SequenceWithQuality.h

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// 
// File:    SequenceWithQuality.h
// Authors: Sylvain Gaillard
//          Vincent Cahais
//          Julien Dutheil
// Created: 19/01/2010 16:01:20
// 

/*
Copyright or © or Copr. Bio++ Development Team, (January 19, 2010)

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 _SEQUENCEQUALITY_H_
#define _SEQUENCEQUALITY_H_

#include "SequenceWithAnnotation.h"
#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/VectorExceptions.h>

// From the STL

#include <string>
#include <vector>

namespace bpp {
  class SequenceQuality :
    public virtual SequenceAnnotation
  {
    private:
      bool removable_;
      std::vector<int> qualScores_;

    public:
      static const std::string QUALITY_SCORE; 
      static const int DEFAULT_QUALITY_VALUE;

    public:

      SequenceQuality(size_t size = 0, bool removable = true) :
        removable_(removable),
        qualScores_(size, DEFAULT_QUALITY_VALUE) {}


      SequenceQuality(const std::vector<int>& quality, bool removable = true) :
        removable_(removable),
        qualScores_(quality)
      {
      //    if (size() != qualScores_.size())
      //      throw DimensionException("SequenceWithQuality constructor: sequence and quality must have the same length", qualScores_.size(), size());
      }

      virtual ~SequenceQuality() {}
#ifdef NO_VIRTUAL_COV
      Clonable*
#else
      SequenceQuality*
#endif
      clone() const { return new SequenceQuality(*this); }
    public:
      void init(const Sequence& seq)
      {
        qualScores_.resize(seq.size());
        std::fill(qualScores_.begin(), qualScores_.end(), DEFAULT_QUALITY_VALUE);
      }

      const std::string& getType() const { return QUALITY_SCORE; }

      bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const
      {
        if (throwException && qualScores_.size() != sequence.size()) throw Exception("SequenceQuality. Quality scores must match the sequence size.");
        return (qualScores_.size() == sequence.size());
      }

      bool isRemovable() const { return removable_; }
      bool isShared() const { return false; }
      void beforeSequenceChanged(const SymbolListEditionEvent& event) {}
      void afterSequenceChanged(const SymbolListEditionEvent& event);
      void beforeSequenceInserted(const SymbolListInsertionEvent& event) {}
      void afterSequenceInserted(const SymbolListInsertionEvent& event);
      void beforeSequenceDeleted(const SymbolListDeletionEvent& event) {}
      void afterSequenceDeleted(const SymbolListDeletionEvent& event);
      void beforeSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}
      void afterSequenceSubstituted(const SymbolListSubstitutionEvent& event) {}

      size_t getSize() const { return qualScores_.size(); }

      const int& operator[](size_t i) const { return qualScores_[i]; }
      int& operator[](size_t i) { return qualScores_[i]; }

      void setScores(const std::vector<int>& scores) {
        if (scores.size() != qualScores_.size())
          throw DimensionException("SequenceQuality::setScores. Trying to replace score by a vector with different length.", scores.size(), qualScores_.size());
        qualScores_ = scores;
      }

      const std::vector<int>& getScores() const { return qualScores_; }

      void setScore(size_t pos, int score) {
        if (pos >= qualScores_.size())
          throw Exception("SequenceQuality::setScore. Vector overflow. Scores number: " + TextTools::toString(qualScores_.size()) + ", but trying to insert score at position " + TextTools::toString(pos) + ".");
        qualScores_[pos] = score;
      }
      
      void setScores(size_t pos, const std::vector<int>& scores) {
        if (pos + scores.size() > qualScores_.size())
          throw Exception("SequenceQuality::setScores. Vector overflow. Scores number: " + TextTools::toString(qualScores_.size()) + ", but trying to insert " + TextTools::toString(scores.size()) + " scores at position " + TextTools::toString(pos) + ".");
        std::copy(scores.begin(), scores.end(), qualScores_.begin() + pos); 
      }
    
      bool merge(const SequenceAnnotation& anno) {
        try {
          const SequenceQuality* qual = & dynamic_cast<const SequenceQuality&>(anno);
          VectorTools::append(qualScores_, qual->getScores());
          return true;
        } catch (std::exception& e) {
          return false;
        }
      }

