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// File: PatternTools.h
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// Created by: Julien Dutheil
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// Created on: Thu Mar 20 13:36:53 2003
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _PATTERNTOOLS_H_
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#define _PATTERNTOOLS_H_
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#include <Bpp/Numeric/VectorTools.h>
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#include <Bpp/Seq/Site.h>
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#include <Bpp/Seq/Container/SiteContainer.h>
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* @brief Utilitary methods to compute site patterns.
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* Theses methods are mainly designed to save computation in likelihood
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* and parsimony methods.
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* @brief Extract the sequences corresponding to a given subtree.
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* @param sequenceSet The container to look in.
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* @param node The root node of the subtree to check.
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* @return A new site container with corresponding sequences.
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* @throw Exception if an error occured.
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static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
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* @brief Extract the sequences corresponding to a given set of names.
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* @param sequenceSet The container to look in.
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* @param names The names of the sequences to look for.
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* @return A new site container with corresponding sequences.
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* @throw Exception if an error occured.
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static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
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* @brief Compress a site container by removing duplicated sites.
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* @param sequenceSet The container to look in.
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* @return A new site container with unique sites.
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* @throw Exception if an error occured.
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static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
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* @brief Look for the occurence of each site in sequences1 in sequences2 and send the
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* position of the first occurence, or -1 if not found.
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* @param sequences1 First container.
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* @param sequences2 Second container.
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* @return A vecotr of positions.
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static Vint getIndexes(const SiteContainer& sequences1, const SiteContainer& sequences2);
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} //end of namespace bpp.
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#endif //_PATTERNTOOLS_H_