CMakeLists.txt

@@ -35,7 +35,7 @@ ELSE(NO_DEP_CHECK)
 #           library implements.
 # In other words, the library implements all the interface numbers in the
 # range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "11")
+SET(${PROJECT_NAME}_VERSION_CURRENT "12")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
 SET(${PROJECT_NAME}_VERSION_AGE "0")
 
@@ -53,7 +53,7 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-seq 11.0.0 REQUIRED)
+find_package (bpp-seq 12.0.0 REQUIRED)
 
 # CMake package
 set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-phyl")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION "2.4.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetics library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -107,6 +107,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
 # /!\ This assumes that an external build is used
 SET(CPACK_SOURCE_IGNORE_FILES 
        "/build/" 
+       "/html/" 
+       "/BppPhyl.tag" 
        "/\\\\.git/" 
        "/\\\\.gitignore" 
        ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+20/02/18 -*- Version 2.4.0 -*-
+
+10/12/17 -*- Version 2.3.2 -*-
+
 10/05/17 -*- Version 2.3.0 -*-
 
 23/09/16 Laurent Gueguen

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-phyl
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.3.0
+PROJECT_NUMBER         = 2.4.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

bpp-phyl.spec

-%define _basename bpp-phyl
-%define _version 2.3.1
-%define _release 1
 %define _prefix /usr
 
-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-phyl
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-phyl
+Version: 1.4.0
+Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
 Summary: Bio++ Phylogenetics library
 Group: Development/Libraries/C and C++
-Requires: bpp-core = %{_version}
-Requires: bpp-seq = %{_version}
+Requires: bpp-core = %{version}
+Requires: bpp-seq = %{version}
 
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
-BuildRequires: libbpp-core3 = %{_version}
-BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq11 = %{_version}
-BuildRequires: libbpp-seq-devel = %{_version}
+BuildRequires: libbpp-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
 
 AutoReq: yes
 AutoProv: yes
@@ -31,11 +28,11 @@ AutoProv: yes
 This library contains utilitary and classes for phylogenetics and molecular evolution analysis.
 It is part of the Bio++ project.
 
-%package -n libbpp-phyl11
+%package -n libbpp-phyl12
 Summary: Bio++ Phylogenetics library
 Group: Development/Libraries/C and C++
 
-%description -n libbpp-phyl11
+%description -n libbpp-phyl12
 This library contains utilitary and classes for phylogenetics and molecular evolution analysis.
 It is part of the Bio++ project.
 
@@ -43,15 +40,15 @@ It is part of the Bio++ project.
 %package -n libbpp-phyl-devel
 Summary: Libraries, includes to develop applications with %{_basename}
 Group: Development/Libraries/C and C++
-Requires: libbpp-phyl11 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core3 = %{_version}
-Requires: libbpp-core-devel = %{_version}
+Requires: libbpp-phyl12 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-seq-devel = %{version}
+Requires: libbpp-core4 = %{version}
+Requires: libbpp-core-devel = %{version}
 
 %description -n libbpp-phyl-devel
 The libbpp-phyl-devel package contains the header files and static libraries for
-building applications which use %{_basename}.
+building applications which use %{name}.
 
 %prep
 %setup -q
@@ -68,11 +65,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
 %clean
 rm -rf $RPM_BUILD_ROOT
 
-%post -n libbpp-phyl11 -p /sbin/ldconfig
+%post -n libbpp-phyl12 -p /sbin/ldconfig
 
-%postun -n libbpp-phyl11 -p /sbin/ldconfig
+%postun -n libbpp-phyl12 -p /sbin/ldconfig
 
-%files -n libbpp-phyl11
+%files -n libbpp-phyl12
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
 %{_prefix}/%{_lib}/lib*.so.*
@@ -88,6 +85,9 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions specifications.
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 - Increased interface number
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

debian/changelog

-libbpp-phyl (2.3.2-3) UNRELEASED; urgency=medium
+libbpp-phyl (2.4.0-1) UNRELEASED; urgency=medium
 
+  * New upstream update.
   * Reduced execution time of test_likelihood_nh
     Closes: #890136
+  * Added symbol list.
 