      SequenceQuality* getPartAnnotation(size_t pos, size_t len) const throw (Exception) {
        return new SequenceQuality(std::vector<int>(qualScores_.begin() + pos, qualScores_.begin() + pos + len), removable_);
      }
  };



  class SequenceWithQuality :
    public SequenceWithAnnotation
  {
    private:
      SequenceQuality* qualScores_;

    public:

      SequenceWithQuality(
          const Alphabet* alpha
          ):
        SequenceWithAnnotation(alpha),
        qualScores_(new SequenceQuality(0, false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::string& sequence,
          const Alphabet* alpha
          ) throw (BadCharException):
        SequenceWithAnnotation(name, sequence, alpha),
        qualScores_(new SequenceQuality(sequence.size(), false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::string& sequence,
          const Comments& comments,
          const Alphabet* alpha
          ) throw (BadCharException):
        SequenceWithAnnotation(name, sequence, comments, alpha),
        qualScores_(new SequenceQuality(sequence.size(), false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::string& sequence,
          const std::vector<int>& quality,
          const Alphabet* alpha)
        throw (BadCharException, DimensionException):
        SequenceWithAnnotation(name, sequence, alpha),
        qualScores_(new SequenceQuality(quality, false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::string& sequence,
          const std::vector<int>& quality,
          const Comments& comments,
          const Alphabet* alpha)
        throw (BadCharException, DimensionException):
        SequenceWithAnnotation(name, sequence, comments, alpha),
        qualScores_(new SequenceQuality(quality, false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::vector<int>& sequence,
          const Alphabet* alpha)
        throw (BadIntException):
        SequenceWithAnnotation(name, sequence, alpha),
        qualScores_(new SequenceQuality(sequence.size(), false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::vector<int>& sequence,
          const Comments& comments,
          const Alphabet* alpha)
        throw (BadIntException):
        SequenceWithAnnotation(name, sequence, comments, alpha),
        qualScores_(new SequenceQuality(sequence.size(), false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::vector<int>& sequence,
          const std::vector<int>& quality,
          const Alphabet* alpha)
        throw (BadIntException, DimensionException):
        SequenceWithAnnotation(name, sequence, alpha),
        qualScores_(new SequenceQuality(quality, false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const std::string& name,
          const std::vector<int>& sequence,
          const std::vector<int>& quality,
          const Comments& comments,
          const Alphabet* alpha)
        throw (BadIntException, DimensionException):
        SequenceWithAnnotation(name, sequence, comments, alpha),
        qualScores_(new SequenceQuality(quality, false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(const Sequence& s) :
        SequenceWithAnnotation(s), qualScores_(new SequenceQuality(s.size(), false))
      {
        addAnnotation(qualScores_);
      }

      SequenceWithQuality(
          const Sequence& s,
          const std::vector<int>& sc)
        throw (DimensionException):
        SequenceWithAnnotation(s),
        qualScores_(new SequenceQuality(sc, false))
      {
        addAnnotation(qualScores_);
      }

      virtual ~SequenceWithQuality() {}
      SequenceWithQuality(const SequenceWithQuality& sequence) : 
        SequenceWithAnnotation(sequence), qualScores_(0)
      {
        qualScores_ = dynamic_cast<SequenceQuality*>(&getAnnotation(SequenceQuality::QUALITY_SCORE));                  
      }

      SequenceWithQuality& operator=(const SequenceWithQuality& sequence)
      { 
        SequenceWithAnnotation::operator=(sequence);
        qualScores_ = dynamic_cast<SequenceQuality*>(&getAnnotation(SequenceQuality::QUALITY_SCORE));
        return *this;
      }

