Julien Y. Dutheil · Julien Y. Dutheil · Julien Y. Dutheil · Julien Y. Dutheil · cd13f67d · cd13f67d
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
 project (bpp-core CXX)

 # Compile options
-set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
+#set (CMAKE_CXX_FLAGS "-std=c++11 -g")

 IF(NOT CMAKE_BUILD_TYPE)
  SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
@@ -25,7 +25,7 @@ ENDIF(NOT CMAKE_BUILD_TYPE)
 #           library implements.
 # In other words, the library implements all the interface numbers in the
 # range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "3")
+SET(${PROJECT_NAME}_VERSION_CURRENT "4")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
 SET(${PROJECT_NAME}_VERSION_AGE "0")

@@ -77,10 +77,10 @@ ENDIF (DOXYGEN_FOUND)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-core")
 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++ Core library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -89,6 +89,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
 # /!\ This assumes that an external build is used
 SET(CPACK_SOURCE_IGNORE_FILES 
       "/build/" 
+       "/html/"
+       "/BppCore.tag"
       "/\\\\.git/" 
       "/\\\\.gitignore" 
       ${CPACK_SOURCE_IGNORE_FILES}

--- a/ChangeLog
+++ b/ChangeLog
-10/0(/17 -*- Version 2.3.0 -*-
+19/02/17 -*- Version 2.4.0 -*-
+
+04/01/18 Laurent Guéguen
+* Several bug fixes and improvements (interface break)
+
+18/12/17 Laurent Guéguen 
+* TreeGraphs improvements
+
+08/12/17 -*- Version 2.3.2 -*-
+
+10/05/17 -*- Version 2.3.0 -*-

 26/04/16 Julien Dutheil
 * Upgrading to C++11

--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-core
 # 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

--- a/bpp-core.spec
+++ b/bpp-core.spec
-%define _basename bpp-core
-%define _version 2.3.1
-%define _release 1
 %define _prefix /usr

-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-core

-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-core
+Version: 2.4.0
+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++ Core library
 Group: Development/Libraries/C and C++

-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
 AutoReq: yes
@@ -23,17 +20,17 @@ AutoProv: yes
 %description
 This library contains the core classes and utilitary functions of the Bio++ project.

-%package -n libbpp-core3
+%package -n libbpp-core4
 Summary: Bio++ Core library
 Group: Development/Libraries/C and C++

-%description -n libbpp-core3
+%description -n libbpp-core4
 This library contains the core classes and utilitary functions of the Bio++ project.

 %package -n libbpp-core-devel
-Summary: Libraries, includes to develop applications with %{_basename}
+Summary: Libraries, includes to develop applications with %{name}
 Group: Development/Libraries/C and C++
-Requires: libbpp-core3 = %{_version}
+Requires: libbpp-core4 = %{version}

 %description -n libbpp-core-devel
 The libbpp-core-devel package contains the header files and static libraries for
@@ -54,11 +51,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
 %clean
 rm -rf $RPM_BUILD_ROOT

-%post -n libbpp-core3 -p /sbin/ldconfig
+%post -n libbpp-core4 -p /sbin/ldconfig

-%postun -n libbpp-core3 -p /sbin/ldconfig
+%postun -n libbpp-core4 -p /sbin/ldconfig

-%files -n libbpp-core3
+%files -n libbpp-core4
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
 %{_prefix}/%{_lib}/lib*.so.*
@@ -74,6 +71,10 @@ 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.
+- Graphs classes improvements
 * 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

--- a/cmake/doc-cmake-for-developpers.cmake
+++ b/cmake/doc-cmake-for-developpers.cmake
@@ -31,7 +31,7 @@ set (CMAKE_CXX_FLAGS "std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
 # -> It also provides a "feature" property on targets which annotates, and auto selects the right -std=...

 SET(${PROJECT_NAME}_VERSION_CURRENT "2")
-SET(${PROJECT_NAME}_VERSION_REVISION "3")
+SET(${PROJECT_NAME}_VERSION_REVISION "4")
 SET(${PROJECT_NAME}_VERSION_AGE "0")
 MATH(EXPR ${PROJECT_NAME}_VERSION_MAJOR "${${PROJECT_NAME}_VERSION_CURRENT} - ${${PROJECT_NAME}_VERSION_AGE}")
 SET(${PROJECT_NAME}_VERSION_MINOR ${${PROJECT_NAME}_VERSION_AGE})

