libopenms-dev 1.11.1-3 / usr / include / OpenMS / CHEMISTRY / EdwardsLippertIterator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: $
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#ifndef OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
#define OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H

#include <OpenMS/CHEMISTRY/PepIterator.h>

namespace OpenMS
{

  /**
  @brief finds all Peptide Candidates with given masses and given fasta file

  The used algorithm was described by Edwards and Lippert. The algorithm uses two pointers to iterator over a sequence. One pointer represents the start the other the end.
  */
  class OPENMS_DLLAPI EdwardsLippertIterator :
    public PepIterator
  {

public:

    typedef std::pair<String, String> FASTAEntry;
    /**
    @brief Constructor
    */
    EdwardsLippertIterator();
    /**
    @brief Copy Constructor
    */
    EdwardsLippertIterator(const EdwardsLippertIterator &);
    /**
    @brief Destructor
    */
    virtual ~EdwardsLippertIterator();

    /**
    @brief * operator for getting the value of the iterator
    @return FASTAEntry with specific candidate
    @throw InvalidIterator if iterator has not been initialized
    */
    virtual FASTAEntry operator*();

    /**
    @brief opperator ++ for postincrement
    @return Reference to PepIterator
    @throw InvalidIterator if iterator has not been initialized
    */
    virtual PepIterator & operator++();

    /**
    @brief opperator ++ for preincrement
    @return pointer to PepIterator
    @throw InvalidIterator if iterator has not been initialized
    */
    virtual PepIterator * operator++(int i);

    /**
    @brief setter for fasta file
    @param f String with fasta file location
    @throw FileNotFound if file could not be found
    */
    virtual void setFastaFile(const String & f);

    /**
    @brief getter for FASTA file
    @return String with file location
    */
    virtual String getFastaFile();

    /**
    @brief setter for tolerance
    @param t tolerance
    @throw InvalidValue if tolerance is negative
    */
    virtual void setTolerance(DoubleReal t);

    /**
    @brief getter for tolerance
    @return tolerance
    */
    virtual DoubleReal getTolerance();

    /**
    @brief setter for spectrum
    @param s spectrum as a vector of DoubleReals
    @throw InvalidValue if spectrum is not sorted
    */
    virtual void setSpectrum(const std::vector<DoubleReal> & s);

    /**
    @brief getter for spectrum
    @return the used spectrum
    */
    virtual const std::vector<DoubleReal> & getSpectrum();

    /**
    @brief initializing iterator
    @return true if everything was ok
    @throw InvalidIterator is thrown if the begin iterator is invalid
    */
    virtual bool begin();

    /**
    @brief indicates whether iterator is at end
    @return true if iterator is at end
    @see hasNext
    */
    virtual bool isAtEnd();

    /**
    @brief indicated if a digesting enzyme will cut at this position
    @return true if digenting enzym cuts the sequence
    */
    virtual bool isDigestingEnd(char, char);

    /**
    @brief needed by Factory
    @return const string name of class
    */
    static const String getProductName()
    {
      return "EdwardsLippertIterator";
    }

    /**
    @brief needed by Factory
    @return poiter to new object
    */
    static PepIterator * create()
    {
      return new EdwardsLippertIterator;
    }

protected:
    /**
    @brief getting the next candidate
    @return string with next sequence
    */
    virtual std::string next_();

    /**
    @brief indicates if there will be a next element
    @return true if iterator has more elements
    */
    bool hasNext_();

    /**
    @brief finds the next starting position where a digesting enzyme will cut the sequence
    */
    void goToNextAA_();

    /**
    @brief indicates if a mass is in spectrum
    @return true if a given mass is in spectrum
    */
    virtual bool isInSpectrum_(DoubleReal & mass);

    String f_file_;         ///< fasta file location

    std::string actual_pep_;         ///< actual peptide

    std::vector<DoubleReal> spec_;         ///< given spectrum

    DoubleReal tol_;         ///< tolerance

    DoubleReal masse_[255];         ///< mass table

    bool is_at_end_;         ///< indicates if iterator is at end

    PepIterator * f_iterator_;         ///< FastaIterator

    FASTAEntry f_entry_;         ///< actual fasta entry

    unsigned int b_, e_;        ///< to ints representing a position within the actual string (b = begin, e = end)

    DoubleReal m_, massMax_;         ///< mass and maximum masse


  };

}
#endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H