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Viewing changes to src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp

  • Committer: Package Import Robot
  • Author(s): Julien Dutheil
  • Date: 2013-03-05 14:31:00 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20130305143100-2jox395vr1ghao46
Tags: 2.1.0-1
* 'omics' tools now in bpp-seq-omics
* Extended BppO support
* StateProperties renamed to AlphabetIndex

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src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
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//
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/*
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Copyright or © or Copr. CNRS, (November 17, 2004)
 
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Copyright or © or Copr. Bio++ Development Team, (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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ProteicAlphabet::ProteicAlphabet()
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{
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        // Alphabet size definition
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        resize(27);
 
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        resize(28);
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        // Alphabet content definition
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  setState( 0, ProteicAlphabetState(-1, "-", "GAP", "Gap"));
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  setState(24, ProteicAlphabetState(22, "O", "O", "Unresolved amino acid"));
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  setState(25, ProteicAlphabetState(22, "0", "0", "Unresolved amino acid"));
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  setState(26, ProteicAlphabetState(22, "?", "?", "Unresolved amino acid"));
 
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  setState(27, ProteicAlphabetState(-2, "*", "STOP", "Stop"));
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}
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/******************************************************************************/
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string ProteicAlphabet::getAbbr(const string & aa) const throw (AlphabetException)
 
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string ProteicAlphabet::getAbbr(const string& aa) const throw (AlphabetException)
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{
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        string AA = TextTools::toUpper(aa);
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  return (getState(aa).getAbbreviation());