[med-svn] [libbpp-seq] 03/05: Version 2.3.2.
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Mon Feb 5 19:47:55 UTC 2018
This is an automated email from the git hooks/post-receive script.
jdutheil-guest pushed a commit to branch master
in repository libbpp-seq.
commit 2bfb7c7abf508d7619c6c6ba23f5ebe577e0f5ff
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Mon Feb 5 17:36:50 2018 +0100
Version 2.3.2.
---
debian/changelog | 7 +
debian/control | 6 +-
.../rm_VectorProbabilisticSiteContainer.patch | 322 ---------------------
debian/patches/series | 1 -
debian/rules | 1 -
5 files changed, 10 insertions(+), 327 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index ed75da8..cd96451 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-seq (2.3.2-1) UNRELEASED; urgency=medium
+
+ * Rebuild with gcc-7
+ * Standards-Version: 4.0.1
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 05 Feb 2018 17:36:38 +0200
+
libbpp-seq (2.3.1-8) unstable; urgency=medium
* Rebuild with gcc-7
diff --git a/debian/control b/debian/control
index 313aff8..b4e076f 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 10),
cmake,
d-shlibs (>= 0.80),
- libbpp-core-dev (>= 2.3.1)
+ libbpp-core-dev (>= 2.3.2)
Standards-Version: 4.0.1
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq.git
@@ -18,7 +18,7 @@ Architecture: any
Section: libdevel
Depends: libbpp-seq11 (= ${binary:Version}),
${misc:Depends},
- libbpp-core-dev (>= 2.3.1)
+ libbpp-core-dev (>= 2.3.2)
Description: Bio++ Sequence library development files
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
@@ -36,7 +36,7 @@ Pre-Depends: ${misc:Pre-Depends}
Multi-Arch: same
Depends: ${shlibs:Depends},
${misc:Depends},
- libbpp-core3 (>= 2.3.1)
+ libbpp-core3 (>= 2.3.2)
Description: Bio++ Sequence library
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
diff --git a/debian/patches/rm_VectorProbabilisticSiteContainer.patch b/debian/patches/rm_VectorProbabilisticSiteContainer.patch
deleted file mode 100644
index a869f0a..0000000
--- a/debian/patches/rm_VectorProbabilisticSiteContainer.patch
+++ /dev/null
@@ -1,322 +0,0 @@
-Author: Julien Dutheil <julien.dutheil at univ-montp2.fr>
-Last-Update: Wed, 12 Jul 2017 13:21:07 +0000
-Description: Removed unused class VectorProbabilisticSiteContainer
- This class was moved to a dedicated branch but these files were left on
- the master branch. Yet they were not listed by cmake for compilation.
-
---- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
-+++ /dev/null
-@@ -1,187 +0,0 @@
--//
--// File: VectorProbabilisticSiteContainer.cpp
--// Created by: Murray Patterson
--// Created on: Mon Oct 19 2015
--//
--
--/*
-- Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
--
-- This software is a computer program whose purpose is to provide classes
-- for sequences analysis.
--
-- This software is governed by the CeCILL license under French law and
-- abiding by the rules of distribution of free software. You can use,
-- modify and/ or redistribute the software under the terms of the CeCILL
-- license as circulated by CEA, CNRS and INRIA at the following URL
-- "http://www.cecill.info".
--
-- As a counterpart to the access to the source code and rights to copy,
-- modify and redistribute granted by the license, users are provided only
-- with a limited warranty and the software's author, the holder of the
-- economic rights, and the successive licensors have only limited
-- liability.
--
-- In this respect, the user's attention is drawn to the risks associated
-- with loading, using, modifying and/or developing or reproducing the
-- software by the user in light of its specific status of free software,
-- that may mean that it is complicated to manipulate, and that also
-- therefore means that it is reserved for developers and experienced
-- professionals having in-depth computer knowledge. Users are therefore
-- encouraged to load and test the software's suitability as regards their
-- requirements in conditions enabling the security of their systems and/or
-- data to be ensured and, more generally, to use and operate it in the
-- same conditions as regards security.
--
-- The fact that you are presently reading this means that you have had
-- knowledge of the CeCILL license and that you accept its terms.