--- a/debian/changelog
+++ b/debian/changelog
-libbpp-core (2.3.2-2) UNRELEASED; urgency=medium
+libbpp-core (2.4.0-1) UNRELEASED; urgency=medium

+  [ Julien Dutheil ]
+  * Version 2.4.0.
+
+  [ Andreas Tille ]
  * Bump soversion due to ABI change
    Closes: #890400
  * Add symbols file

- -- Andreas Tille <tille@debian.org>  Thu, 15 Feb 2018 15:34:56 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 21 Mar 2018 15:55:44 +0100

 libbpp-core (2.3.2-1) unstable; urgency=medium


--- a/debian/libbpp-core4.symbols
+++ b/debian/libbpp-core4.symbols
--- a/debian/patches/bump_soversion.patch
+++ b/debian/patches/bump_soversion.patch
-Description: Bump soversion due to ABI change
-Bug-Debian: https://bugs.debian.org/890400
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 15 Feb 2018 15:34:56 +0100
-
--- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -25,7 +25,7 @@ ENDIF(NOT CMAKE_BUILD_TYPE)
- #           library implements.
- # In other words, the library implements all the interface numbers in the
- # range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "3")
-+SET(${PROJECT_NAME}_VERSION_CURRENT "4")
- SET(${PROJECT_NAME}_VERSION_REVISION "0")
- SET(${PROJECT_NAME}_VERSION_AGE "0")
- 
--- a/debian/patches/gcc-7.patch
+++ b/debian/patches/gcc-7.patch
-Author: Julien Y. Dutheil
-Last-Update: 2018-02-05 13:11:51 +0100
-Description: Fix issues with gcc-7
-
--- a/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
-+++ b/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
-@@ -58,7 +58,7 @@ namespace bpp
-    */
-   class AbstractDiscreteDistribution :
-     public virtual DiscreteDistribution,
-    public virtual AbstractParameterAliasable
-+    public AbstractParameterAliasable
-   {
- 
-   public:
--- a/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
-@@ -52,7 +52,6 @@ using namespace std;
- /** Constructor: **************************************************************/
- 
- BetaDiscreteDistribution::BetaDiscreteDistribution(size_t n, double alpha, double beta) :
-  AbstractParameterAliasable("Beta."),
-   AbstractDiscreteDistribution(n,NumConstants::VERY_TINY(),"Beta."), alpha_(alpha), beta_(beta), diffln_(0)
- {
-   addParameter_(new Parameter("Beta.alpha", alpha, new IntervalConstraint(1, 0.0001, true), true));
-@@ -67,14 +66,12 @@ BetaDiscreteDistribution::BetaDiscreteDi
- }
- 
- BetaDiscreteDistribution::BetaDiscreteDistribution(const BetaDiscreteDistribution& bdd) :
-  AbstractParameterAliasable(bdd),
-   AbstractDiscreteDistribution(bdd), alpha_(bdd.alpha_), beta_(bdd.beta_), diffln_(bdd.diffln_)
- {
- }
- 
- BetaDiscreteDistribution& BetaDiscreteDistribution::operator=(const BetaDiscreteDistribution& bdd)
- {
-  AbstractParameterAliasable::operator=(bdd);
-   AbstractDiscreteDistribution::operator=(bdd);
- 
-   alpha_=bdd.alpha_;
--- a/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
-@@ -48,7 +48,6 @@ using namespace std;
- /******************************************************************************/
- 
- ConstantDistribution::ConstantDistribution(double value):
-  AbstractParameterAliasable("Constant."),
-   AbstractDiscreteDistribution(1, "Constant."),
-   value_(value)
- {
-@@ -57,14 +56,12 @@ ConstantDistribution::ConstantDistributi
- }
- 
- ConstantDistribution::ConstantDistribution(const ConstantDistribution& cd) :
-  AbstractParameterAliasable(cd),
-   AbstractDiscreteDistribution(cd),
-   value_(cd.value_)
- {}
- 
- ConstantDistribution& ConstantDistribution::operator=(const ConstantDistribution& cd)
- {
-  AbstractParameterAliasable::operator=(cd);
-   AbstractDiscreteDistribution::operator=(cd);
-   value_=cd.value_;
- 
--- a/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
-@@ -52,7 +52,6 @@ using namespace std;
- /** Constructor: **************************************************************/
- 
- GammaDiscreteDistribution::GammaDiscreteDistribution(size_t n, double alpha, double beta, double minimumAlpha, double minimumBeta, bool paramOffset, double offset) :
-  AbstractParameterAliasable("Gamma."),
-   AbstractDiscreteDistribution(n, "Gamma."),
-   alpha_(alpha),
-   beta_(beta),
-@@ -76,7 +75,6 @@ GammaDiscreteDistribution::GammaDiscrete
- }
- 
- GammaDiscreteDistribution::GammaDiscreteDistribution(const GammaDiscreteDistribution& gdd) :
-  AbstractParameterAliasable(gdd),
-   AbstractDiscreteDistribution(gdd),
-   alpha_(gdd.alpha_),
-   beta_(gdd.beta_),
-@@ -87,7 +85,6 @@ GammaDiscreteDistribution::GammaDiscrete
- 
