SuffixArray.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_SUFFIXARRAY_H
#define OPENMS_DATASTRUCTURES_SUFFIXARRAY_H

#include <vector>
#include <OpenMS/CONCEPT/Exception.h>


namespace OpenMS
{
  class String;

  class OPENMS_DLLAPI SuffixArray
  {

public:

    SuffixArray(const String & st, const String & filename);

    SuffixArray(const SuffixArray & sa);

    virtual ~SuffixArray() = 0;

    virtual String toString() = 0;

    virtual void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>, DoubleReal> > > & candidates, const std::vector<DoubleReal> & spec) = 0;

    virtual bool save(const String & filename) = 0;
    virtual bool open(const String & filename) = 0;

    virtual void setTolerance(DoubleReal t) = 0;

    virtual DoubleReal getTolerance() const  = 0;

    virtual bool isDigestingEnd(const char aa1, const char aa2) const = 0;

    virtual void setTags(const std::vector<String> & tags) = 0;

    virtual const std::vector<String> & getTags() = 0;

    virtual void setUseTags(bool use_tags) = 0;

    virtual bool getUseTags() = 0;

    virtual void setNumberOfModifications(Size number_of_mods) = 0;

    virtual Size getNumberOfModifications() = 0;

    virtual void printStatistic() = 0;

    SuffixArray();


  };
}

#endif //OPENMS_DATASTRUCTURES_SUFARRAY_H