[med-svn] [libbpp-seq] 01/01: Removed unused class VectorProbabilisticSiteContainer.
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Wed Jul 12 13:21:07 UTC 2017
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 d4d4ce2f27747441d8011292ba0fd877a1307a7a
Author: Julien Y. Dutheil <jdutheil at virtualdeb.evolbio.mpg.de>
Date: Wed Jul 12 15:13:42 2017 +0200
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.
---
.../Container/VectorProbabilisticSiteContainer.cpp | 187 ---------------------
.../Container/VectorProbabilisticSiteContainer.h | 123 --------------
2 files changed, 310 deletions(-)
diff --git a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp b/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
deleted file mode 100644
index b40a379..0000000
--- 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();
-}
diff --git a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h b/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
deleted file mode 100644
index 5f93474..0000000
--- 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_
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-seq.git
More information about the debian-med-commit
mailing list