automaton-manipulate Manipulation
  *

src/matrix.hh

@@ -15,8 +15,9 @@
  *  @ref matrix<T> are (just) a more compact way to store @ref automata<T> attributes, once letters are not needed anymore.
  *  Default @ref matrix<T> constructor is almost empty, but several methods from @ref automaton<T> are proposed to produce matrices. They must be used first!
  *
+ *  The set of rows is stored in the @ref matrix::_rows vector. The set of cells per row is stored either in the  @ref row::_cells_dense  or  @ref row::_cells_sparse  vector.
  *  Several methods are also proposed to manipulate theses matrices (@ref local-matrix-manipulation or @ref global-matrices-manipulation), compute properties (@ref matrix-computed-properties),
- *   and an additional class is given (@ref matrices-slicer) for specific computations.
+ *  and an additional class is given (@ref matrices-slicer) for specific computations.
  *
  *  @section local-matrix-manipulation Local matrix manipulation
  *

src/polynomial.hh

@@ -10,10 +10,10 @@
  *  This part describes a polynomial\<C\> : each @ref polynomial<C> is mainly represented by an inner vector of pairs, where each pair represents a @e monomial.
  *
  *  Each monomial is composed (as a pair) by those two elements :
- *     @li a vector of int, to store the different degrees of variables @e x, @e y @e z (variables names are stored in the static @ref polynomial::_var_names list).
- *     @li a templated coefficient \<C\> (that could be, for example, a \<long long\> or an @ref infint<long long>) : this last one could be @b positive @b is C @b allows @b them.
+ *  @li a vector of int, to store the different degrees of variables @e x, @e y @e z (variables names are stored in the static @ref polynomial::_var_names list).
+ *  @li a templated coefficient \<C\> (that could be, for example, a \<long long\> or an @ref infint<long long>) : this last one could be @b positive @b is C @b allows @b them.
  *
- *   The set of monomials is stored in the @ref polynomial::_coefs vector. The set of variables used is stored in the static variable @ref polynomial::_var_names list.
+ *  The set of monomials is stored in the @ref polynomial::_coefs vector. The set of variables used is stored in the static variable @ref polynomial::_var_names list.
  *
  *  Several methods are also proposed to build (@ref polynomial-construction), or operate (@ref polynomial-operators) theses polynomials,
  *