--*/
--
--#include "VectorProbabilisticSiteContainer.h"
--
--#include <Bpp/Text/TextTools.h>
--#include <Bpp/Numeric/DataTable.h>
--
--using namespace bpp;
--
--/********************************************************************************/
--
--VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(const Alphabet * alpha) :
-- VectorSiteContainer(alpha),
-- p_sites_(0),
-- p_sequences_(0)
--{}
--
--/********************************************************************************/
--
--const ProbabilisticSite & VectorProbabilisticSiteContainer::getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException)
--{
-- if(i >= getNumberOfProbabilisticSites())
-- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSite.", i, 0, getNumberOfProbabilisticSites() - 1);
--
-- return *p_sites_[i];
--}
--
--/********************************************************************************/
--
--void VectorProbabilisticSiteContainer::addSite(const ProbabilisticSite & site, bool checkPosition) throw (Exception)
--{
-- // check size :
-- if(site.size() != getNumberOfProbabilisticSequences())
-- throw Exception("VectorProbabilisticSiteContainer::addSite. Site does not have the appropriate length: " + TextTools::toString(site.size()) + ", should be " + TextTools::toString(getNumberOfProbabilisticSequences()) + ".");
--
-- // new site's alphabet and site container's alphabet must match :
-- if(site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
-- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSite.", getAlphabet(), site.getAlphabet());
--
-- // check position :
-- if(checkPosition) {
--
-- int position = site.getPosition();
-- // for all positions in vector : throw exception if position already exists
-- for(std::size_t i = 0; i < p_sites_.size(); ++i)
-- if(p_sites_[i]->getPosition() == position)
-- throw Exception("VectorSiteContainer::addSite. Site position: " + TextTools::toString(position) + ", already exists in container.");
-- }
--
-- p_sites_.push_back(dynamic_cast<ProbabilisticSite *>(site.clone()));
--}
--
--/********************************************************************************/
--
--const ProbabilisticSequence & VectorProbabilisticSiteContainer::getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException)
--{
--
-- if(i >= getNumberOfProbabilisticSequences())
-- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSequence.", i, 0, getNumberOfProbabilisticSequences() - 1);
--
-- // main loop : for all sites
-- std::size_t n = getNumberOfProbabilisticSites();
-- DataTable sequence(getAlphabet()->getResolvedChars());
-- for(std::size_t j = 0; j < n; ++j)
-- sequence.addRow(p_sites_[j]->getContent().getRow(i));
--
-- if(p_sequences_[i])
-- delete p_sequences_[i];
--
-- p_sequences_[i] = new BasicProbabilisticSequence(names_[i], sequence, *comments_[i], getAlphabet());
--
-- return *p_sequences_[i];
--}
--
--/********************************************************************************/
--
--void VectorProbabilisticSiteContainer::addSequence(const ProbabilisticSequence & sequence, bool checkName) throw (Exception)
--{
--
-- // if the container has no sequence, we set the size to the size of this sequence :
-- if(getNumberOfProbabilisticSequences() == 0)
-- pRealloc(sequence.size());
--
-- // new sequence's alphabet and site container's alphabet must match :
-- if(sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
-- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSequence.", getAlphabet(), sequence.getAlphabet());
--
-- if(sequence.size() != p_sites_.size())
-- throw Exception("VectorProbabilisticSiteContainer::addSequence. Sequence does not have the appropriate length: " + TextTools::toString(sequence.size()) + ", should be " + TextTools::toString(p_sites_.size()) + ".");
--
-- // check name :
-- if(checkName)
-- for(std::size_t i = 0; i < names_.size(); ++i)
-- if(sequence.getName() == names_[i])
-- throw Exception("VectorProbabilisticSiteContainer::addSequence. Name: " + sequence.getName() + ", already exists in the container.");
--
-- // append name :
-- names_.push_back(sequence.getName());
--
-- // append elements at each site :
-- for(size_t i = 0; i < p_sites_.size(); ++i)
-- p_sites_[i]->addElement(sequence.getContent().getRow(i));
--
-- // append comments :
-- comments_.push_back(new Comments(sequence.getComments()));
--
-- // sequence pointers :
-- p_sequences_.push_back(0);
--}
--
--/********************************************************************************/
--
--void VectorProbabilisticSiteContainer::pClear()
--{
-- clear(); // call VectorSiteContainer clear
--
-- // now clear all probabilistic sites / sequences
-- for(std::size_t i = 0; i < p_sites_.size(); ++i)
-- delete p_sites_[i];
--
-- for(std::size_t i = 0; i < p_sequences_.size(); ++i)
-- delete p_sequences_[i];
--
-- // and delete the corresponding pointers
-- p_sites_.clear();
-- p_sequences_.clear();
--}
--
--/********************************************************************************/
--
--void VectorProbabilisticSiteContainer::reindexpSites()
--{
-- int pos = 1; // start at position 1
-- std::vector<ProbabilisticSite *>::iterator i = p_sites_.begin();
-- for(; i != p_sites_.end(); ++i)
-- (*i)->setPosition(++pos);
--}
--
--/********************************************************************************/
--
--void VectorProbabilisticSiteContainer::pRealloc(std::size_t n)
--{
-- pClear();
-- p_sites_.resize(n);
--
-- for(std::size_t i = 0; i < n; ++i)
-- p_sites_[i] = new BasicProbabilisticSite(getAlphabet());
--
-- reindexpSites();
--}
---- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
-+++ /dev/null
-@@ -1,123 +0,0 @@
--//
--// File: VectorProbabilisticSiteContainer.h
--// Created by: Murray Patterson
--// Created on: Mon Oct 19 2015
--//
--
--/*
-- Copyright or © or Copr. CNRS, (November 17, 2004)
--
-- This software is a computer program whose purpose is to provide classes
-- for sequences analysis.
