Merge branch 'multivariate_polynomial'

laurentnoe · May 28, 2020 · 6970578 · 6970578
2 parents 654cf20 + 4e74e53
commit 6970578
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diff --git a/Makefile.am b/Makefile.am
@@ -1,3 +1,5 @@
 # Makefile.am
 EXTRA_DIST = README doxygenconfig
 SUBDIRS = src tests
+
+test: check
diff --git a/Makefile.in b/Makefile.in
@@ -746,6 +746,8 @@ uninstall-am:
 .PRECIOUS: Makefile
 
 
+test: check
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:
diff --git a/NEWS b/NEWS
@@ -149,7 +149,11 @@ Version 1.06
 
 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
+- Multivariate polynomial are command-lined (output only, no seed selection)
+- A automaton<void> templating has been enabled (no additional unused values
+  are stored on transitions)
+- Adding the "-pF" polynomial computation : it will output polynomials according
+   to a probabilistic model in several variables.
+
diff --git a/README.rst b/README.rst
@@ -31,7 +31,9 @@ Installation
 
 (more at  <http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#downloadiedera>)
 
-You need a C++ compiler and the autotools. On Linux, you can install
+Binaries for Windows (x64) and OS X (x64) are available at <https://github.com/laurentnoe/iedera/releases>.
+
+Otherwise, you need a C++ compiler and the autotools. On Linux, you can install
 ``g++``, ``autoconf``, ``automake``. On Mac, you can install
 ``xcode``, or the command line developer tools (or you can use
 ``macports`` to install ``g++-mp-5`` for example).
@@ -61,6 +63,7 @@ or copy the binary directly to your homedir::
    
   cp src/iedera ~/.
 
+
 Command-line
 ------------
 
@@ -184,14 +187,38 @@ will also probably improve the sensitivity result.
 Polynomial form
 ---------------
 
-When the probability *p* to generate a *match* is not fixed (for example *p=0.7* was set in all the previous examples), Mak & Benson have proposed to use a polynomial form and select what they called **dominant seeds**. We have noticed that this dominance applies as well for any other i.i.d criteria as the *Hit Integration* (Chung & Park), for *Lossless seeds*, and several discrete models ... (see <http://doi.org/10.1186/s13015-017-0092-1>) so the flag :
+Bernoulli model
+~~~~~~~~~~~~~~~
+
+When the probability *p* to generate a *match* is not fixed (for example *p=0.7* was set in all the previous examples), Mak & Benson have proposed to use a polynomial form and select what they called **dominant seeds**. We have noticed that this dominance applies as well for any other i.i.d criteria as the *Hit Integration* (Chung & Park), for *Lossless seeds*, and several discrete models ... (see <http://doi.org/10.1186/s13015-017-0092-1>) so the flag:
 
 -p
   to activate dominant selection and output polynomial coefficients
- 
+
 
 is added in the current commited version of iedera (master branch).
 
+Other multivariate models 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+When the probabilitic model is more complex compared to a simple Bernoulli model on a binary alphabet, it is possible to compute the probability as a multivariate polynomial form. For a given seed provided with the *-m* parameter, the output will contain this polynomial form set in square brackets. *Selection of the best seeds is left as an exercice for the reader.*  The flag ``-pF <filename>``  activates the output of the multivariate polynomial on the given model. This flag is added on this local branch. The next example gives sensitivity of the seed 1101 on alignments of length 8 ::
+
+  iedera -spaced -pF model_bernoulli_simple_x_xp.txt  -m "##-#" -l 8
+
+on the bernoulli model provided by the file *model_bernoulli_simple_x_xp.txt* ::
+
+  2
+     0   1
+        0   1
+           0   x
+        1   1
+           0   xp
+     1   0
+        0   1
+           1   x
+        1   1
+           1   xp
+
 
 References
 ----------

diff --git a/configure b/configure
@@ -3883,8 +3883,8 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++0x is needed" >&5
-$as_echo_n "checking for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++0x is needed... " >&6; }
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++11 is needed" >&5
+$as_echo_n "checking for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++11 is needed... " >&6; }
   acx_type_traits=no
 
