Commit d9174eb5 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.1

parent 6bfddcbf

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-popgen")

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++ Population Genetics library")

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

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

Doxyfile

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

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



Name: bpp-popgen

Version: 2.4.0

Version: 2.4.1

Release: 1%{?dist}

License: CECILL-2.0

Vendor: The Bio++ Project
@@ -84,6 +84,8 @@ rm -rf $RPM_BUILD_ROOT 
%{_prefix}/include/*



%changelog

* Mon Aug 13 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1

- Compatibility update gcc8.

* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1

- Remove deprecated dynamic exception specifications

- Increased interface number

src/Bpp/PopGen/DataSet/DataSet.cpp

+23 −23
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ 
//



/*

   Copyright or © or Copr. CNRS, (November 17, 2004)

   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)



   This software is a computer program whose purpose is to provide classes

   for population genetics analysis.
@@ -453,7 +453,7 @@ size_t DataSet::getIndividualPositionInGroup(size_t group_position, const std::s 
  {

    return groups_[group_position]->getIndividualPosition(individual_id);

  }

  catch (IndividualNotFoundException infe)

  catch (IndividualNotFoundException& infe)

  {

    throw IndividualNotFoundException("DataSet::getIndividualPositionFromGroup: individual_id not found.", infe.getIdentifier());

  }
@@ -469,7 +469,7 @@ const Individual* DataSet::getIndividualAtPositionFromGroup(size_t group_positio 
  {

    return &groups_[group_position]->getIndividualAtPosition(individual_position);

  }

  catch (IndexOutOfBoundsException ioobe)

  catch (IndexOutOfBoundsException& ioobe)

  {

    throw IndexOutOfBoundsException("DataSet::getIndividualAtPositionFromGroup: individual_position out of bouds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }
@@ -485,7 +485,7 @@ const Individual* DataSet::getIndividualByIdFromGroup(size_t group_position, con 
  {

    return &groups_[group_position]->getIndividualById(individual_id);

  }

  catch (IndividualNotFoundException infe)

  catch (IndividualNotFoundException& infe)

  {

    throw IndividualNotFoundException("DataSet::getIndividualByIdFromGroup: individual_id not found.", infe.getIdentifier());

  }
@@ -501,7 +501,7 @@ void DataSet::deleteIndividualAtPositionFromGroup(size_t group_position, size_t 
  {

    groups_[group_position]->deleteIndividualAtPosition(individual_position);

  }

  catch (IndexOutOfBoundsException ioobe)

  catch (IndexOutOfBoundsException& ioobe)

  {

    throw IndexOutOfBoundsException("DataSet::deleteIndividualAtPositionFromGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }
@@ -517,7 +517,7 @@ void DataSet::deleteIndividualByIdFromGroup(size_t group_position, const std::st 
  {

    groups_[group_position]->deleteIndividualById(individual_id);

  }

  catch (IndividualNotFoundException infe)

  catch (IndividualNotFoundException& infe)

  {

    throw IndividualNotFoundException("DataSet::deleteIndividualByIdFromGroup: individual_id not found.", infe.getIdentifier());

  }
@@ -585,7 +585,7 @@ const Date* DataSet::getIndividualDateInGroup(size_t group_position, size_t indi 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualDateInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualDateInGroup: individual has no date.");

  }
@@ -621,7 +621,7 @@ const Point2D<double>* DataSet::getIndividualCoordInGroup(size_t group_position, 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualCoordAtPosition: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualCoordInGroup: individual has no coordinate.");

  }
@@ -661,7 +661,7 @@ const Locality<double>* DataSet::getIndividualLocalityInGroup(size_t group_posit 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualLocalityInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualLocalityInGroup: individual has no locality.");

  }
@@ -710,7 +710,7 @@ const Sequence& DataSet::getIndividualSequenceByNameInGroup(size_t group_positio 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualSequenceByNameInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualSequenceByNameInGroup: individual has no sequences.");

  }
@@ -738,7 +738,7 @@ const Sequence& DataSet::getIndividualSequenceAtPositionInGroup(size_t group_pos 
    else

      throw IndexOutOfBoundsException("DataSet::getIndividualSequenceAtPositionInGroup: sequence_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualSequenceAtPositionInGroup: individual has no sequences.");

