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.clang-format 0 → 100644
View file @ 8cff27ae
BasedOnStyle: Mozilla
Cpp11BracedListStyle: true
BreakBeforeBraces: Allman
NamespaceIndentation: All
AlwaysBreakAfterReturnType: None
AlwaysBreakAfterDefinitionReturnType: None
CommentPragmas: ^\*
ColumnLimit: 120
.gitignore 0 → 100644
View file @ 8cff27ae
.clang_complete
CMakeLists.txt
View file @ 8cff27ae
......@@ -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-core 3.0.0 REQUIRED)
find_package (bpp-core 4.0.0 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-seq")
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 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/"
"/BppSeq.tag/"
"/\\\\.git/"
"/\\\\.gitignore"
${CPACK_SOURCE_IGNORE_FILES}
......
ChangeLog
View file @ 8cff27ae
19/02/18 -*- Version 2.4.0 -*-
19/02/18 Julien Dutheil
* Increased interface number (new 12)
10/12/17 -*- Version 2.3.2 -*-
08/11/17 Laurent Guéguen
* More efficient codon models.
27/06/17 François Grindaud
* Removed all dynamic exceptions specification
10/05/17 -*- Version 2.3.0 -*-
18/12/16 Julien Dutheil
......
Doxyfile
View file @ 8cff27ae
......@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-seq
# 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-seq.spec
View file @ 8cff27ae
%define _basename bpp-seq
%define _version 2.3.1
%define _release 1
%define _prefix /usr
URL: http://biopp.univ-montp2.fr/
URL: https://github.com/BioPP/bpp-seq
Name: %{_basename}
Version: %{_version}
Release: %{_release}
Name: bpp-seq
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
Group: Development/Libraries/C and C++
Requires: bpp-core = %{_version}
Requires: bpp-core = %{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-core4 = %{version}
BuildRequires: libbpp-core-devel = %{version}
AutoReq: yes
AutoProv: yes
......@@ -27,24 +24,24 @@ AutoProv: yes
This library contains utilitary and classes for bio-sequence analysis.
It is part of the Bio++ project.
%package -n libbpp-seq11
%package -n libbpp-seq12
Summary: Bio++ Sequence library
Group: Development/Libraries/C and C++
%description -n libbpp-seq11
%description -n libbpp-seq12
This library contains utilitary and classes for bio-sequence analysis.
It is part of the Bio++ project.
%package -n libbpp-seq-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-seq11 = %{_version}
Requires: libbpp-core3 = %{_version}
Requires: libbpp-core-devel = %{_version}
Requires: libbpp-seq12 = %{version}
Requires: libbpp-core4 = %{version}
Requires: libbpp-core-devel = %{version}
%description -n libbpp-seq-devel
The libbpp-seq-devel package contains the header files and static libraries for
building applications which use %{_basename}.
building applications which use %{name}.
%prep
%setup -q
......@@ -61,11 +58,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
%clean
rm -rf $RPM_BUILD_ROOT
%post -n libbpp-seq11 -p /sbin/ldconfig
%post -n libbpp-seq12 -p /sbin/ldconfig
%postun -n libbpp-seq11 -p /sbin/ldconfig
%postun -n libbpp-seq12 -p /sbin/ldconfig
%files -n libbpp-seq11
%files -n libbpp-seq12
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%{_prefix}/%{_lib}/lib*.so.*
......@@ -81,6 +78,9 @@ rm -rf $RPM_BUILD_ROOT
%{_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
......
debian/changelog
View file @ 8cff27ae
libbpp-seq (2.3.2-2) UNRELEASED; urgency=medium
libbpp-seq (2.4.0-1) UNRELEASED; urgency=medium
[ Julien Dutheil ]
* New upstream version
[ Andreas Tille ]
* Add symbols file
-- Andreas Tille <tille@debian.org> Thu, 15 Feb 2018 16:08:01 +0100
-- Andreas Tille <tille@debian.org> Sun, 25 Mar 2018 14:14:44 +0100
libbpp-seq (2.3.2-1) unstable; urgency=medium
......
debian/control
View file @ 8cff27ae
......@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.80),
libbpp-core-dev (>= 2.3.2)
libbpp-core-dev (>= 2.4.0)
Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq.git
......@@ -16,9 +16,9 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Package: libbpp-seq-dev
Architecture: any
Section: libdevel
Depends: libbpp-seq11 (= ${binary:Version}),
Depends: libbpp-seq12 (= ${binary:Version}),
${misc:Depends},
libbpp-core-dev (>= 2.3.2)
libbpp-core-dev (>= 2.4.0)
Description: Bio++ Sequence library development files
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
......@@ -29,13 +29,13 @@ Description: Bio++ Sequence library development files
This package contains the static library and the header files of Bio++
classes for sequence analysis classes.