- -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Fri, 09 Feb 2018 09:10:11 +0200
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Tue, 27 Mar 2018 09:44:33 +0200
 
 libbpp-phyl (2.3.2-2) unstable; urgency=medium
 

debian/control

@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
-               libbpp-seq-dev (>= 2.3.2)
+               libbpp-seq-dev (>= 2.4.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-phyl.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-phyl.git
@@ -16,9 +16,9 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 Package: libbpp-phyl-dev
 Architecture: any
 Section: libdevel
-Depends: libbpp-phyl11 (= ${binary:Version}),
+Depends: libbpp-phyl12 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-seq-dev (>= 2.3.2)
+         libbpp-seq-dev (>= 2.4.0)
 Description: Bio++ Phylogenetic library development files
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.
@@ -29,7 +29,7 @@ Description: Bio++ Phylogenetic library development files
  This package contains the static library and the header files of the
  Bio++ classes for phylogenetics.
 
-Package: libbpp-phyl11
+Package: libbpp-phyl12
 Architecture: any
 Multi-Arch: same
 Section: libs

debian/copyright

 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Phyl
+Upstream-Name: Bpp-Phyl
 Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-phyl/
 
 Files: *
 Copyright: 2010-2016 Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>

debian/patches/correct_constructors_inheritance.patch

-Author: Julien Y. Dutheil
-Last-Update: 2018-02-06 13:42:17 +0100
-Description: correct constructors inheritance to comply with gcc-7
-
-diff --git a/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
-index 93e8f47..593441d 100644
---- a/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
-+++ b/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
-@@ -50,7 +50,6 @@ class ConstantRateDistribution:
- {
-   public:
-     ConstantRateDistribution():
--      AbstractParameterAliasable("Constant."),
-       ConstantDistribution(1.)
-     {
-       resetParameters_();
-diff --git a/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
-index e647f63..7373643 100644
---- a/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
-+++ b/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
-@@ -50,7 +50,6 @@ class ExponentialDiscreteRateDistribution:
- {
-   public:
-     ExponentialDiscreteRateDistribution(size_t nbClasses):
--      AbstractParameterAliasable("Exponential."),
-       ExponentialDiscreteDistribution(nbClasses, 1.)
-     {
-       deleteParameter_(0);
-diff --git a/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
-index 5159ec1..7cbb799 100644
---- a/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
-+++ b/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
-@@ -50,7 +50,6 @@ class GammaDiscreteRateDistribution:
- {
-   public:
-     GammaDiscreteRateDistribution(size_t nbClasses, double alpha = 1.):
--      AbstractParameterAliasable("Gamma."),
-       GammaDiscreteDistribution(nbClasses, alpha, alpha)
-     {
-       aliasParameters("alpha", "beta");
-diff --git a/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
-index 75eb37e..bde7c9c 100644
---- a/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
-+++ b/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
-@@ -50,7 +50,6 @@ class GaussianDiscreteRateDistribution:
- {
-   public:
-     GaussianDiscreteRateDistribution(size_t nbClasses, double sigma):
--      AbstractParameterAliasable("Gaussian."),
-       GaussianDiscreteDistribution(nbClasses, 1., sigma)
-     {
-       deleteParameter_(0);