- GammaDiscreteDistribution& GammaDiscreteDistribution::operator=(const GammaDiscreteDistribution& gdd)
- {
-  AbstractParameterAliasable::operator=(gdd);
-   AbstractDiscreteDistribution::operator=(gdd);
-   alpha_=gdd.alpha_;
-   beta_=gdd.beta_;
--- a/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
-@@ -51,7 +51,6 @@ using namespace std;
- /** Constructor: **************************************************************/
- 
- UniformDiscreteDistribution::UniformDiscreteDistribution(unsigned int n, double min, double max) :
-  AbstractParameterAliasable("Uniform."),
-   AbstractDiscreteDistribution(n,"Uniform."),
-   min_((min<max)?min:max),
-   max_((min<max)?max:min) 
-@@ -63,7 +62,6 @@ UniformDiscreteDistribution::UniformDisc
- }
- 
- UniformDiscreteDistribution::UniformDiscreteDistribution(const UniformDiscreteDistribution& udd) : 
-  AbstractParameterAliasable(udd),
-   AbstractDiscreteDistribution(udd),
-   min_(udd.min_),
-   max_(udd.max_)
-@@ -72,7 +70,6 @@ UniformDiscreteDistribution::UniformDisc
- 
- UniformDiscreteDistribution& UniformDiscreteDistribution::operator=(const UniformDiscreteDistribution& udd) 
- {
-  AbstractParameterAliasable::operator=(udd);
-   AbstractDiscreteDistribution::operator=(udd);
-   min_=udd.min_;
-   max_=udd.max_;
--- a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
-@@ -51,7 +51,6 @@ using namespace std;
- /****************************************************************/
- 
- ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(size_t n, double lambda) :
-  AbstractParameterAliasable("Exponential."),
-   AbstractDiscreteDistribution(n, "Exponential."),
-   lambda_(lambda)
- {
--- a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
-@@ -48,7 +48,6 @@ using namespace std;
- 
- InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(
-   DiscreteDistribution* dist, double p, double invariant) :
-  AbstractParameterAliasable("Invariant."),
-   AbstractDiscreteDistribution(1, "Invariant."),
-   dist_(dist),
-   invariant_(invariant),
--- a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
-@@ -51,7 +51,6 @@ using namespace std;
- /** Constructor: **************************************************************/
- 
- TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(size_t n, double lambda, double truncationPoint) :
-  AbstractParameterAliasable("TruncExponential."),
-   AbstractDiscreteDistribution(n, "TruncExponential."),
-   lambda_(lambda),
-   tp_(truncationPoint),
--- a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
-+++ b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
-@@ -70,14 +70,12 @@ public:
-   ExponentialDiscreteDistribution(size_t n, double lambda = 1.);
- 
-   ExponentialDiscreteDistribution(const ExponentialDiscreteDistribution& dist) :
-    AbstractParameterAliasable(dist),
-     AbstractDiscreteDistribution(dist),
-     lambda_(dist.lambda_)
-   {}
- 
-   ExponentialDiscreteDistribution& operator=(const ExponentialDiscreteDistribution& dist)
-   {
-    AbstractParameterAliasable::operator=(dist);    
-     AbstractDiscreteDistribution::operator=(dist);
-     lambda_ = dist.lambda_;
-     return *this;
--- a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
-+++ b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
-@@ -76,7 +76,6 @@ public:
-   }
- 
-   InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd) :
-    AbstractParameterAliasable(imdd),
-     AbstractDiscreteDistribution(imdd),
-     dist_(dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone())),
-     invariant_(imdd.invariant_),
-@@ -86,7 +85,6 @@ public:
- 
-   InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
-   {
-    AbstractParameterAliasable::operator=(imdd);
-     AbstractDiscreteDistribution::operator=(imdd);
-     dist_         = dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone());
-     invariant_    = imdd.invariant_;
--- a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
-+++ b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
-@@ -85,7 +85,6 @@ public:
-   TruncatedExponentialDiscreteDistribution(size_t n, double lambda = 1., double truncationPoint = 10);
- 
-   TruncatedExponentialDiscreteDistribution(const TruncatedExponentialDiscreteDistribution& dist) :
-    AbstractParameterAliasable(dist),
-     AbstractDiscreteDistribution(dist),
-     lambda_(dist.lambda_),
-     tp_(dist.tp_),
-@@ -94,7 +93,6 @@ public:
- 
-   TruncatedExponentialDiscreteDistribution& operator=(const TruncatedExponentialDiscreteDistribution& dist)
-   {
-    AbstractParameterAliasable::operator=(dist);