Package: libbpp-seq11
Package: libbpp-seq12
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
libbpp-core3 (>= 2.3.2)
libbpp-core4 (>= 2.4.0)
Pre-Depends: ${misc:Pre-Depends}
Description: Bio++ Sequence library
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
......
debian/copyright
View file @ 8cff27ae
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: B++-Seq
Upstream-Name: Bpp-Seq
Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
Source: http://biopp.univ-montp2.fr/Repositories/sources/
Source: https://github.com/BioPP/bpp-seq/
Files: *
Copyright: 2010-2016 Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
......
debian/libbpp-seq11.symbols deleted 100644 → 0
View file @ 3929f00a
This diff is collapsed.
debian/libbpp-seq12.symbols 0 → 100644
View file @ 8cff27ae
Source diff could not be displayed: it is too large. Options to address this: view the blob.
debian/patches/unforce-cxxflags.patch
View file @ 8cff27ae
......@@ -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
debian/rules
View file @ 8cff27ae
......@@ -2,10 +2,10 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
%:
dh $@
......
src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
View file @ 8cff27ae
......@@ -67,7 +67,7 @@ void AbstractAlphabet::updateMaps_(size_t pos, const AlphabetState& st) {
/******************************************************************************/
void AbstractAlphabet::registerState(AlphabetState* st) throw (Exception) {
void AbstractAlphabet::registerState(AlphabetState* st) {
// Add the state to the vector
alphabet_.push_back(st);
// Update the maps
......@@ -76,8 +76,7 @@ void AbstractAlphabet::registerState(AlphabetState* st) throw (Exception) {
/******************************************************************************/
void AbstractAlphabet::setState(size_t pos, AlphabetState* st)
throw (Exception, IndexOutOfBoundsException) {
void AbstractAlphabet::setState(size_t pos, AlphabetState* st) {
if (pos > alphabet_.size())
throw IndexOutOfBoundsException("AbstractAlphabet::setState: incorrect position", pos, 0, alphabet_.size());
// Delete the state if not empty
......@@ -91,7 +90,7 @@ void AbstractAlphabet::setState(size_t pos, AlphabetState* st)
/******************************************************************************/
const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const throw (BadCharException) {
const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const {
map<string, size_t>::const_iterator it = letters_.find(letter);
if (it == letters_.end())
throw BadCharException(letter, "AbstractAlphabet::getState(string): Specified base unknown", this);
......@@ -100,7 +99,7 @@ const AlphabetState& AbstractAlphabet::getState(const std::string& letter) const
/******************************************************************************/
size_t AbstractAlphabet::getStateIndex(const std::string& letter) const throw (BadCharException) {
size_t AbstractAlphabet::getStateIndex(const std::string& letter) const {
map<string, size_t>::const_iterator it = letters_.find(letter);
if (it == letters_.end())
throw BadCharException(letter, "AbstractAlphabet::getStateIndex(string): Specified base unknown", this);
......@@ -109,7 +108,7 @@ size_t AbstractAlphabet::getStateIndex(const std::string& letter) const throw (B
/******************************************************************************/
const AlphabetState& AbstractAlphabet::getState(int num) const throw (BadIntException) {
const AlphabetState& AbstractAlphabet::getState(int num) const {
map<int, size_t>::const_iterator it = nums_.find(num);
if (it == nums_.end())
throw BadIntException(num, "AbstractAlphabet::getState(int): Specified base unknown", this);
......@@ -118,7 +117,7 @@ const AlphabetState& AbstractAlphabet::getState(int num) const throw (BadIntExce
/******************************************************************************/
size_t AbstractAlphabet::getStateIndex(int num) const throw (BadIntException) {
size_t AbstractAlphabet::getStateIndex(int num) const {
map<int, size_t>::const_iterator it = nums_.find(num);
if (it == nums_.end())
throw BadIntException(num, "AbstractAlphabet::getStateIndex(int): Specified base unknown", this);
......@@ -127,7 +126,7 @@ size_t AbstractAlphabet::getStateIndex(int num) const throw (BadIntException) {
/******************************************************************************/
AlphabetState& AbstractAlphabet::getState(const std::string& letter) throw (BadCharException) {
AlphabetState& AbstractAlphabet::getState(const std::string& letter) {
map<string, size_t>::iterator it = letters_.find(letter);
if (it == letters_.end())
throw BadCharException(letter, "AbstractAlphabet::getState(string): Specified base unknown", this);
