Commit afa6b0ca authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.0

parent 70a2715e

CMakeLists.txt

+7 −5
Original line number Diff line number Diff line
@@ -36,7 +36,7 @@ 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 "3")

SET(${PROJECT_NAME}_VERSION_CURRENT "4")

SET(${PROJECT_NAME}_VERSION_REVISION "0")

SET(${PROJECT_NAME}_VERSION_AGE "0")
@@ -54,7 +54,7 @@ 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)



# Find the zlib installation (define zlib imported target)

find_package(ZLIB REQUIRED)
@@ -104,10 +104,10 @@ ENDIF(NO_DEP_CHECK) 
# Packager

SET(CPACK_PACKAGE_NAME "libbpp-raa")

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++ Remote Acnuc Access library")

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

SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -116,6 +116,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ") 
# /!\ This assumes that an external build is used

SET(CPACK_SOURCE_IGNORE_FILES 

       "/build/" 

       "/html/" 

       "/BppRaa.tag" 

       "/\\\\.git/" 

       "/\\\\.gitignore" 

       ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+7 −0
Original line number Diff line number Diff line 
25/02/18 -*- version 2.4.0 -*-



25/02/18 Julien Dutheil



* Removed all dynamic exception specifications

* Increased inerface number to 4.



10/05/17 -*- version 2.3.0 -*-



28/09/14 -*- Version 2.2.0 -*-

Doxyfile

+1 −1
Original line number Diff line number Diff line
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-raa 
# 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-raa.spec

+28 −26
Original line number Diff line number Diff line 
%define _basename bpp-raa

%define _version 2.3.1

%define _release 1

%define _prefix /usr



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

URL: https://github.com/BioPP/bpp-raa



Name: %{_basename}

Version: %{_version}

Release: %{_release}

Name: bpp-raa

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++ Remote Acnuc Access 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}

BuildRequires: zlib >= 1.2.3

BuildRequires: zlib-devel >= 1.2.3
@@ -33,28 +30,30 @@ AutoProv: yes 
This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.

It is part of the Bio++ project.



%package -n libbpp-raa3

%package -n libbpp-raa4

Summary: Bio++ Remote Acnuc Access library

Group: Development/Libraries/C and C++



%description -n libbpp-raa3

%description -n libbpp-raa4

This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.

It is part of the Bio++ project.



%package -n libbpp-raa-devel

Summary: Libraries, includes to develop applications with %{_basename}

Group: Development/Libraries/C and C++

Requires: libbpp-raa3 = %{_version}

Requires: libbpp-seq11 = %{_version}

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

Requires: libbpp-core3 = %{_version}

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

Requires: libbpp-raa4 = %{version}

Requires: libbpp-seq12 = %{version}

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

Requires: libbpp-core4 = %{version}

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

Requires: zlib >= 1.2.3

Requires: zlib-devel >= 1.2.3



%description -n libbpp-raa-devel

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

building applications which use %{_basename}.

building applications which use %{name}.



%global debug_package %{nil}



%prep

%setup -q
@@ -71,11 +70,11 @@ make DESTDIR=$RPM_BUILD_ROOT install 
%clean

rm -rf $RPM_BUILD_ROOT



%post -n libbpp-raa3 -p /sbin/ldconfig

%post -n libbpp-raa4 -p /sbin/ldconfig



%postun -n libbpp-raa3 -p /sbin/ldconfig

%postun -n libbpp-raa4 -p /sbin/ldconfig



%files -n libbpp-raa3

%files -n libbpp-raa4

%defattr(-,root,root)

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

%{_prefix}/%{_lib}/lib*.so.*
@@ -91,6 +90,9 @@ rm -rf $RPM_BUILD_ROOT 
%{_prefix}/include/*



%changelog

* Mon Feb 26 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

src/Bpp/Raa/RAA.cpp

+7 −7
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ int sock_printf(raa_db_access* raa_current_db, const char* fmt, ...); 
using namespace std;

using namespace bpp;



RAA::RAA(const string& dbname, int port, const string& server) throw (int)

RAA::RAA(const string& dbname, int port, const string& server)

{

  kw_pattern = NULL;

  current_address.div = -1;
@@ -27,7 +27,7 @@ RAA::RAA(const string& dbname, int port, const string& server) throw (int) 
}





RAA::RAA(int port, const string& server) throw (int)

RAA::RAA(int port, const string& server)

{

  kw_pattern = NULL;

  int error = raa_open_socket((char*)server.c_str(), port, (char*)"Bio++", &raa_data);
@@ -241,7 +241,7 @@ string RAA::getAnnotLineAtAddress(RaaAddress address) 
}





Sequence* RAA::translateCDS(int seqrank) throw (BadCharException)

Sequence* RAA::translateCDS(int seqrank)

{

  char* descript;

  if (seqrank < 2 || seqrank > raa_data->nseq)
@@ -276,7 +276,7 @@ Sequence* RAA::translateCDS(int seqrank) throw (BadCharException) 
}





Sequence* RAA::translateCDS(const string& name) throw (BadCharException)

Sequence* RAA::translateCDS(const string& name)

{

  int rank;

  rank = raa_isenum(raa_data, (char*)name.c_str());
@@ -303,7 +303,7 @@ char RAA::translateInitCodon(int seqrank) 
}





RaaList* RAA::processQuery(const string& query, const string& listname) throw (string)

RaaList* RAA::processQuery(const string& query, const string& listname)

{

  char* message;

  int type, rank;
@@ -329,7 +329,7 @@ RaaList* RAA::processQuery(const string& query, const string& listname) throw (s 
}





RaaList* RAA::createEmptyList(const string& listname, const string& kind) throw (int)

RaaList* RAA::createEmptyList(const string& listname, const string& kind)

{

  int err, lrank;

  char type, * p = 0, * q = 0;
@@ -552,7 +552,7 @@ struct extract_data 
};





void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey) throw (string)

void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey)

{

  char* p, * line;

  int l;