  }
@@ -758,7 +758,7 @@ void DataSet::deleteIndividualSequenceByNameInGroup(size_t group_position, size_ 
  {

    throw IndexOutOfBoundsException("DataSet::deleteIndividualSequenceByNameInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::deleteIndividualSequenceByNameInGroup: individual has no sequences.");

  }
@@ -786,7 +786,7 @@ void DataSet::deleteIndividualSequenceAtPositionInGroup(size_t group_position, s 
    else

      throw IndexOutOfBoundsException("DataSet::deleteIndividualSequenceAtPositionInGroup: sequence_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::deleteIndividualSequenceAtPositionInGroup: individual has no sequences.");

  }
@@ -806,7 +806,7 @@ std::vector<std::string> DataSet::getIndividualSequencesNamesInGroup(size_t grou 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualSequencesNamesInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualSequencesNamesInGroup: individual has no sequences.");

  }
@@ -826,7 +826,7 @@ size_t DataSet::getIndividualSequencePositionInGroup(size_t group_position, size 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualSequencePositionInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualSequencePositionInGroup: individual has no sequences.");

  }
@@ -850,7 +850,7 @@ size_t DataSet::getIndividualNumberOfSequencesInGroup(size_t group_position, siz 
  {

    throw IndexOutOfBoundsException("DataSet::getIndividualNumberOfSequencesInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualNumberOfSequencesInGroup: individual has no sequences.");

  }
@@ -890,11 +890,11 @@ void DataSet::initIndividualGenotypeInGroup(size_t group_position, size_t indivi 
  {

    throw BadIntegerException("DataSet::initIndividualGenotypeInGroup: number of loci must be > 0.", bie.getBadInteger());

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::initIndividualGenotypeInGroup: analyzed_loci is NULL.");

  }

  catch (Exception)

  catch (Exception&)

  {

    throw Exception("DataSet::initIndividualGenotypeInGroup: individual already has a genotype.");

  }
@@ -934,7 +934,7 @@ void DataSet::setIndividualMonolocusGenotypeInGroup(size_t group_position, size_ 
    else

      throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::setIndividualMonolocusGenotypeInGroup: individual has no genotype.");

  }
@@ -958,11 +958,11 @@ void DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup(size_t group_posi 
    else

      throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: individual has no genotype.");

  }

  catch (Exception)

  catch (Exception&)

  {

    throw Exception("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: no key in allele_keys.");

  }
@@ -987,7 +987,7 @@ void DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t group_posit 
    else

      throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup: individual has no genotype.");

  }
@@ -1015,7 +1015,7 @@ const MonolocusGenotype* DataSet::getIndividualMonolocusGenotypeInGroup(size_t g 
    else

      throw IndexOutOfBoundsException("DataSet::getIndividualMonolocusGenotypeInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (NullPointerException)

  catch (NullPointerException&)

  {

    throw NullPointerException("DataSet::getIndividualMonolocusGenotypeInGroup: individual has no genotype.");

  }

src/Bpp/PopGen/DataSet/Group.cpp

+3 −3
Original line number Diff line number Diff line
@@ -5,7 +5,7 @@ 
//



/*

   Copyright or © or Copr. CNRS, (November 17, 2004)

   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)





   This software is a computer program whose purpose is to provide classes
@@ -473,7 +473,7 @@ void Group::initIndividualGenotype(size_t individual_position, size_t loci_numbe 
  {

    throw BadIntegerException("Group::initIndividualGenotype: loci_number must be > 0.", bie.getBadInteger());

  }

  catch (Exception)

  catch (Exception&)

  {

    throw Exception("Group::initIndividualGenotype: individual already has a genotype.");

  }
@@ -527,7 +527,7 @@ void Group::setIndividualMonolocusGenotypeByAlleleKey(size_t individual_position 
  {

    throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleKey: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);

  }

  catch (Exception)

  catch (Exception&)

  {

    throw Exception("Group::setIndividualMonolocusGenotypeByAlleleKey: no key in allele_keys.");

  }