--
-- This software is governed by the CeCILL license under French law and
-- abiding by the rules of distribution of free software. You can use,
-- modify and/ or redistribute the software under the terms of the CeCILL
-- license as circulated by CEA, CNRS and INRIA at the following URL
-- "http://www.cecill.info".
--
-- As a counterpart to the access to the source code and rights to copy,
-- modify and redistribute granted by the license, users are provided only
-- with a limited warranty and the software's author, the holder of the
-- economic rights, and the successive licensors have only limited
-- liability.
--
-- In this respect, the user's attention is drawn to the risks associated
-- with loading, using, modifying and/or developing or reproducing the
-- software by the user in light of its specific status of free software,
-- that may mean that it is complicated to manipulate, and that also
-- therefore means that it is reserved for developers and experienced
-- professionals having in-depth computer knowledge. Users are therefore
-- encouraged to load and test the software's suitability as regards their
-- requirements in conditions enabling the security of their systems and/or
-- data to be ensured and, more generally, to use and operate it in the
-- same conditions as regards security.
--
-- The fact that you are presently reading this means that you have had
-- knowledge of the CeCILL license and that you accept its terms.
--*/
--
--#ifndef _VECTORPROBABILISTICSITECONTAINER_H_
--#define _VECTORPROBABILISTICSITECONTAINER_H_
--
--#include "VectorSiteContainer.h"
--
--#include "../ProbabilisticSite.h"
--#include "../ProbabilisticSequence.h"
--
--// From the STL :
--#include <vector>
--
--namespace bpp
--{
--
--/**
-- * @brief The VectorProbabilisticSiteContainer class.
-- *
-- * ProbabilisticSites are stored in a std::vector of pointers.
-- * ProbabilisticSite access is hence in \f$O(1)\f$, and sequence
-- * access in \f$O(l)\f$, where \f$l\f$ is the number of sites in the
-- * container.
-- *
-- * This is a modified copy of VectorSiteContainer with the minimum
-- * changes necessary for it to work with bppML and bppAncestor
-- *
-- * @see ProbabilisticSequence, ProbabilisticSite, VectorSiteContainer
-- */
--class VectorProbabilisticSiteContainer :
-- public VectorSiteContainer
--{
--
-- protected :
--
-- std::vector<ProbabilisticSite *> p_sites_;
-- mutable std::vector<ProbabilisticSequence *> p_sequences_;
--
-- public :
--
-- /**
-- * @brief Build a new emtpy container.
-- *
-- * @param alpha The alphabet for this container.
-- */
-- VectorProbabilisticSiteContainer(const Alphabet * alpha);
--
-- /**
-- * @name The Clonable interface.
-- *
-- * @{
-- */
-- VectorSiteContainer* clone() const { return new VectorSiteContainer(*this); }
--
-- /**
-- * @}
-- */
--
-- // class destructor
-- virtual ~VectorProbabilisticSiteContainer() { pClear(); }
--
-- public :
--
-- const ProbabilisticSite & getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException);
--
-- void addSite(const ProbabilisticSite & site, bool checkPosition = true) throw (Exception);
--
-- const ProbabilisticSequence & getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException);
--
-- void addSequence(const ProbabilisticSequence & sequence, bool checkName = true) throw (Exception);
--
-- std::size_t getNumberOfProbabilisticSites() const { return p_sites_.size(); }
-- std::size_t getNumberOfProbabilisticSequences() const { return p_sequences_.size(); }
--
-- void pClear();
-- void reindexpSites();
--
-- protected :
--
-- // create n void probabilistic sites :
-- void pRealloc(std::size_t n);
--};
--
--} // end of namespace bpp
--
--#endif // _VECTORPROBABILISTICSITECONTAINER_H_
diff --git a/debian/patches/series b/debian/patches/series
index 1704a6b..4ff7e79 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
unforce-cxxflags.patch
-rm_VectorProbabilisticSiteContainer.patch
relax_test_timeout.patch
diff --git a/debian/rules b/debian/rules
index aa1cdb9..ecd2fa6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,7 +12,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_install:
# Broken header, don't install (if we do, the postinst will pull it
# into generic include files)
- rm -f debian/tmp/usr/include/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
dh_install
d-shlibmove --commit \
--multiarch \
--
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