-     AbstractDiscreteDistribution::operator=(dist);
-     lambda_= dist.lambda_;
-     tp_ = dist.tp_;
--- a/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
-@@ -52,7 +52,6 @@ using namespace std;
- /** Constructor: **************************************************************/
- 
- GaussianDiscreteDistribution::GaussianDiscreteDistribution(size_t n, double mu, double sigma) :
-  AbstractParameterAliasable("Gaussian."),
-   AbstractDiscreteDistribution(n,"Gaussian."), mu_(mu), sigma_(sigma)
- {
-   addParameter_(new Parameter("Gaussian.mu", mu));
-@@ -61,7 +60,6 @@ GaussianDiscreteDistribution::GaussianDi
- }
- 
- GaussianDiscreteDistribution::GaussianDiscreteDistribution(const GaussianDiscreteDistribution& gdd) :
-  AbstractParameterAliasable(gdd),
-   AbstractDiscreteDistribution(gdd),
-   mu_(gdd.mu_),
-   sigma_(gdd.sigma_)
-@@ -70,7 +68,6 @@ GaussianDiscreteDistribution::GaussianDi
- 
- GaussianDiscreteDistribution& GaussianDiscreteDistribution::operator=(const GaussianDiscreteDistribution& gdd) 
- {
-  AbstractParameterAliasable::operator=(gdd);
-   AbstractDiscreteDistribution::operator=(gdd);
-   mu_=gdd.mu_;
-   sigma_=gdd.sigma_;
--- a/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
-+++ b/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
-@@ -47,7 +47,6 @@ using namespace std;
- 
- MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const vector<DiscreteDistribution*>& distributions,
-                                                                const vector<double>& probas ) :
-  AbstractParameterAliasable("Mixture."),
-   AbstractDiscreteDistribution(1, "Mixture."),
-   vdd_(),
-   probas_(),
-@@ -108,7 +107,6 @@ MixtureOfDiscreteDistributions::MixtureO
- }
- 
- MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const MixtureOfDiscreteDistributions& mdd) :
-  AbstractParameterAliasable(mdd),
-   AbstractDiscreteDistribution(mdd),
-   vdd_(),
-   probas_(),
-@@ -124,7 +122,6 @@ MixtureOfDiscreteDistributions::MixtureO
- 
- MixtureOfDiscreteDistributions& MixtureOfDiscreteDistributions::operator=(const MixtureOfDiscreteDistributions& mdd)
- {
-  AbstractParameterAliasable::operator=(mdd);
-   AbstractDiscreteDistribution::operator=(mdd);
-   vdd_.clear();
-   probas_.clear();
--- a/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
-+++ b/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
-@@ -49,7 +49,6 @@ using namespace std;
- SimpleDiscreteDistribution::SimpleDiscreteDistribution(const map<double, double>& distribution,
-                                                        double prec,
-                                                        bool fixed) :
-  AbstractParameterAliasable("Simple."),
-   AbstractDiscreteDistribution(distribution.size(), prec, "Simple."),
-   givenRanges_()
- {
-@@ -87,7 +86,6 @@ SimpleDiscreteDistribution::SimpleDiscre
-                                                        double prec,
-                                                        bool fixed
-                                                        ) :
-  AbstractParameterAliasable("Simple."),
-   AbstractDiscreteDistribution(values.size(), prec, "Simple."),
-   givenRanges_()
- {
-@@ -129,7 +127,6 @@ SimpleDiscreteDistribution::SimpleDiscre
-                                                        const std::vector<double>& probas,
-                                                        double prec,
-                                                        bool fixed) :
-  AbstractParameterAliasable("Simple."),
-   AbstractDiscreteDistribution(values.size(), prec, "Simple."),
-   givenRanges_()
- {
-@@ -193,14 +190,12 @@ SimpleDiscreteDistribution::SimpleDiscre
- 
- 
- SimpleDiscreteDistribution::SimpleDiscreteDistribution(const SimpleDiscreteDistribution& sdd) :
-  AbstractParameterAliasable(sdd),
-   AbstractDiscreteDistribution(sdd),
-   givenRanges_(sdd.givenRanges_)
- {}
- 
- SimpleDiscreteDistribution& SimpleDiscreteDistribution::operator=(const SimpleDiscreteDistribution& sdd)
- {
-  AbstractParameterAliasable::operator=(sdd);
-   AbstractDiscreteDistribution::operator=(sdd);
-   givenRanges_ = sdd.givenRanges_;
- 
--- a/debian/patches/series
+++ b/debian/patches/series
 unforce-cxxflags.patch
-gcc-7.patch
-bump_soversion.patch
--- a/debian/patches/unforce-cxxflags.patch
+++ b/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
--- a/src/Bpp/App/ApplicationTools.cpp
+++ b/src/Bpp/App/ApplicationTools.cpp
@@ -49,9 +49,9 @@ using namespace std;