......@@ -136,7 +135,7 @@ AlphabetState& AbstractAlphabet::getState(const std::string& letter) throw (BadC
/******************************************************************************/
AlphabetState& AbstractAlphabet::getState(int num) throw (BadIntException) {
AlphabetState& AbstractAlphabet::getState(int num) {
map<int, size_t>::iterator it = nums_.find(num);
if (it == nums_.end())
throw BadIntException(num, "AbstractAlphabet::getState(int): Specified base unknown", this);
......@@ -145,7 +144,7 @@ AlphabetState& AbstractAlphabet::getState(int num) throw (BadIntException) {
/******************************************************************************/
AlphabetState& AbstractAlphabet::getStateAt(size_t pos) throw (IndexOutOfBoundsException) {
AlphabetState& AbstractAlphabet::getStateAt(size_t pos) {
if (pos > alphabet_.size())
throw IndexOutOfBoundsException("AbstractAlphabet::getStateAt: incorrect position", pos, 0, alphabet_.size());
return * (alphabet_[pos]);
......@@ -153,7 +152,7 @@ AlphabetState& AbstractAlphabet::getStateAt(size_t pos) throw (IndexOutOfBoundsE
/******************************************************************************/
const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const throw (IndexOutOfBoundsException) {
const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const {
if (pos > alphabet_.size())
throw IndexOutOfBoundsException("AbstractAlphabet::getStateAt: incorrect position", pos, 0, alphabet_.size());
return * (alphabet_[pos]);
......@@ -161,28 +160,28 @@ const AlphabetState& AbstractAlphabet::getStateAt(size_t pos) const throw (Index
/******************************************************************************/
std::string AbstractAlphabet::getName(const std::string& state) const throw (BadCharException)
std::string AbstractAlphabet::getName(const std::string& state) const
{
return (getState(state)).getName();
}
/******************************************************************************/
std::string AbstractAlphabet::getName(int state) const throw (BadIntException)
std::string AbstractAlphabet::getName(int state) const
{
return (getState(state)).getName();
}
/******************************************************************************/
int AbstractAlphabet::charToInt(const std::string& state) const throw (BadCharException)
int AbstractAlphabet::charToInt(const std::string& state) const
{
return getState(state).getNum();
}
/******************************************************************************/
std::string AbstractAlphabet::intToChar(int state) const throw (BadIntException)
std::string AbstractAlphabet::intToChar(int state) const
{
return (getState(state)).getLetter();
}
......@@ -209,7 +208,7 @@ bool AbstractAlphabet::isCharInAlphabet(const std::string& state) const
/******************************************************************************/
std::vector<int> AbstractAlphabet::getAlias(int state) const throw (BadIntException)
std::vector<int> AbstractAlphabet::getAlias(int state) const
{
if (!isIntInAlphabet(state)) throw BadIntException(state, "AbstractAlphabet::getAlias(int): Specified base unknown.");
vector<int> v(1);
......@@ -219,7 +218,7 @@ std::vector<int> AbstractAlphabet::getAlias(int state) const throw (BadIntExcept
/******************************************************************************/
std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) const throw (BadCharException)
std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) const
{
if (!isCharInAlphabet(state)) throw BadCharException(state, "AbstractAlphabet::getAlias(char): Specified base unknown.");
vector<string> v(1);
......@@ -229,7 +228,7 @@ std::vector<std::string> AbstractAlphabet::getAlias(const std::string& state) co
/******************************************************************************/
int AbstractAlphabet::getGeneric(const std::vector<int>& states) const throw (BadIntException) {
int AbstractAlphabet::getGeneric(const std::vector<int>& states) const {
map<int, int> m;
for (unsigned int i = 0 ; i < states.size() ; ++i) {
vector<int> tmp_s = this->getAlias(states[i]); // get the states for generic characters
......@@ -255,7 +254,7 @@ int AbstractAlphabet::getGeneric(const std::vector<int>& states) const throw (Ba
/******************************************************************************/
std::string AbstractAlphabet::getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) {
std::string AbstractAlphabet::getGeneric(const std::vector<std::string>& states) const {
map <string, int> m;
for (unsigned int i = 0 ; i < states.size() ; ++i) {
vector<string> tmp_s = this->getAlias(states[i]); // get the states for generic characters
......