debian/patches/fix_covariant_return.patch

-Author: Julien Y. Dutheil <dutheil@evolbio.mpg.de>
-Date:   Fri Feb 9 09:34:02 2018 +0100
-Bug-Debian: https://bugs.debian.org/889953
-Description: Fixed covariant return error on 32bits arch.
-
-diff --git a/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h b/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
-index 9d20298..fe0bc51 100644
---- a/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
-+++ b/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
-@@ -151,12 +151,12 @@ namespace bpp
-       return AbstractWrappedSubstitutionModel::getAlphabetStates();
-     }
-     
--    std::vector<long unsigned int> getModelStates(int i) const
-+    std::vector<size_t> getModelStates(int i) const
-     {
-       return AbstractWrappedSubstitutionModel::getModelStates(i);
-     }
- 
--    std::vector<long unsigned int> getModelStates(const std::string& s) const
-+    std::vector<size_t> getModelStates(const std::string& s) const
-     {
-       return AbstractWrappedSubstitutionModel::getModelStates(s);
-     }

debian/patches/series

 unforce-cxxflags.patch
-correct_constructors_inheritance.patch
-fix_covariant_return.patch
 reduce_test_time.patch

debian/patches/unforce-cxxflags.patch

@@ -11,7 +11,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
  
  # Compile options
 -set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
-+set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g")
++#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
  
  IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp

@@ -102,7 +102,7 @@ Tree* PhylogeneticsApplicationTools::getTree(
   const string& suffix,
   bool suffixIsOptional,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   string format = ApplicationTools::getStringParameter(prefix + "tree.format", params, "Newick", suffix, suffixIsOptional, warn);
   string treeFilePath = ApplicationTools::getAFilePath(prefix + "tree.file", params, true, true, suffix, suffixIsOptional, "none", warn);
@@ -126,7 +126,7 @@ vector<Tree*> PhylogeneticsApplicationTools::getTrees(
   const string& suffix,
   bool suffixIsOptional,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   string format = ApplicationTools::getStringParameter(prefix + "trees.format", params, "Newick", suffix, suffixIsOptional, warn);
   string treeFilePath = ApplicationTools::getAFilePath(prefix + "trees.file", params, true, true, suffix, suffixIsOptional, "none", warn);
@@ -163,7 +163,7 @@ SubstitutionModel* PhylogeneticsApplicationTools::getSubstitutionModel(
   const string& suffix,
   bool suffixIsOptional,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   BppOSubstitutionModelFormat bIO(BppOSubstitutionModelFormat::ALL, true, true, true, verbose, warn + 1);
   string modelDescription;
@@ -192,7 +192,7 @@ TransitionModel* PhylogeneticsApplicationTools::getTransitionModel(
   const string& suffix,
   bool suffixIsOptional,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   BppOTransitionModelFormat bIO(BppOSubstitutionModelFormat::ALL, true, true, true, verbose, warn + 1);
   string modelDescription;
@@ -221,7 +221,7 @@ void PhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesW
   size_t modelNumber,
   const SiteContainer* data,
   std::map<std::string, std::string>& sharedParams,
-  bool verbose) throw (Exception)
+  bool verbose)
 {
   string initFreqs = ApplicationTools::getStringParameter(model.getNamespace() + "initFreqs", unparsedParameterValues, "", "", true, 2);
 
@@ -258,7 +258,7 @@ void PhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesW
   for (size_t i = 0; i < pl.size(); ++i)
   {
     AutoParameter ap(pl[i]);
-    ap.setMessageHandler(ApplicationTools::warning);
+    ap.setMessageHandler(ApplicationTools::warning.get());
     pl.setParameter(i, ap);
   }
 
