Modify "mode change"

Makefile.am

@@ -1,6 +1,6 @@
 # Makefile.am
 bin_PROGRAMS   = iedera
-iedera_SOURCES = main.cc automaton.cc seed.cc macro.cc \
-		         automaton.h  seed.h  macro.h  \
+iedera_SOURCES = main.cc seed.cc macro.cc \
+		         seed.h  macro.h  \
                  matrix.hh cost.hh automaton.hh polynomial.hh infint.hh
 EXTRA_DIST = binomial_weight.h lcm.cc 

Makefile.in

@@ -101,8 +101,7 @@ CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
-am_iedera_OBJECTS = main.$(OBJEXT) automaton.$(OBJEXT) seed.$(OBJEXT) \
-	macro.$(OBJEXT)
+am_iedera_OBJECTS = main.$(OBJEXT) seed.$(OBJEXT) macro.$(OBJEXT)
 iedera_OBJECTS = $(am_iedera_OBJECTS)
 iedera_LDADD = $(LDADD)
 AM_V_P = $(am__v_P_@AM_V@)
@@ -280,8 +279,8 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-iedera_SOURCES = main.cc automaton.cc seed.cc macro.cc \
-		         automaton.h  seed.h  macro.h  \
+iedera_SOURCES = main.cc seed.cc macro.cc \
+		         seed.h  macro.h  \
                  matrix.hh cost.hh automaton.hh polynomial.hh infint.hh
 
 EXTRA_DIST = binomial_weight.h lcm.cc 
@@ -375,7 +374,6 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/automaton.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/macro.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seed.Po@am__quote@

NEWS

@@ -143,3 +143,13 @@ Version 1.06
   variance
   [Not Command Lined yet : set "gv_covariance_flag = true;"]
 
+- Missing infint file added to the package
+- Missing lcm.cc and binomial_weight.h with the correct name added to the package
+- True Polynomial computations have been added but not command lined yet
+
+Version 1.07
+============
+
+- A Full Templating of the automaton class has been applied to the program
+  (it can handle <double>,<cost<int>>, <polynomial<long int>>,...)
+- Polynomial ongoing

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for iedera 1.06.
+# Generated by GNU Autoconf 2.69 for iedera 1.07.
 #
 # Report bugs to <laurent DT noe AT univ-lille1 DT fr>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='iedera'
 PACKAGE_TARNAME='iedera'
-PACKAGE_VERSION='1.06'
-PACKAGE_STRING='iedera 1.06'
+PACKAGE_VERSION='1.07'
+PACKAGE_STRING='iedera 1.07'
 PACKAGE_BUGREPORT='laurent DT noe AT univ-lille1 DT fr'
 PACKAGE_URL='http://bioinfo.lifl.fr/yass/iedera'
 
@@ -1267,7 +1267,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures iedera 1.06 to adapt to many kinds of systems.
+\`configure' configures iedera 1.07 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1333,7 +1333,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of iedera 1.06:";;
+     short | recursive ) echo "Configuration of iedera 1.07:";;
    esac
   cat <<\_ACEOF
 
@@ -1425,7 +1425,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-iedera configure 1.06
+iedera configure 1.07
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1794,7 +1794,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by iedera $as_me 1.06, which was
+It was created by iedera $as_me 1.07, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2664,7 +2664,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='iedera'
- VERSION='1.06'
+ VERSION='1.07'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -4742,7 +4742,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by iedera $as_me 1.06, which was
+This file was extended by iedera $as_me 1.07, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4800,7 +4800,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-iedera config.status 1.06
+iedera config.status 1.07
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -182,7 +182,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
 
 
 
-AC_INIT([iedera],[1.06],[laurent DT noe AT univ-lille1 DT fr],[iedera],[http://bioinfo.lifl.fr/yass/iedera])
+AC_INIT([iedera],[1.07],[laurent DT noe AT univ-lille1 DT fr],[iedera],[http://bioinfo.lifl.fr/yass/iedera])
 AC_CONFIG_SRCDIR([main.cc])
 AC_LANG([C++])
 AM_INIT_AUTOMAKE

cost.hh

@@ -6,7 +6,7 @@
  *  and in the @f$ (\oplus = min, \otimes = plus) @f$ tropical semi-ring
  *
  *
- *  @see matrix
+ *  @see matrix, automaton 
  */
 
 // @{
@@ -35,7 +35,7 @@ using namespace std;
  *  (C++ operators  @f$+@f$ and @f$\times@f$) can be used in both cases : either on costs, otherwise on more
  *  traditional floating point values...
  *
- *  @see matrix
+ *  @see matrix, automaton 
  */
 
 template<typename C> class cost {
@@ -49,17 +49,17 @@ template<typename C> class cost {
 
