SuffixArrayPeptideFinder.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: Chris Bauer $
// --------------------------------------------------------------------------


#ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
#define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H

#include <vector>
#include <OpenMS/DATASTRUCTURES/BigString.h>
#include <OpenMS/CHEMISTRY/WeightWrapper.h>

namespace OpenMS
{
  class String;
  class SuffixArray;
  class OPENMS_DLLAPI SuffixArrayPeptideFinder :
    public WeightWrapper
  {

public:

    typedef std::pair<String, String> FASTAEntry;

    SuffixArrayPeptideFinder(const String & filename, const String & method, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);

    SuffixArrayPeptideFinder(const SuffixArrayPeptideFinder & source);

    virtual ~SuffixArrayPeptideFinder();

    void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates, const std::vector<DoubleReal> & spec);

    void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates, const String & DTA_file);

    void setTolerance(const DoubleReal t);

    DoubleReal getTolerance() const;

    void setNumberOfModifications(Size number_of_mods) const;

    Size getNumberOfModifications() const;

    void setTags(const std::vector<String> & tags);

    const std::vector<String> & getTags();

    void setUseTags(bool use_tags);

    bool getUseTags();

    void setModificationOutputMethod(const String & s);

    String getModificationOutputMethod();

protected:

    String vToString_(std::vector<String> v);

    BigString big_string_;  

    SuffixArray * sa_;   

    String modification_output_method_; 

  };

}

#endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H