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// Author : Guillaume Deuchst
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// Last modification : Tuesday August 21 2003
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Copyright or © or Copr. CNRS, (November 17, 2004)
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This software is a computer program whose purpose is to provide classes
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for sequences 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 "../StringSequenceTools.h"
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/****************************************************************************************/
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void Mase::appendFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
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if (!input) { throw IOException ("Mase::read : fail to open file"); }
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Comments seqComments, fileComments;
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string temp, name, sequence = "";
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bool comments = false;
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// Get current general comments is VectorSequenceContainer
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fileComments = vsc.getGeneralComments();
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// Main loop : for all file lines
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getline(input, temp, '\n'); // Copy current line in temporary string
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// If first character is ;
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// If second character is also ;
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// File comments isolation
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temp.erase(0,2); // Characters ;; deletion
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if(temp != "") fileComments.push_back(temp);
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// If a name and a sequence were founded
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if ((name != "") && (sequence != ""))
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// New sequence creation, and addition in existing VectorSequenceContainer
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vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
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// Sequence commentaries isolation
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temp.erase(temp.begin()); // Character ; deletion
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if (temp != "") seqComments.push_back(temp);
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// If sequence commentaries were just isolated
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// Sequence name isolation
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else sequence += temp; // Sequence isolation
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// Addition of the last sequence in file
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if ((name != "") && (sequence != ""))
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vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
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// Set new general comments in VectorSequenceContainer (old + new comments)
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vsc.setGeneralComments(fileComments);
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/****************************************************************************************/
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void Mase::write(ostream& output, const SequenceContainer& sc) 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 (!output) { throw IOException ("Mase::write : failed to open file"); }
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Comments comments = sc.getGeneralComments();
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// Writing all general commentaries in file
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for (unsigned int i = 0 ; i < comments.size() ; i++)
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output << ";;" << comments[i] << endl;
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string seq, temp = ""; // Initialization
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// Main loop : for all sequences
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vector<string> names = sc.getSequencesNames();
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for (unsigned int i = 0 ; i < names.size() ; i ++)
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comments = sc.getComments(names[i]);
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// Writing all sequence comments in file
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// If no comments are associated with current sequence, an empy commentary line will be writed
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if (comments.size() == 0)
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output << ";" << endl;
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for (unsigned int j = 0 ; j < comments.size() ; j++)
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output << ";" << comments[j] << endl;
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// Sequence name writing
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output << names[i] << endl;
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// Sequence cutting to specified characters number per line
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seq = sc.toString(names[i]);
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if (seq.size() > charsByLine_)
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temp.erase(temp.begin() + charsByLine_ , temp.end());
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output << temp << endl;
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seq.erase(seq.begin(), seq.begin() + charsByLine_);
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output << seq << endl;
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/****************************************************************************************/
added
removed
src/Bpp/Seq/Io/Mase.cpp
