New upstream version 2.4.0

#           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 "2")

SET(${PROJECT_NAME}_VERSION_CURRENT "3")

SET(${PROJECT_NAME}_VERSION_REVISION "0")

SET(${PROJECT_NAME}_VERSION_AGE "0")

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})

# Packager

SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")

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++ Sequence-Omics library")

SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")

SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

# /!\ This assumes that an external build is used

SET(CPACK_SOURCE_IGNORE_FILES 

       "/build/" 

       "/html/" 

       "/BppSeqOmics.tag" 

       "/\\\\.git/" 

       "/\\\\.gitignore" 

       ${CPACK_SOURCE_IGNORE_FILES}

02/03/18 -*- Version 2.4.0 -*-

02/03/18 Julien Dutheil

* Removed all dynamic exception specifications

* Increased interface number to 3

21/01/18 Julien Dutheil

* Added OrderFilterMafIterator class.

03/01/18 Julien Dutheil

* Fixed bug in AlnFilter when relative proportions are set. Proportion was relative to block and not to window, which was incorrect.

22/12/17 Julien Dutheil

* Improved GTF parser, bug fixed when empty token in last column.

10/12/17 -*- Version 2.3.2 -*-

10/05/17 -*- Version 2.3.0 -*-

# 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

%define _basename bpp-seq-omics

%define _version 2.3.1

%define _release 1

%define _prefix /usr

URL: http://biopp.univ-montp2.fr/

URL: https://github.com/BioPP/bpp-seq-omics

Name: %{_basename}

Version: %{_version}

Release: %{_release}

Name: bpp-seq-omics

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++ Sequence library: genomics components

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

This library contains the genomics components of the Bio++ sequence library.

It is part of the Bio++ project.

%package -n libbpp-seq-omics2

%package -n libbpp-seq-omics3

Summary: Bio++ Sequence library: genomics components

Group: Development/Libraries/C and C++

%description -n libbpp-seq-omics2

%description -n libbpp-seq-omics3

This library contains the genomics components of the Bio++ sequence library.

It is part of the Bio++ project.

%package -n libbpp-seq-omics-devel

Summary: Bio++ Sequence library: genomics components

Group: Development/Libraries/C and C++

Requires: libbpp-seq-omics2 = %{_version}

Requires: libbpp-seq11 = %{_version}

Requires: libbpp-seq-devel = %{_version}

Requires: libbpp-core3 = %{_version}

Requires: libbpp-core-devel = %{_version}

Requires: libbpp-seq-omics3 = %{version}

Requires: libbpp-seq12 = %{version}

Requires: libbpp-seq-devel = %{version}

Requires: libbpp-core4 = %{version}

Requires: libbpp-core-devel = %{version}

%description -n libbpp-seq-omics-devel

The libbpp-seq-omics-devel package contains the header files and static libraries for

building applications which use %{_basename}.

building applications which use %{name}.

%prep

%setup -q

%clean

rm -rf $RPM_BUILD_ROOT

%post -n libbpp-seq-omics2 -p /sbin/ldconfig

%post -n libbpp-seq-omics3 -p /sbin/ldconfig

%postun -n libbpp-seq-omics2 -p /sbin/ldconfig

%postun -n libbpp-seq-omics3 -p /sbin/ldconfig

%files -n libbpp-seq-omics2

%files -n libbpp-seq-omics3

%defattr(-,root,root)

%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog

%{_prefix}/%{_lib}/lib*.so.*

%{_prefix}/include/*

%changelog

* Fri Mar 03 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1

- Increased interface number

- Removed dynamic exceptions declarations.

* 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

  }

}

const BasicSequenceFeature BedGraphFeatureReader::nextFeature() throw (Exception)

const BasicSequenceFeature BedGraphFeatureReader::nextFeature()

{

  if (!hasMoreFeature())

    throw Exception("BedGraphFeatureReader::nextFeature(). No more feature in file.");