Commit 8ad7c609 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.1

parent 690616d6

CMakeLists.txt

+2 −2
Original line number Diff line number Diff line
@@ -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 "2.4.0")

SET(CPACK_PACKAGE_VERSION "2.4.1")

SET(CPACK_PACKAGE_VERSION_MAJOR "2")

SET(CPACK_PACKAGE_VERSION_MINOR "4")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

SET(CPACK_PACKAGE_VERSION_PATCH "1")

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")

Doxyfile

+1 −1
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@@ -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         = 2.4.0

PROJECT_NUMBER         = 2.4.1



# 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

+3 −1
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@@ -3,7 +3,7 @@ 
URL: https://github.com/BioPP/bpp-seq



Name: bpp-seq

Version: 2.4.0

Version: 2.4.1

Release: 1%{?dist}

License: CECILL-2.0

Vendor: The Bio++ Project
@@ -78,6 +78,8 @@ rm -rf $RPM_BUILD_ROOT 
%{_prefix}/include/*



%changelog

* Fri Aug 10 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1

- Compatibility update gcc8

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

- Increased interface number

- Removed dynamic exceptions declarations.

src/Bpp/Seq/Alphabet/DefaultAlphabet.h

+0 −3
Original line number Diff line number Diff line
@@ -55,9 +55,6 @@ namespace bpp 
    public LetterAlphabet

  {

  protected:

    void registerState(AlphabetState* st) {

      AbstractAlphabet::registerState(st);

    }

    std::string chars_;

		

  public:

src/Bpp/Seq/Alphabet/LetterAlphabet.h

+9 −9
Original line number Diff line number Diff line
@@ -83,7 +83,7 @@ namespace bpp { 


  public:

    bool isCharInAlphabet(char state) const {

      return letters_[static_cast<unsigned int>(state)] != LETTER_UNDEF_VALUE;

      return letters_[static_cast<size_t>(state)] != LETTER_UNDEF_VALUE;

    }

    bool isCharInAlphabet(const std::string& state) const {

      return isCharInAlphabet(state[0]);
@@ -98,20 +98,20 @@ namespace bpp { 
    void registerState(AlphabetState* st) {

      AbstractAlphabet::registerState(st);

      if (caseSensitive_) {

        letters_[static_cast<unsigned int>(st->getLetter()[0])] = st->getNum();

        letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();

      } else {

        letters_[static_cast<unsigned int>(tolower(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<unsigned int>(toupper(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();

      }

    }



    void setState(size_t pos, AlphabetState* st) {

      AbstractAlphabet::setState(pos, st);

      if (caseSensitive_) {

        letters_[static_cast<unsigned int>(st->getLetter()[0])] = st->getNum();

        letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();

      } else {

        letters_[static_cast<unsigned int>(tolower(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<unsigned int>(toupper(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();

        letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();

      }

    }