@@ -311,7 +311,7 @@ FrequenciesSet* PhylogeneticsApplicationTools::getRootFrequenciesSet(
   const std::string& suffix,
   bool suffixIsOptional,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   string freqDescription = ApplicationTools::getStringParameter("nonhomogeneous.root_freq", params, "Full(init=observed)", suffix, suffixIsOptional, warn);
   if (freqDescription == "None")
@@ -347,7 +347,7 @@ FrequenciesSet* PhylogeneticsApplicationTools::getFrequenciesSet(
   std::map<std::string, std::string>& sharedparams,
   const std::vector<double>& rateFreqs,
   bool verbose,
-  int warn) throw (Exception)
+  int warn)
 {
   map<string, string> unparsedParameterValues;
   BppOFrequenciesSetFormat bIO(BppOFrequenciesSetFormat::ALL, verbose, warn);
@@ -698,7 +698,7 @@ DiscreteDistribution* PhylogeneticsApplicationTools::getRateDistribution(
   map<string, string>& params,
   const string& suffix,
   bool suffixIsOptional,
-  bool verbose) throw (Exception)
+  bool verbose)
 {
   string distDescription = ApplicationTools::getStringParameter("rate_distribution", params, "Constant()", suffix, suffixIsOptional);
 
@@ -733,7 +733,6 @@ TreeLikelihood* PhylogeneticsApplicationTools::optimizeParameters(
   bool suffixIsOptional,
   bool verbose,
   int warn)
-throw (Exception)
 {
   string optimization = ApplicationTools::getStringParameter("optimization", params, "FullD(derivatives=Newton)", suffix, suffixIsOptional, warn);
   if (optimization == "None")
@@ -747,7 +746,7 @@ throw (Exception)
   string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);
   OutputStream* messageHandler =
     (mhPath == "none") ? 0 :
-    (mhPath == "std") ? ApplicationTools::message :
+    (mhPath == "std") ? ApplicationTools::message.get() :
     new StlOutputStream(new ofstream(mhPath.c_str(), ios::out));
   if (verbose)
     ApplicationTools::displayResult("Message handler", mhPath);
@@ -755,7 +754,7 @@ throw (Exception)
   string prPath = ApplicationTools::getAFilePath("optimization.profiler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);
   OutputStream* profiler =
     (prPath == "none") ? 0 :
-    (prPath == "std") ? ApplicationTools::message :
+    (prPath == "std") ? ApplicationTools::message.get() :
     new StlOutputStream(new ofstream(prPath.c_str(), ios::out));
   if (profiler)
     profiler->setPrecision(20);
@@ -978,10 +977,15 @@ throw (Exception)
           }
           string pname  = stp.nextToken();
           string pvalue = stp.nextToken();
+          try {
             size_t p = pl.whichParameterHasName(pname);
             pl.setParameter(p, AutoParameter(pl[p]));
             pl[p].setValue(TextTools::toDouble(pvalue));
           }
+          catch(Exception& e)
+          {
+          }
+        }
       }
       bck.close();
       tl->setParameters(pl);
@@ -1156,7 +1160,6 @@ void PhylogeneticsApplicationTools::optimizeParameters(
   bool suffixIsOptional,
   bool verbose,
   int warn)
-throw (Exception)
 {
   string optimization = ApplicationTools::getStringParameter("optimization", params, "FullD(derivatives=Newton)", suffix, suffixIsOptional, warn);
   if (optimization == "None")
@@ -1170,7 +1173,7 @@ throw (Exception)
   string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);
   OutputStream* messageHandler =
     (mhPath == "none") ? 0 :
-    (mhPath == "std") ? ApplicationTools::message :
+    (mhPath == "std") ? ApplicationTools::message.get() :
     new StlOutputStream(new ofstream(mhPath.c_str(), ios::out));
   if (verbose)
     ApplicationTools::displayResult("Message handler", mhPath);
@@ -1178,7 +1181,7 @@ throw (Exception)
   string prPath = ApplicationTools::getAFilePath("optimization.profiler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);
   OutputStream* profiler =
     (prPath == "none") ? 0 :
-    (prPath == "std") ? ApplicationTools::message :
+    (prPath == "std") ? ApplicationTools::message.get() :
     new StlOutputStream(new ofstream(prPath.c_str(), ios::out));
   if (profiler)
     profiler->setPrecision(20);
@@ -1398,7 +1401,7 @@ void PhylogeneticsApplicationTools::writeTree(
   bool suffixIsOptional,
   bool verbose,
   bool checkOnly,
-  int warn) throw (Exception)
+  int warn)
 {
   string format = ApplicationTools::getStringParameter(prefix + "tree.format", params, "Newick", suffix, suffixIsOptional, warn);
   string file = ApplicationTools::getAFilePath(prefix + "tree.file", params, false, false, suffix, suffixIsOptional, "none", warn);
@@ -1424,7 +1427,7 @@ void PhylogeneticsApplicationTools::writeTrees(
   bool suffixIsOptional,
   bool verbose,
   bool checkOnly,
-  int warn) throw (Exception)
+  int warn)
 {
   string format = ApplicationTools::getStringParameter(prefix + "trees.format", params, "Newick", suffix, suffixIsOptional, warn);
   string file = ApplicationTools::getAFilePath(prefix + "trees.file", params, true, false, suffix, suffixIsOptional, "none", warn);