   // @{
   /// Operator + (min) for two costs
-  template<typename U> friend cost<U> operator+ (cost<U> l, cost<U> r);
+  template<typename U> friend cost<U> operator+ (const cost<U> l,const cost<U> r);
   /// Operator @f$ \times @f$ (add) for two costs
-  template<typename U> friend cost<U> operator* (cost<U> l, cost<U> r);
+  template<typename U> friend cost<U> operator* (const cost<U> l,const cost<U> r);
   /// Operator @f$ != @f$ for two costs
-  template<typename U> friend bool    operator!= (cost<U> l, cost<U> r);
+  template<typename U> friend bool    operator!= (const cost<U> l,const cost<U> r);
   /// Operator @f$ == @f$ for two costs
-  template<typename U> friend bool    operator== (cost<U> l, cost<U> r);
+  template<typename U> friend bool    operator== (const cost<U> l,const cost<U> r);
   /// Operator @f$ < @f$ for two costs
-  template<typename U> friend bool    operator< (cost<U> l, cost<U> r);
+  template<typename U> friend bool    operator< (const cost<U> l,const cost<U> r);
   /// Operator @f$ > @f$ for two costs
-  template<typename U> friend bool    operator> (cost<U> l, cost<U> r);
+  template<typename U> friend bool    operator> (const cost<U> l,const cost<U> r);
   // @}
 
   // @{
@@ -77,34 +77,34 @@ protected:
 };
 
 /// Operator + (min) for two costs
-template<typename C> inline cost<C> operator+ (cost<C> l, cost<C> r) {
+template<typename C> inline cost<C> operator+ (const cost<C> l, const cost<C> r) {
   cost<C> x(MIN(l._c,r._c));
   return x;
 }
 
 /// Operator @f$ \times @f$ (add) for two costs
-template<typename C> inline cost<C> operator* (cost<C> l, cost<C> r) {
+template<typename C> inline cost<C> operator* (const cost<C> l, const cost<C> r) {
   cost<C> x(l._c + r._c);
   return x;
 }
 
 /// Operator @f$ == @f$ for two costs
-template<typename C> inline bool    operator== (cost<C> l, cost<C> r) {
+template<typename C> inline bool    operator== (const cost<C> l, const cost<C> r) {
   return l._c == r._c;
 }
 
 /// Operator @f$ != @f$ for two costs
-template<typename C> inline bool    operator!= (cost<C> l, cost<C> r) {
+template<typename C> inline bool    operator!= (const cost<C> l, const cost<C> r) {
   return l._c != r._c;
 }
 
 /// Operator @f$ < @f$ for two costs
-template<typename C> inline bool    operator< (cost<C> l, cost<C> r) {
+template<typename C> inline bool    operator< (const cost<C> l, const cost<C> r) {
   return l._c < r._c;
 }
 
 /// Operator @f$ > @f$ for two costs
-template<typename C> inline bool    operator> (cost<C> l, cost<C> r) {
+template<typename C> inline bool    operator> (const cost<C> l, const cost<C> r) {
   return l._c > r._c;
 }
 

macro.cc

@@ -14,7 +14,6 @@ int                    gv_nbruns = 0;
 bool                   gv_matching_symbol_flag = true;
 int                    gv_alignment_length = 64;
 int                    gv_verbose = 1;
-#ifndef NOMATRIX
 bool                   gv_subalignment_flag = false;
 int                    gv_subalignment_length = 0;
 int                    gv_subalignment_function_index = 0;
@@ -38,7 +37,6 @@ subalignment_function_double gv_subalignment_functions_double[SUBALIGNMENT_FUNCT
   (subalignment_function_double)  &avg_vector<double>,
   (subalignment_function_double)  &med_vector<double>
 };
-#endif
 
 int                    gv_align_alphabet_size = 2;
 int                    gv_seed_alphabet_size = 2;

macro.h

@@ -37,18 +37,15 @@ using namespace std;
 /// use a sampling on some alignments before computing the sensitivity (better when many seeds are designed together)
 #define SAMPLING_STRATEGY_MF
 #undef SAMPLING_STRATEGY_MF
-/// keep product of seeds that are less sujbect to change in future (usefull when many seeds are designed together: faster for hillclimbing and full enumeration, but requires more memory)
+/// keep product of seeds that are less subject to change in future (usefull when many seeds are designed together: faster for hillclimbing and full enumeration, but requires more memory)
 #define KEEP_PRODUCT_MF
-#undef KEEP_PRODUCT_MF
 /// compute correlation coefficients for coverage or multi-hit automaton
 #define COMPUTE_CORRELATION_LN
 #undef COMPUTE_CORRELATION_LN
 /// use the InfInt Header
 #define USEINFINT
 #undef USEINFINT
 
-/// dont use a matrix (slower and disable the -ll option)
-#undef NOMATRIX
 /// dont use the matrix slicer (slower than the slicer version)
 #define NOSLICER
 #undef NOSLICER
@@ -70,8 +67,6 @@ using namespace std;
 // @}
 
 
-#ifndef NOMATRIX
-
 /** @name subalignments computation
  *  @brief parameters used for the sub-alignment computation and selection of the sensitivity/lossless value
  */
@@ -97,8 +92,6 @@ extern subalignment_function_double gv_subalignment_functions_double[SUBALIGNMEN
 extern char *                 gv_subalignment_functions_names[SUBALIGNMENT_FUNCTIONS_NUMBER];
 // @}
 
-#endif
-
 /** @name verbosity
  *  @brief verbosity level and macros
  */