SuffixArrayTrypticCompressed.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: Chris Bauer $
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#ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
#define OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/SuffixArray.h>
#include <OpenMS/CHEMISTRY/WeightWrapper.h>

namespace OpenMS
{
  class String;

  class OPENMS_DLLAPI SuffixArrayTrypticCompressed :
    public SuffixArray
    , public WeightWrapper
  {

public:

    SuffixArrayTrypticCompressed(const String & st, const String & filename, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);

    SuffixArrayTrypticCompressed(const SuffixArrayTrypticCompressed & sa);

    virtual ~SuffixArrayTrypticCompressed();

    String toString();

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

    bool save(const String & file_name);
    bool open(const String & file_name);

    void setTolerance(DoubleReal t);

    DoubleReal getTolerance() const;

    bool isDigestingEnd(const char aa1, const char aa2) const;

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

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

    void setUseTags(bool use_tags);

    bool getUseTags();

    void setNumberOfModifications(Size number_of_mods);

    Size getNumberOfModifications();

    void printStatistic();

protected:

    SuffixArrayTrypticCompressed();

    SignedSize getNextSep_(const SignedSize p) const;

    SignedSize getLCP_(const std::pair<SignedSize, SignedSize> & last_point, const std::pair<SignedSize, SignedSize> & current_point);

    SignedSize findFirst_(const std::vector<DoubleReal> & spec, DoubleReal & m);

    SignedSize findFirst_(const std::vector<DoubleReal> & spec, DoubleReal & m, SignedSize start, SignedSize end);

    void parseTree_(SignedSize start_index, SignedSize stop_index, SignedSize depth, SignedSize walked_in, SignedSize edge_len, std::vector<std::pair<SignedSize, SignedSize> > & out_number, std::vector<std::pair<SignedSize, SignedSize> > & edge_length, std::vector<SignedSize> & leafe_depth);

    bool hasMoreOutgoings_(SignedSize start_index, SignedSize stop_index, SignedSize walked_in);

    const String & s_; 

    DoubleReal tol_; 

    std::vector<std::pair<SignedSize, SignedSize> > indices_; 

    std::vector<SignedSize> lcp_; 

    std::vector<SignedSize> skip_; 

    //const SignedSize getIndex_ (const String & s);

    DoubleReal masse_[256]; 

    Size number_of_modifications_; 

    std::vector<String> tags_; 

    bool use_tags_;  

    SignedSize progress_;
  };
}

#endif //OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H