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h

@@ -107,7 +107,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Build a list ofTree objects according to options.
@@ -129,7 +129,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Build a SubstitutionModel object according to options.
@@ -161,7 +161,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   
   static TransitionModel* getTransitionModel(
@@ -172,7 +172,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Set parameter initial values of a given model in a set according to options.
@@ -199,7 +199,7 @@ public:
     size_t modelNumber,
     const SiteContainer* data,
     std::map<std::string, std::string>& sharedParams,
-    bool verbose) throw (Exception);
+    bool verbose);
 
   /**
    * @brief Get A FrequenciesSet object for root frequencies (NH models) according to options.
@@ -231,7 +231,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Get A FrequenciesSet object according to options.
@@ -260,8 +260,7 @@ public:
     std::map<std::string, std::string>& sharedParams,
     const std::vector<double>& rateFreqs,
     bool verbose = true,
-    int warn = 1)
-  throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Get A FrequenciesSet object according to options.
@@ -289,7 +288,6 @@ public:
     const std::vector<double>& rateFreqs,
     bool verbose = true,
     int warn = 1)
-  throw (Exception)
   {
     std::map<std::string, std::string> sharedParams;
     return getFrequenciesSet(alphabet, gCode, freqDescription, data, sharedParams, rateFreqs, verbose, warn);
@@ -487,8 +485,7 @@ public:
     std::map<std::string, std::string>& params,
     const std::string& suffix = "",
     bool suffixIsOptional = true,
-    bool verbose = true)
-  throw (Exception);
+    bool verbose = true);
 
   /**
    * @brief Optimize parameters according to options.
@@ -517,8 +514,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1)
-  throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Optimize parameters according to options, with a molecular clock.
@@ -540,8 +536,7 @@ public:
     const std::string& suffix = "",
     bool suffixIsOptional = true,
     bool verbose = true,
-    int warn = 1)
-  throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Check if parameter values are close to their definition boundary.
@@ -580,7 +575,6 @@ public:
    * @param verbose if outputs  reading
    * @return A SubstitutionRegister object.
    */
-  
   static SubstitutionRegister* getSubstitutionRegister(const std::string& regTypeDesc, const SubstitutionModel* model, bool verbose = true);
   
 
@@ -608,7 +602,7 @@ public:
     bool suffixIsOptional = true,
     bool verbose = true,
     bool checkOnly = false,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
   /**
    * @brief Write a tree according to options.
@@ -634,7 +628,7 @@ public:
     bool suffixIsOptional = true,
     bool verbose = true,
     bool checkOnly = false,
-    int warn = 1) throw (Exception);
+    int warn = 1);
 
 
   /**

src/Bpp/Phyl/BipartitionList.cpp

@@ -240,7 +240,7 @@ BipartitionList::~BipartitionList()
 
 /******************************************************************************/
 
-map<string, bool> BipartitionList::getBipartition(size_t i) const throw (Exception)
+map<string, bool> BipartitionList::getBipartition(size_t i) const
 {
   map<string, bool> bip;
 