 /******************************************************************************/

-OutputStream* ApplicationTools::error   = new StdErr();
-OutputStream* ApplicationTools::message = new StdOut();
-OutputStream* ApplicationTools::warning = new StdOut();
+std::shared_ptr<OutputStream> ApplicationTools::error(new StdErr());
+std::shared_ptr<OutputStream> ApplicationTools::message(new StdOut());
+std::shared_ptr<OutputStream> ApplicationTools::warning(new StdOut());
 time_t ApplicationTools::startTime;
 size_t ApplicationTools::terminalWidth = 80;
 float ApplicationTools::terminalSplit = 0.5;

--- a/src/Bpp/App/ApplicationTools.h
+++ b/src/Bpp/App/ApplicationTools.h
@@ -96,15 +96,15 @@ namespace bpp
    /**
     * @brief The output stream where errors have to be displayed.
     */
-    static OutputStream* error;
+    static std::shared_ptr<OutputStream> error;
    /**
     * @brief The output stream where messages have to be displayed.
     */
-    static OutputStream* message;
+    static std::shared_ptr<OutputStream> message;
    /**
     * @brief The output stream where warnings have to be displayed.
     */
-    static OutputStream* warning;
+    static std::shared_ptr<OutputStream> warning;

    /**
     * @brief Timer variable.

--- a/src/Bpp/App/NumCalcApplicationTools.cpp
+++ b/src/Bpp/App/NumCalcApplicationTools.cpp
@@ -48,10 +48,10 @@ using namespace std;
 vector<int> NumCalcApplicationTools::seqFromString(const std::string& s, const std::string& delim, const std::string& seqdelim)
 {
  vector<int> seq;
-  StringTokenizer * st = new StringTokenizer(s, delim, true);
+  unique_ptr<StringTokenizer> st(new StringTokenizer(s, delim, true));
  while (st->hasMoreToken())
  {
-    StringTokenizer * st2 = new StringTokenizer(st->nextToken(), seqdelim, true);
+    unique_ptr<StringTokenizer> st2(new StringTokenizer(st->nextToken(), seqdelim, true));

    if (st2->numberOfRemainingTokens() > 1)
    {
@@ -62,7 +62,7 @@ vector<int> NumCalcApplicationTools::seqFromString(const std::string& s, const s
    {
      seq.push_back(TextTools::toInt(st2->getToken(0)));
    }  
-  }  
+  }
  return seq;
 }


--- a/src/Bpp/Graph/AssociationGraphImplObserver.h
+++ b/src/Bpp/Graph/AssociationGraphImplObserver.h
@@ -197,7 +197,7 @@ public:
   */

  AssociationGraphImplObserver(bool directed = false) :
-    subjectGraph_(new GraphImpl(directed)),
+    subjectGraph_(std::shared_ptr<GraphImpl>(new GraphImpl(directed))),
    graphidToN_(),
    graphidToE_(),
    NToGraphid_(),
@@ -216,7 +216,7 @@ public:
   */

  AssociationGraphImplObserver(std::shared_ptr<GraphImpl> subjectGraph = 00) :
-    subjectGraph_(subjectGraph ? subjectGraph : new GraphImpl()),
+    subjectGraph_(subjectGraph ? subjectGraph : std::shared_ptr<GraphImpl>(new GraphImpl(true))),
    graphidToN_(),
    graphidToE_(),
    NToGraphid_(),
@@ -1039,6 +1039,22 @@ public:
    return leavesToReturn;
  }

