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// Created by: Julien Dutheil
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// Created on: Thu Oct 23 15:35:03 2003
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Copyright or © or Copr. Bio++ Development Team, (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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#include "../TreeTemplate.h"
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#include "../TreeTemplateTools.h"
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#include <Bpp/Text/TextTools.h>
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/******************************************************************************/
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const string Newick::getFormatName() const { return "Newick"; }
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/******************************************************************************/
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const string Newick::getFormatDescription() const
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return string("New hampshire parenthesis format. ") +
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"See http://evolution.genetics.washington.edu/phylip/newicktree.html for more info.";
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/******************************************************************************/
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#if defined(NO_VIRTUAL_COV)
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Newick::read(istream& in) const throw (Exception)
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// Checking the existence of specified file
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if (! in) { throw IOException ("Newick::read: failed to read from stream"); }
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//We concatenate all line in file till we reach the ending semi colon:
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string temp, description;// Initialization
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// Main loop : for all file lines
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getline(in, temp, '\n'); // Copy current line in temporary string
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string::size_type index = temp.find(";");
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if(index != string::npos)
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description += temp.substr(0, index + 1);
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else description += temp;
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if (allowComments_) description = TextTools::removeSubstrings(description, '[', ']');
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return TreeTemplateTools::parenthesisToTree(description, useBootstrap_, bootstrapPropertyName_);
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/******************************************************************************/
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void Newick::write_(const Tree& tree, ostream& out) const throw (Exception)
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// Checking the existence of specified file, and possibility to open it in write mode
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if (! out) { throw IOException ("Newick::writeTree: failed to write to stream"); }
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out << TreeTools::treeToParenthesis(tree, writeId_);
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out << TreeTools::treeToParenthesis(tree, false, bootstrapPropertyName_);
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/******************************************************************************/
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void Newick::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
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// Checking the existence of specified file, and possibility to open it in write mode
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if (! out) { throw IOException ("Newick::writeTree: failed to write to stream"); }
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out << TreeTemplateTools::treeToParenthesis(tree, writeId_);
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out << TreeTemplateTools::treeToParenthesis(tree, false, bootstrapPropertyName_);
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/******************************************************************************/
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void Newick::read(istream& in, vector<Tree*>& trees) const throw (Exception)
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// Checking the existence of specified file
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if (! in) { throw IOException ("Newick::read: failed to read from stream"); }
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// Main loop : for all file lines
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string temp, description;// Initialization
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string::size_type index;
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//We concatenate all line in file till we reach the ending semi colon:
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getline(in, temp, '\n'); // Copy current line in temporary string
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index = temp.find(";");
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if (index != string::npos)
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description += temp.substr(0, index + 1);
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if (allowComments_) description = TextTools::removeSubstrings(description, '[', ']');
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trees.push_back(TreeTemplateTools::parenthesisToTree(description, useBootstrap_, bootstrapPropertyName_));
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description = temp.substr(index + 1);
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else description += temp;
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/******************************************************************************/
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void Newick::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
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// Checking the existence of specified file, and possibility to open it in write mode
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if (! out) { throw IOException ("Newick::write: failed to write to stream"); }
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for(unsigned int i = 0; i < trees.size(); i++)
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out << TreeTools::treeToParenthesis(*trees[i], writeId_);
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out << TreeTools::treeToParenthesis(*trees[i], false, bootstrapPropertyName_);
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/******************************************************************************/
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void Newick::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
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// Checking the existence of specified file, and possibility to open it in write mode
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if (! out) { throw IOException ("Newick::write: failed to write to stream"); }
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for(unsigned int i = 0; i < trees.size(); i++)
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out << TreeTemplateTools::treeToParenthesis(*trees[i], writeId_);
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out << TreeTemplateTools::treeToParenthesis(*trees[i], false, bootstrapPropertyName_);
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/******************************************************************************/
added
removed
src/Bpp/Phyl/Io/Newick.cpp