@@ -259,7 +259,7 @@ map<string, bool> BipartitionList::getBipartition(size_t i) const throw (Excepti
 
 /******************************************************************************/
 
-int* BipartitionList::getBitBipartition(size_t i) throw (Exception)
+int* BipartitionList::getBitBipartition(size_t i)
 {
   if (i >= bitBipartitionList_.size())
     throw Exception("Bipartition index exceeds BipartitionList size");
@@ -291,7 +291,7 @@ bool BipartitionList::haveSameElementsThan(map<string, bool>& bipart) const
 
 /******************************************************************************/
 
-void BipartitionList::addBipartition(map<string, bool>& bipart, bool checkElements) throw (Exception)
+void BipartitionList::addBipartition(map<string, bool>& bipart, bool checkElements)
 {
   if (checkElements && !BipartitionList::haveSameElementsThan(bipart))
     throw Exception("Distinct bipartition element sets");
@@ -317,7 +317,7 @@ void BipartitionList::addBipartition(map<string, bool>& bipart, bool checkElemen
 
 /******************************************************************************/
 
-void BipartitionList::deleteBipartition(size_t i) throw (Exception)
+void BipartitionList::deleteBipartition(size_t i)
 {
   if (i >= bitBipartitionList_.size())
     throw Exception("Bipartition index exceeds BipartitionList size");
@@ -328,7 +328,7 @@ void BipartitionList::deleteBipartition(size_t i) throw (Exception)
 
 /******************************************************************************/
 
-bool BipartitionList::containsBipartition(map<string, bool>& bipart, bool checkElements) const throw (Exception)
+bool BipartitionList::containsBipartition(map<string, bool>& bipart, bool checkElements) const
 {
   size_t i, j;
   bool dac, padac;
@@ -366,7 +366,7 @@ bool BipartitionList::containsBipartition(map<string, bool>& bipart, bool checkE
 
 /******************************************************************************/
 
-bool BipartitionList::areIdentical(size_t k1, size_t k2) const throw (Exception)
+bool BipartitionList::areIdentical(size_t k1, size_t k2) const
 {
   bool dac, padac;
 
@@ -400,7 +400,7 @@ bool BipartitionList::areIdentical(size_t k1, size_t k2) const throw (Exception)
 
 /******************************************************************************/
 
-bool BipartitionList::areCompatible(size_t k1, size_t k2) const throw (Exception)
+bool BipartitionList::areCompatible(size_t k1, size_t k2) const
 {
   bool uu, uz, zu, zz;
 
@@ -451,7 +451,7 @@ bool BipartitionList::areAllCompatible() const
 
 /******************************************************************************/
 
-bool BipartitionList::areAllCompatibleWith(map<string, bool>& bipart, bool checkElements) const throw (Exception)
+bool BipartitionList::areAllCompatibleWith(map<string, bool>& bipart, bool checkElements) const
 {
   if (checkElements && !haveSameElementsThan(bipart))
     throw Exception("Distinct bipartition element sets");
@@ -525,7 +525,7 @@ void BipartitionList::sortElements()
 
 /******************************************************************************/
 
-size_t BipartitionList::getPartitionSize(size_t k) const throw (Exception)
+size_t BipartitionList::getPartitionSize(size_t k) const
 {
   size_t size = 0;
   if (k >= bitBipartitionList_.size())
@@ -602,7 +602,7 @@ void BipartitionList::sortByPartitionSize()
 
 /******************************************************************************/
 
-void BipartitionList::flip(size_t k) throw (Exception)
+void BipartitionList::flip(size_t k)
 {
   if (k >= bitBipartitionList_.size())
     throw Exception("Bipartition index exceeds BipartitionList size");
@@ -647,7 +647,7 @@ void BipartitionList::removeRedundantBipartitions()
 