+  std::vector<typename AssociationGraphObserver<N, E>::NodeIndex > getAllLeavesIndexes() const
+  {
+    std::vector<typename AssociationGraphObserver<N, E>::NodeIndex > leavesToReturn;
+
+    // fetching all the graph Leaves
+    std::vector<NodeGraphid> graphLeaves = getGraph()->getAllLeaves();
+    // testing if they are defined in this observer
+    for (typename std::vector<NodeGraphid>::iterator currGraphLeave = graphLeaves.begin(); currGraphLeave != graphLeaves.end(); currGraphLeave++)
+    {
+      std::shared_ptr<N>  foundLeafObject = graphidToN_.at(*currGraphLeave);
+      if (foundLeafObject != 00)
+        leavesToReturn.push_back(getNodeIndex(foundLeafObject));
+    }
+    return leavesToReturn;
+  }
+
  /**
   * Get all the inner nodes of a graph, ie, nodes with degree >= 2.
   * @return a vector containing the inner nodes.

--- a/src/Bpp/Graph/AssociationGraphObserver.h
+++ b/src/Bpp/Graph/AssociationGraphObserver.h
@@ -400,6 +400,7 @@ public:
   * @return a vector containing the leaves
   */
  virtual std::vector<std::shared_ptr<N> > getAllLeaves() const = 0;
+  virtual std::vector<NodeIndex> getAllLeavesIndexes() const = 0;

  /**
   * Get all the inner nodes of a graph, ie, nodes with degree >= 2.

--- a/src/Bpp/Graph/AssociationTreeGraphImplObserver.h
+++ b/src/Bpp/Graph/AssociationTreeGraphImplObserver.h
@@ -62,6 +62,7 @@ public:
  typedef typename AssociationGraphObserver<N, E>::EdgeIndex EdgeIndex;

  typedef typename Graph::NodeId NodeGraphid;
+
  typedef typename Graph::EdgeId EdgeGraphid;

 public:
@@ -77,10 +78,11 @@ public:
   * Constructor
   * @param subjectTreeGraph the graph which is observed
   */
+
  AssociationTreeGraphImplObserver(std::shared_ptr<TreeGraphImpl> subjectTreeGraph = 00) :
    AssociationGraphImplObserver<N, E, TreeGraphImpl>(subjectTreeGraph)
  {}
-
+  
  /**
   * Copy Constructor
   * @param treeGraphObserver the treeGraphObserver to be copied

--- a/src/Bpp/Io/BppODiscreteDistributionFormat.cpp
+++ b/src/Bpp/Io/BppODiscreteDistributionFormat.cpp
@@ -426,7 +426,7 @@ void BppODiscreteDistributionFormat::initialize_(
  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);
  }


--- a/src/Bpp/Numeric/AbstractParameterAliasable.cpp
+++ b/src/Bpp/Numeric/AbstractParameterAliasable.cpp
@@ -172,7 +172,7 @@ void AbstractParameterAliasable::aliasParameters(map<string, string>& unparsedPa
  for (size_t i = 0; i < pl.size(); i++)
  {
    if (unparsedParams.find(pl[i].getName()) == unparsedParams.end())
-      plpars.addParameter(*pl[i].clone());
+      plpars.addParameter(pl[i].clone());
  }

  size_t unp_s = unparsedParams.size();

--- a/src/Bpp/Numeric/AutoParameter.cpp
+++ b/src/Bpp/Numeric/AutoParameter.cpp
@@ -59,9 +59,9 @@ string AutoParameter::CONSTRAINTS_KEEP   = "keep";
 /** Constructors: *************************************************************/

 AutoParameter::AutoParameter(const std::string& name, double value, Constraint* constraint, bool attachConstraint):
-Parameter(name, value, constraint, attachConstraint), messageHandler_(ApplicationTools::message) {}
+  Parameter(name, value, constraint, attachConstraint), messageHandler_(ApplicationTools::message.get()) {}

-AutoParameter::AutoParameter(const Parameter& p): Parameter(p), messageHandler_(ApplicationTools::message) {}
+AutoParameter::AutoParameter(const Parameter& p): Parameter(p), messageHandler_(ApplicationTools::message.get()) {}

 AutoParameter::AutoParameter(const AutoParameter& p): Parameter(p), messageHandler_(p.messageHandler_) {}