src/Bpp/Seq/Alphabet/AbstractAlphabet.h
View file @ 8cff27ae
......@@ -142,16 +142,16 @@ namespace bpp
*/
size_t getNumberOfStates() const { return alphabet_.size(); }
unsigned int getNumberOfChars() const { return static_cast<unsigned int>(alphabet_.size()); }
std::string getName(const std::string& state) const throw (BadCharException);
std::string getName(int state) const throw (BadIntException);
int charToInt(const std::string& state) const throw (BadCharException);
std::string intToChar(int state) const throw (BadIntException);
std::string getName(const std::string& state) const;
std::string getName(int state) const;
int charToInt(const std::string& state) const;
std::string intToChar(int state) const;
bool isIntInAlphabet(int state) const;
bool isCharInAlphabet(const std::string& state) const;
std::vector<int> getAlias(int state) const throw (BadIntException);
std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
int getGeneric(const std::vector<int>& states) const throw (BadIntException);
std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException);
std::vector<int> getAlias(int state) const;
std::vector<std::string> getAlias(const std::string& state) const;
int getGeneric(const std::vector<int>& states) const;
std::string getGeneric(const std::vector<std::string>& states) const;
const std::vector<int>& getSupportedInts() const;
const std::vector<std::string>& getSupportedChars() const;
const std::vector<std::string> & getResolvedChars() const;
......@@ -173,7 +173,7 @@ namespace bpp
* @param stateIndex The index of the state in the alphabet_ vector.
* @throw IndexOutOfBoundsException If the index is invalid.
*/
virtual AlphabetState& getStateAt(size_t stateIndex) throw (IndexOutOfBoundsException);
virtual AlphabetState& getStateAt(size_t stateIndex);
/**
* @brief Get a state at a position in the alphabet_ vector.
......@@ -184,7 +184,7 @@ namespace bpp
* @param stateIndex The index of the state in the alphabet_ vector.
* @throw IndexOutOfBoundsException If the index is invalid.
*/
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
virtual const AlphabetState& getStateAt(size_t stateIndex) const;
/**
* @brief Get a state by its letter.
......@@ -195,9 +195,9 @@ namespace bpp
* @param letter The letter of the state to find.
* @throw BadCharException If the letter is not in the Alphabet.
*/
const AlphabetState& getState(const std::string& letter) const throw (BadCharException);
const AlphabetState& getState(const std::string& letter) const;
AlphabetState& getState(const std::string& letter) throw (BadCharException);
AlphabetState& getState(const std::string& letter);
/**
* @brief Get a state by its num.
......@@ -208,21 +208,21 @@ namespace bpp
* @param num The num of the state to find.
* @throw BadIntException If the num is not in the Alphabet.
*/
const AlphabetState& getState(int num) const throw (BadIntException);
const AlphabetState& getState(int num) const;
AlphabetState& getState(int num) throw (BadIntException);
AlphabetState& getState(int num);
int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
int getIntCodeAt(size_t stateIndex) const {
return getStateAt(stateIndex).getNum();
}
const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) {
const std::string& getCharCodeAt(size_t stateIndex) const {
return getStateAt(stateIndex).getLetter();
}
size_t getStateIndex(int state) const throw (BadIntException);
size_t getStateIndex(int state) const;
size_t getStateIndex(const std::string& state) const throw (BadCharException);
size_t getStateIndex(const std::string& state) const;
/** @} */
protected:
......@@ -232,7 +232,7 @@ namespace bpp
* @param st The state to add.
* @throw Exception If a wrong alphabet state is provided.
*/
virtual void registerState(AlphabetState* st) throw (Exception);
virtual void registerState(AlphabetState* st);
/**
* @brief Set a state in the Alphabet.
......@@ -242,7 +242,7 @@ namespace bpp
* @throw Exception If a wrong alphabet state is provided.
* @throw IndexOutOfBoundsException If an incorrect index is provided.