 /******************************************************************************/
 
-TreeTemplate<Node>* BipartitionList::toTree() const throw (Exception)
+TreeTemplate<Node>* BipartitionList::toTree() const
 {
   BipartitionList* sortedBipL;
   vector<int*> sortedBitBipL;

src/Bpp/Phyl/BipartitionList.h

@@ -132,23 +132,23 @@ class BipartitionList:
 
     const std::vector<int*> & getBitBipartitionList() const { return bitBipartitionList_; }
 
-    std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
+    std::map<std::string, bool> getBipartition(size_t i) const;
 
-    int* getBitBipartition(size_t i) throw (Exception);
+    int* getBitBipartition(size_t i);
 
     bool haveSameElementsThan(std::map<std::string, bool>& bipart) const;
 
-    void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
+    void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1);
 
-    void deleteBipartition(size_t i) throw(Exception);
+    void deleteBipartition(size_t i);
 
     bool isSorted() const { return sorted_; }
 
     void sortElements();
 
-    bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
+    bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const;
 
-    bool areIdentical(size_t k1, size_t k2) const throw(Exception);
+    bool areIdentical(size_t k1, size_t k2) const;
 
     void removeRedundantBipartitions();
 
@@ -160,7 +160,7 @@ class BipartitionList:
      * and B1 contains A2) or (B1 contains A1 and A2 contains B2) or (B2 contains A1 and A2
      * contains B1). Only compatible bipartitions can belong to the same tree.
      */
-    bool areCompatible(size_t k1, size_t k2) const throw(Exception);
+    bool areCompatible(size_t k1, size_t k2) const;
 
     /**
      * @brief Tells whether all bipartitions in the list are compatible with each other
@@ -173,7 +173,7 @@ class BipartitionList:
      * @param bipart A map representing a bipartition.
      * @param checkElements Check the correspondance of element sets or not.
      */
-    bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
+    bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const;
 
     /**
      * @brief Removes bipartitions corresponding to external branches (1 vs n-1)
@@ -189,12 +189,12 @@ class BipartitionList:
     /**
      * @brief Replaces ones by zeros and zeros by ones in the ith bipartition
      */
-    void flip(size_t i) throw(Exception);
+    void flip(size_t i);
 
     /**
      * @brief Returns the size of the smallest of the two partitions (e.g. 1 for external branches)
      */
-    size_t getPartitionSize(size_t i) const throw(Exception);
+    size_t getPartitionSize(size_t i) const;
 
     /**
      * @brief Sort bipartitions by partition size
@@ -204,7 +204,7 @@ class BipartitionList:
     /**
      * @brief Translate into a tree
      */
-    TreeTemplate<Node>* toTree() const throw(Exception);
+    TreeTemplate<Node>* toTree() const;
 
     /**
      * @brief Create a matrix representation of the bifurcations.

src/Bpp/Phyl/BipartitionTools.cpp

@@ -126,7 +126,7 @@ bool BipartitionTools::testBit(int* plist, int num)
 BipartitionList* BipartitionTools::buildBipartitionPair(
   const BipartitionList& bipartL1, size_t i1,
   const BipartitionList& bipartL2, size_t i2,
-  bool checkElements) throw (Exception)
+  bool checkElements)
 {
   vector<int*> bitBipL1, bitBipL2, twoBitBipL;
   vector<string> elements;
@@ -204,7 +204,7 @@ bool BipartitionTools::areCompatible(
 
 BipartitionList* BipartitionTools::mergeBipartitionLists(
   const vector<BipartitionList*>& vecBipartL,
-  bool checkElements) throw (Exception)
+  bool checkElements)
 {
   vector<string> elements;
   vector<int*> mergedBitBipL;
@@ -264,7 +264,7 @@ BipartitionList* BipartitionTools::mergeBipartitionLists(
 /******************************************************************************/
 