 # (1) =========================== no compiler option ===========================
@@ -3897,7 +3897,7 @@ $as_echo_n "checking for type traits <tr1/type_traits> or <type_trait>, for std
 int
 main ()
 {
-typedef std::is_arithmetic<double> isArithmeticT;
+typedef std::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -3927,7 +3927,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 int
 main ()
 {
-typedef std::tr1::is_arithmetic<double> isArithmeticT;
+typedef std::tr1::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -3957,7 +3957,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 int
 main ()
 {
-typedef std::is_arithmetic<double> isArithmeticT;
+typedef std::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -3987,7 +3987,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 int
 main ()
 {
-typedef std::tr1::is_arithmetic<double> isArithmeticT;
+typedef std::tr1::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -4013,15 +4013,15 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
         #include <type_traits>
 int
 main ()
 {
-typedef std::is_arithmetic<double> isArithmeticT;
+typedef std::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -4050,15 +4050,15 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
         #include <type_traits>
 int
 main ()
 {
-typedef std::tr1::is_arithmetic<double> isArithmeticT;
+typedef std::tr1::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -4087,15 +4087,15 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
         #include <tr1/type_traits>
 int
 main ()
 {
-typedef std::is_arithmetic<double> isArithmeticT;
+typedef std::is_void<double> isVoidT;
 
   ;
   return 0;
@@ -4124,15 +4124,15 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
         #include <tr1/type_traits>
 int
 main ()
 {
-typedef std::tr1::is_arithmetic<double> isArithmeticT;
+typedef std::tr1::is_void<double> isVoidT;
 
   ;
   return 0;

diff --git a/configure.ac b/configure.ac
@@ -1,10 +1,9 @@
 
 # Check for type traits in <type_traits> and std namespace
-
-AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
+AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX11], [
   AC_LANG_PUSH([C++])
 
-  AC_MSG_CHECKING([for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++0x is needed])
+  AC_MSG_CHECKING([for type traits <tr1/type_traits> or <type_trait>, for std or std:tr1, and if compiler option -std=c++11 is needed])
   acx_type_traits=no
 
 # (1) =========================== no compiler option ===========================
@@ -14,7 +13,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
       [
         AC_LANG_PROGRAM(
       	  [[#include <type_traits>]],
-          [[typedef std::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::is_void<double> isVoidT;]]
       	)	  
       ],		    
       [
@@ -30,7 +29,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
       [
         AC_LANG_PROGRAM(
           [[#include <type_traits>]],
-          [[typedef std::tr1::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::tr1::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -46,7 +45,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
       [
         AC_LANG_PROGRAM(
           [[#include <tr1/type_traits>]],
-          [[typedef std::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -62,7 +61,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
       [
         AC_LANG_PROGRAM(
           [[#include <tr1/type_traits>]],
-          [[typedef std::tr1::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::tr1::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -77,12 +76,12 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
   
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     AC_COMPILE_IFELSE(
       [
         AC_LANG_PROGRAM(
       	  [[#include <type_traits>]],
-          [[typedef std::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::is_void<double> isVoidT;]]
       	)	  
       ],		    
       [
@@ -100,12 +99,12 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
 
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     AC_COMPILE_IFELSE(
       [
         AC_LANG_PROGRAM(
           [[#include <type_traits>]],
-          [[typedef std::tr1::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::tr1::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -123,12 +122,12 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
   
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     AC_COMPILE_IFELSE(
       [
         AC_LANG_PROGRAM(
           [[#include <tr1/type_traits>]],
-          [[typedef std::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -146,12 +145,12 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX0X], [
   
   if test "$acx_type_traits" = no; then
     ac_save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -std=c++0x"
+    CXXFLAGS="$CXXFLAGS -std=c++11"
     AC_COMPILE_IFELSE(
       [
         AC_LANG_PROGRAM(
           [[#include <tr1/type_traits>]],
-          [[typedef std::tr1::is_arithmetic<double> isArithmeticT;]]
+          [[typedef std::tr1::is_void<double> isVoidT;]]
         )
       ],
       [
@@ -193,7 +192,7 @@ CXXFLAGS=""
 AC_PROG_CXX
 AC_CHECK_HEADERS([stdlib.h string.h sys/time.h unistd.h])
 AC_CHECK_FUNCS([gettimeofday sqrt strdup strtol])
-ACX_CHECK_TYPE_TRAITS_CXX0X
+ACX_CHECK_TYPE_TRAITS_CXX11
 LIBS="$LIBS -lm"
 AC_SUBST(CXXFLAGS)
 AC_SUBST(LIBS)