*/
virtual void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException);
virtual void setState(size_t pos, AlphabetState* st);
/**
* @brief Resize the private alphabet_ vector.
......
src/Bpp/Seq/Alphabet/Alphabet.h
View file @ 8cff27ae
......@@ -154,7 +154,7 @@ namespace bpp
* @return The name of the state.
* @throw BadIntException When state is not a valid integer.
*/
virtual std::string getName(int state) const throw (BadIntException) = 0;
virtual std::string getName(int state) const = 0;
/**
* @brief Get the complete name of a state given its string description.
......@@ -166,29 +166,29 @@ namespace bpp
* @return The name of the state.
* @throw BadCharException When state is not a valid char description.
*/
virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;
virtual std::string getName(const std::string& state) const = 0;
/**
* @return The int code of a given state.
* @param stateIndex The index of the state to fetch.
*/
virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
virtual int getIntCodeAt(size_t stateIndex) const = 0;
/**
* @return The char code of a given state.
* @param stateIndex The index of the state to fetch.
*/
virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
virtual const std::string& getCharCodeAt(size_t stateIndex) const = 0;
/**
* @return The indices of the states with corresponding int code.
*/
virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
virtual size_t getStateIndex(int state) const = 0;
/**
* @return The index of the state with corresponding char code.
*/
virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;
virtual size_t getStateIndex(const std::string& state) const = 0;
/**
* @name Tests
......@@ -228,7 +228,7 @@ namespace bpp
* @return The AlphabetState.
* @throw IndexOutOfBoundsException When index is not a valid.
*/
virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;
virtual const AlphabetState& getStateAt(size_t stateIndex) const = 0;
/**
* @brief Get a state given its int description.
......@@ -239,7 +239,7 @@ namespace bpp
* @return The AlphabetState.
* @throw BadIntException When state is not a valid integer.
*/
virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;
virtual const AlphabetState& getState(int state) const = 0;
/**
* @brief Get a state given its string description.
......@@ -248,7 +248,7 @@ namespace bpp
* @return The AlphabetState.
* @throw BadCharException When state is not a valid string.
*/
virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;
virtual const AlphabetState& getState(const std::string& state) const = 0;
/** @} */
......@@ -265,7 +265,7 @@ namespace bpp
* @return The string description.
* @throw BadIntException When state is not a valid integer.
*/
virtual std::string intToChar(int state) const throw (BadIntException) = 0;
virtual std::string intToChar(int state) const = 0;
/**
* @brief Give the int description of a state given its string description.
......@@ -274,7 +274,7 @@ namespace bpp
* @return The int description.
* @throw BadCharException When state is not a valid char description.
*/
virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
virtual int charToInt(const std::string& state) const = 0;
/** @} */
/**
......@@ -332,7 +332,7 @@ namespace bpp
* @return A vector of resolved states.
* @throw BadIntException When state is not a valid integer.
*/
virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
virtual std::vector<int> getAlias(int state) const = 0;
/**
* @brief Get all resolved states that match a generic state.
......@@ -343,7 +343,7 @@ namespace bpp
* @return A vector of resolved states.
* @throw BadCharException When state is not a valid char description.
*/
virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;
virtual std::vector<std::string> getAlias(const std::string& state) const = 0;
/**
* @brief Get the generic state that match a set of states.
......@@ -355,7 +355,7 @@ namespace bpp
* @return A int code for the computed state.
* @throw BadIntException When a state is not a valid integer.
*/
virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;
virtual int getGeneric(const std::vector<int>& states) const = 0;
/**
* @brief Get the generic state that match a set of states.
......@@ -368,7 +368,7 @@ namespace bpp
* @throw BadCharException when a state is not a valid char description.
* @throw CharStateNotSupportedException when the alphabet does not support Char state for unresolved state.
*/
virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;
virtual std::string getGeneric(const std::vector<std::string>& states) const = 0;
/**
* @return A list of all supported int codes.
