SequenceTools.h

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//
// File: SequenceTools.h
// Authors: Guillaume Deuchst
//          Julien Dutheil
//          Sylvain Gaillard
// Created on: Tue Aug 21 2003
//

/*
   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.
 */

#ifndef _SEQUENCETOOLS_H_
#define _SEQUENCETOOLS_H_

#include "Alphabet/Alphabet.h"
#include "Alphabet/DNA.h"
#include "Alphabet/RNA.h"
#include "Alphabet/RNY.h"
#include "Sequence.h"
#include "SymbolListTools.h"
#include "NucleicAcidsReplication.h"
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Random/RandomTools.h>
#include <Bpp/Numeric/Stat/StatTest.h>

// From the STL:
#include <string>
#include <map>
#include <vector>
#include <algorithm>

namespace bpp
{
class BowkerTest :
  public StatTest
{
private:
  double pvalue_;
  double stat_;

public:
  BowkerTest() : pvalue_(1.),
    stat_(0.) {}

  virtual ~BowkerTest() {}

  BowkerTest* clone() const { return new BowkerTest(*this); }

public:
  std::string getName() const { return "Bowker's test for homogeneity."; }
  double getStatistic() const { return stat_; }
  double getPValue() const { return pvalue_; }

  void setStatistic(double stat) { stat_ = stat; }
  void setPValue(double pvalue) { pvalue_ = pvalue; }
};

class SequenceTools :
  public SymbolListTools
{
private:
  static DNA _DNA;
  static RNA _RNA;
  static RNY _RNY;
  static NucleicAcidsReplication _DNARep;
  static NucleicAcidsReplication _RNARep;
  static NucleicAcidsReplication _transc;

public:
  SequenceTools() {}
  virtual ~SequenceTools() {}

public:
  static Sequence* subseq(const Sequence& sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception);

  static Sequence* concatenate(const Sequence& seq1, const Sequence& seq2)
  throw (AlphabetMismatchException, Exception);

  static Sequence& complement(Sequence& seq) throw (AlphabetException);

  static Sequence* getComplement(const Sequence& sequence) throw (AlphabetException);

  static Sequence* transcript(const Sequence& sequence) throw (AlphabetException);

  static Sequence* reverseTranscript(const Sequence& sequence) throw (AlphabetException);

  static Sequence& invert(Sequence& seq);

  static Sequence* getInvert(const Sequence& sequence);

  static Sequence& invertComplement(Sequence& seq);

  static double getPercentIdentity(const Sequence& seq1, const Sequence& seq2, bool ignoreGaps = false) throw (AlphabetMismatchException, SequenceNotAlignedException);

  static size_t getNumberOfSites(const Sequence& seq);

  static size_t getNumberOfCompleteSites(const Sequence& seq);

  static size_t getNumberOfUnresolvedSites(const Sequence& seq);

  static void removeGaps(Sequence& seq);

  static Sequence* getSequenceWithoutGaps(const Sequence& seq);

  static void removeStops(Sequence& seq) throw (Exception);

  static Sequence* getSequenceWithoutStops(const Sequence& seq) throw (Exception);

  static void replaceStopsWithGaps(Sequence& seq) throw (Exception);

  static BowkerTest* bowkerTest(const Sequence& seq1, const Sequence& seq2) throw (SequenceNotAlignedException);

  static void getPutativeHaplotypes(const Sequence& seq, std::vector<Sequence*>& hap, unsigned int level = 2);

  static Sequence* combineSequences(const Sequence& s1, const Sequence& s2) throw (AlphabetMismatchException);

  static Sequence* subtractHaplotype(const Sequence& s, const Sequence& h, std::string name = "", unsigned int level = 1) throw (SequenceNotAlignedException);

  static Sequence* RNYslice(const Sequence& sequence, int ph) throw (AlphabetException);
  static Sequence* RNYslice(const Sequence& sequence) throw (AlphabetException);

  static void getCDS(Sequence& sequence, bool checkInit, bool checkStop, bool includeInit = true, bool includeStop = true);

  static size_t findFirstOf(const Sequence& seq, const Sequence& motif, bool strict = true);
};
} // end of namespace bpp.

#endif // _SEQUENCETOOLS_H_