 VectorSiteContainer* BipartitionTools::MRPEncode(
-  const vector<BipartitionList*>& vecBipartL) throw (Exception)
+  const vector<BipartitionList*>& vecBipartL)
 {
   vector<string> all_elements;
   map<string, bool> bip;
@@ -328,7 +328,7 @@ VectorSiteContainer* BipartitionTools::MRPEncode(
 /******************************************************************************/
 
 VectorSiteContainer* BipartitionTools::MRPEncodeMultilabel(
-                                                 const vector<BipartitionList*>& vecBipartL) throw (Exception)
+                                                 const vector<BipartitionList*>& vecBipartL)
 {
     vector<string> all_elements;
     map<string, bool> bip;

src/Bpp/Phyl/BipartitionTools.h

@@ -139,12 +139,12 @@ public:
    * The input BipartitionList objects must share the same set of elements. This will be checked or not
    * depending on checkElements
    */
-  static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
+  static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true);
 
   /**
    * @brief Construct a BipartitionList containing two bipartitions taken from distinct input lists
    */
-  static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
+  static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true);
 
   /**
    * @brief Tells whether two bipartitions from distinct lists are identical
@@ -163,7 +163,7 @@ public:
    * The output alignment (DNA sequences including only A, C and N)) is ready for maximum parsimony analysis
    * according to the MRP supertree method.
    */
-  static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
+  static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL);
     
     /**
      * @brief Create a sequence data set corresponding to the Matrix Representation of the input BipartitionList objects and accomodates multilabel trees
@@ -172,7 +172,7 @@ public:
      * The output alignment (DNA sequences including only A, C and N)) is ready for maximum parsimony analysis
      * according to the MRP supertree method.
      */
-    static VectorSiteContainer* MRPEncodeMultilabel(                                                                     const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
+    static VectorSiteContainer* MRPEncodeMultilabel(                                                                     const std::vector<BipartitionList*>& vecBipartL);
 
 };
 } // end of namespace bpp.

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp

@@ -50,7 +50,7 @@ using namespace bpp;
 
 using namespace std;
 
-void AbstractAgglomerativeDistanceMethod::setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
+void AbstractAgglomerativeDistanceMethod::setDistanceMatrix(const DistanceMatrix& matrix)
 {
   if (matrix.size() <= 3)
     throw Exception("AbstractAgglomerativeDistanceMethod::setDistanceMatrix(): matrix must be at least of dimension 3.");
@@ -59,7 +59,7 @@ void AbstractAgglomerativeDistanceMethod::setDistanceMatrix(const DistanceMatrix
   if (tree_) delete tree_;
 }
     
-void AbstractAgglomerativeDistanceMethod::computeTree() throw (Exception)
+void AbstractAgglomerativeDistanceMethod::computeTree()
 {
   // Initialization:
   for (size_t i = 0; i < matrix_.size(); ++i)

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h

@@ -111,7 +111,7 @@ class AbstractAgglomerativeDistanceMethod:
     }
 
 	public:
-		virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
+		virtual void setDistanceMatrix(const DistanceMatrix& matrix);
 
     /**
      * @brief Get the computed tree, if there is one.
@@ -139,7 +139,7 @@ class AbstractAgglomerativeDistanceMethod:
      * 6) Return to step 2 while there are more than 3 remaining nodes.
      * 7) Perform the final step, and send a rooted or unrooted tree.
      */
-		virtual void computeTree() throw (Exception);
+		virtual void computeTree();
 
     void setVerbose(bool yn) { verbose_ = yn; }
     bool isVerbose() const { return verbose_; }
@@ -160,7 +160,7 @@ class AbstractAgglomerativeDistanceMethod:
      * @return A size 2 vector with the indices of the nodes.
      * @throw Exception If an error occured.
      */
-		virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
+		virtual std::vector<size_t> getBestPair() = 0;
 		
     /**
      * @brief Compute the branch lengths for two nodes to agglomerate.