......
src/Bpp/Seq/Alphabet/AlphabetExceptions.h
View file @ 8cff27ae
......@@ -78,7 +78,7 @@ class AlphabetException:
return *this;
}
virtual ~AlphabetException() throw () {}
virtual ~AlphabetException() {}
public:
/**
......@@ -108,7 +108,7 @@ class BadCharException:
*/
BadCharException(const std::string & badChar, const std::string & text = "", const Alphabet * alpha = 0);
virtual ~BadCharException() throw() {};
virtual ~BadCharException() {};
public:
/**
......@@ -137,7 +137,7 @@ class BadIntException:
*/
BadIntException(int badInt, const std::string& text = "", const Alphabet* alpha = 0);
virtual ~BadIntException() throw() {}
virtual ~BadIntException() {}
public:
/**
......@@ -179,7 +179,7 @@ class AlphabetMismatchException : public Exception
return *this;
}
virtual ~AlphabetMismatchException() throw() {}
virtual ~AlphabetMismatchException() {}
public:
/**
......@@ -204,7 +204,7 @@ class CharStateNotSupportedException : public AlphabetException
*/
CharStateNotSupportedException(const std::string & text = "", const Alphabet * alpha = 0);
virtual ~CharStateNotSupportedException() throw() {};
virtual ~CharStateNotSupportedException() {};
};
} //end of namespace bpp.
......
src/Bpp/Seq/Alphabet/AlphabetTools.cpp
View file @ 8cff27ae
......@@ -86,7 +86,7 @@ int AlphabetTools::getType(char state)
/**********************************************************************************************/
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet)
{
if (alphabet.getNumberOfChars() == 0)
return true; // Will this really happen?
......@@ -102,14 +102,14 @@ bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (Alp
/**********************************************************************************************/
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet)
{
return checkAlphabetCodingSize(*alphabet);
}
/**********************************************************************************************/
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException)
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet)
{
if (!checkAlphabetCodingSize(alphabet))
throw AlphabetException("Bad alphabet in function Alphabet::getAlphabetCodingSize().");
......@@ -118,7 +118,7 @@ unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet) thro
/**********************************************************************************************/
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException)
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet)
{
return getAlphabetCodingSize(*alphabet);
}
src/Bpp/Seq/Alphabet/AlphabetTools.h
View file @ 8cff27ae
......@@ -101,7 +101,7 @@ public:
* @param alphabet The alphabet to check.
* @return True if all text description have the same length (e.g. 3 for codon alphabet).
*/
static bool checkAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
static bool checkAlphabetCodingSize(const Alphabet& alphabet);
/**
* @brief This checks that all characters in the alphabet are coded by a string of same length.
......@@ -112,7 +112,7 @@ public:
* @param alphabet a pointer toward the alphabet to check.
* @return True if all text description have the same length (e.g. 3 for codon alphabet).
*/
static bool checkAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
static bool checkAlphabetCodingSize(const Alphabet* alphabet);
/**
* @brief In case that all states in the given alphabet have a string description of same length,
......@@ -121,7 +121,7 @@ public:
* @param alphabet The alphabet to analyse.
* @return The common size of all text descriptionif there is one. Else throws an AlphabetException.
*/
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet) throw (AlphabetException);
static unsigned int getAlphabetCodingSize(const Alphabet& alphabet);
/**
* @brief In case that all states in the given alphabet have a string description of same length,
......@@ -133,7 +133,7 @@ public:
* @param alphabet a pointer toward the alphabet to analyse.
* @return The common size of all text descriptionif there is one. Else throws an AlphabetException.
*/
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet) throw (AlphabetException);
static unsigned int getAlphabetCodingSize(const Alphabet* alphabet);
/**
* @return True if the alphabet is an instanciation of the NucleicAlphabet class.
......
src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
View file @ 8cff27ae
......@@ -60,7 +60,7 @@ BinaryAlphabet::BinaryAlphabet()
/******************************************************************************/
std::vector<int> BinaryAlphabet::getAlias(int state) const throw (BadIntException)
std::vector<int> BinaryAlphabet::getAlias(int state) const
{
if (!isIntInAlphabet(state)) throw BadIntException(state, "BinaryAlphabet::getAlias(int): Specified base unknown.");
std::vector<int> v;
......@@ -86,7 +86,7 @@ std::vector<int> BinaryAlphabet::getAlias(int state) const throw (BadIntExceptio
/******************************************************************************/
std::vector<std::string> BinaryAlphabet::getAlias(const std::string& state) const throw (BadCharException)
std::vector<std::string> BinaryAlphabet::getAlias(const std::string& state) const
{
if (!isCharInAlphabet(state)) throw BadCharException(state, "BinaryAlphabet::getAlias(char): Specified base unknown.");
......