BigString.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg$
// $Authors: Andreas Bertsch$
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#ifndef OPENMS_DATASTRUCTURES_BIGSTRING_H
#define OPENMS_DATASTRUCTURES_BIGSTRING_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/OpenMSConfig.h>

#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI BigString
  {

public:

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

    BigString();

    BigString(const BigString& bs);

    virtual ~BigString();

    void add(FASTAEntry const& new_entry);

    void setSeparator(const char sep);

    char getSeparator();

    Size size();

    Size length();

    void getPeptide(FASTAEntry& entry, Size start, Size length);

    const String& getBigString() const;

protected:

    Size getIndex_(Size index, Size start, Size end);

    Size getIndex_(Size index);

    String big_string_; 

    char separator_; 

    Size count_; 

    Size len_; 

    std::vector<Size> sep_indices_; 

    std::vector<String> FASTA_header_; 

  };
}
#endif // OPENMS_DATASTRUCTURES_BIGSTRING_H