#ifdef NO_VIRTUAL_COV
      Clonable*
#else
      SequenceWithQuality*
#endif
      clone() const { return new SequenceWithQuality(*this); }
      void setQuality(size_t pos, int quality) throw (IndexOutOfBoundsException) {
        //if (pos >= qualScores_->getSize())
        //  throw IndexOutOfBoundsException("SequenceWithQuality::setQuality: pos out of bounds", pos, 0, qualScores_->getSize() - 1);
        //qualScores_[pos] = quality;
        qualScores_->setScore(pos, quality);
      }
      
      int getQuality(size_t pos) const throw (IndexOutOfBoundsException) {
        if (pos >= qualScores_->getSize())
          throw IndexOutOfBoundsException("SequenceWithQuality::getQuality: pos out of bounds", pos, 0, qualScores_->getSize() - 1);
        return (*qualScores_)[pos];
      }

      void setQualities(const std::vector<int>& quality) throw (DimensionException) {
        if (quality.size() != qualScores_->getSize())
          throw DimensionException("SequenceWithQuality::setQualities: quality must fit sequence size", quality.size(), qualScores_->getSize());
        qualScores_->setScores(quality);
      }

      const std::vector<int>& getQualities() const {
        return qualScores_->getScores();
      }

      void append(const std::vector<int>& content)
        throw (BadIntException)
      {
        SequenceWithAnnotation::append(content);
      }

      void append(
          const std::vector<int>& content,
          const std::vector<int>& qualities)
        throw (BadIntException, DimensionException)
      {
        if (content.size() != qualities.size())
          throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size());
        size_t pos = qualScores_->getSize();
        append(content); //This automatically extend scores array with default values through the listener
        //Update scores:
        qualScores_->setScores(pos, qualities);
      }

      void append(const std::vector<std::string>& content)
        throw (BadCharException)
      {
        SequenceWithAnnotation::append(content);
      }

      void append(
          const std::vector<std::string>& content,
          const std::vector<int>& qualities)
        throw (BadCharException, DimensionException)
      {
        if (content.size() != qualities.size())
          throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size());
        size_t pos = qualScores_->getSize();
        SequenceWithAnnotation::append(content); //This automatically extend scores array with default values through the listener
        //Update scores:
        qualScores_->setScores(pos, qualities);
      }

      void append(const std::string& content)
        throw (BadCharException)
      {
        SequenceWithAnnotation::append(content);
      }

      void append(
          const std::string& content,
          const std::vector<int>& qualities)
        throw (BadCharException, DimensionException)
      {
        if (content.size() / this->getAlphabet()->getStateCodingSize()
            != qualities.size())
          throw DimensionException("SequenceWithQuality::append: qualities must fit content size", qualities.size(), content.size() / this->getAlphabet()->getStateCodingSize());
        size_t pos = qualScores_->getSize();
        SequenceWithAnnotation::append(content); //This automatically extend scores array with default values through the listener
        //Update scores:
        qualScores_->setScores(pos, qualities);
      }

      void addElement(
          const std::string& c)
        throw (BadCharException)
      {
        SequenceWithAnnotation::addElement(c);
      }

      void addElement(
          const std::string& c, int q)
        throw (BadCharException)
      {
        SequenceWithAnnotation::addElement(c);
        qualScores_->setScore(size() - 1, q);
      }

      void addElement(size_t pos, const std::string& c)
        throw (BadCharException, IndexOutOfBoundsException)
      {
        SequenceWithAnnotation::addElement(pos, c);
      }

      void addElement(
          size_t pos, const std::string& c, int q)
        throw (BadCharException, IndexOutOfBoundsException)
      {
        SequenceWithAnnotation::addElement(pos, c);
        qualScores_->setScore(pos, q);
      }

      void addElement(int v)
        throw (BadIntException)
      {
        SequenceWithAnnotation::addElement(v);
      }

      void addElement(int v, int q)
        throw (BadIntException)
      {
        SequenceWithAnnotation::addElement(v);
        qualScores_->setScore(size() - 1, q);
      }

      void addElement(size_t pos, int v)
        throw (BadIntException, IndexOutOfBoundsException)
      {
        SequenceWithAnnotation::addElement(pos, v);
      }

      void addElement(size_t pos, int v, int q)
        throw (BadCharException, IndexOutOfBoundsException)
      {
        SequenceWithAnnotation::addElement(pos, v);
        qualScores_->setScore(pos, q);
      }

  };

} // end of namespace bpp.

#endif // _SEQUENCEWITHQUALITY_H_