TargetedExperimentHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/Macros.h>

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/METADATA/CVTerm.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/METADATA/CVTermListInterface.h>
#include <OpenMS/CHEMISTRY/Residue.h>

#include <boost/numeric/conversion/cast.hpp>

namespace OpenMS
{
  namespace TargetedExperimentHelper
  {

    struct Configuration :
      public CVTermList
    {
      String contact_ref;
      String instrument_ref;
      std::vector<CVTermList> validations;

      Configuration & operator=(const Configuration & rhs)
      {
        if (this != &rhs)
        {
          CVTermList::operator=(rhs);
          contact_ref = rhs.contact_ref;
          instrument_ref = rhs.instrument_ref;
          validations = rhs.validations;
        }
        return *this;
      }

    };

    struct CV
    {
      CV(const String & new_id, const String & new_fullname, const String & new_version, const String & new_URI) :
        id(new_id),
        fullname(new_fullname),
        version(new_version),
        URI(new_URI)
      {

      }

      String id;
      String fullname;
      String version;
      String URI;

      bool operator==(const CV & cv) const
      {
        return id == cv.id &&
               fullname == cv.fullname &&
               version == cv.version &&
               URI == cv.URI;
      }

    };

    struct Protein :
      public CVTermList
    {
      Protein() :
        CVTermList()
      {
      }

      String id;
      String sequence;

      bool operator==(const Protein & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               id == rhs.id &&
               sequence == rhs.sequence;
      }

      Protein & operator=(const Protein & rhs)
      {
        if (&rhs != this)
        {
          CVTermList::operator=(rhs);
          id = rhs.id;
          sequence = rhs.sequence;
        }
        return *this;
      }

    };

    class OPENMS_DLLAPI RetentionTime :
      public CVTermListInterface
    {
public:

      enum class RTUnit : std::int8_t
      {
        SECOND = 0,        // RT stored in seconds
        MINUTE,            // RT stored in minutes
        UNKNOWN,           // no stored annotation
        SIZE_OF_RTUNIT
      };

      enum class RTType : std::int8_t
      {
        LOCAL = 0,        // undefined local chromatography
        NORMALIZED,       // standardized reference chromatography
        PREDICTED,        // predicted by referenced software
        HPINS,            // H-PINS "The de facto standard providing the retention times"
        IRT,              // iRT retention time standard
        UNKNOWN,          // no stored annotation
        SIZE_OF_RTTYPE
      };

      RetentionTime() :
        CVTermListInterface(),
        software_ref(""),
        retention_time_unit(RTUnit::SIZE_OF_RTUNIT),
        retention_time_type(RTType::SIZE_OF_RTTYPE),
        retention_time_set_(false),
        retention_time_(0.0)
        // retention_time_width(0.0),
        // retention_time_lower(0.0),
        // retention_time_upper(0.0)
      {
      }

      RetentionTime(const RetentionTime & rhs) :
        CVTermListInterface(rhs),
        software_ref(rhs.software_ref),
        retention_time_unit(rhs.retention_time_unit),
        retention_time_type(rhs.retention_time_type),
        retention_time_set_(rhs.retention_time_set_),
        retention_time_(rhs.retention_time_)
      {
      }

      virtual ~RetentionTime()
      {
      }

      RetentionTime & operator=(const RetentionTime & rhs)
      {
        if (&rhs != this)
        {
          CVTermListInterface::operator=(rhs);
          software_ref = rhs.software_ref;
          retention_time_unit = rhs.retention_time_unit;
          retention_time_type = rhs.retention_time_type;
          retention_time_set_ = rhs.retention_time_set_;
          retention_time_ = rhs.retention_time_;
        }
        return *this;
      }

      bool operator==(const RetentionTime & rhs) const
      {
        return CVTermListInterface::operator==(rhs) &&
               software_ref == rhs.software_ref &&
               retention_time_unit == rhs.retention_time_unit &&
               retention_time_type == rhs.retention_time_type &&
               retention_time_set_ == rhs.retention_time_set_ &&
               retention_time_ == rhs.retention_time_;
      }

      bool isRTset() const 
      {
        return retention_time_set_;
      }
      void setRT(double rt)
      {
        retention_time_ = rt;
        retention_time_set_ = true;
      }
      double getRT() const
      {
        OPENMS_PRECONDITION(isRTset(), "RT needs to be set")
        return retention_time_;
      }

      String software_ref;
      RTUnit retention_time_unit;
      RTType retention_time_type;

private:

      bool retention_time_set_;
      double retention_time_;
      // double retention_time_width;
      // double retention_time_lower;
      // double retention_time_upper;
    };

    class OPENMS_DLLAPI PeptideCompound :
      public CVTermList
    {
public:

      PeptideCompound() :
        CVTermList(),
        charge_(0),
        charge_set_(false),
        drift_time_(-1)
      {
      }

      PeptideCompound(const PeptideCompound & rhs) :
        CVTermList(rhs),
        id(rhs.id),
        rts(rhs.rts),
        charge_(rhs.charge_),
        charge_set_(rhs.charge_set_),
        drift_time_(rhs.drift_time_)
      {
      }

      PeptideCompound & operator=(const PeptideCompound & rhs)
      {
        if (this != &rhs)
        {
          CVTermList::operator=(rhs);
          rts = rhs.rts;
          id = rhs.id;
          charge_ = rhs.charge_;
          charge_set_ = rhs.charge_set_;
          drift_time_ = rhs.drift_time_;
        }
        return *this;
      }

      bool operator==(const PeptideCompound & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               rts == rhs.rts &&
               id == rhs.id &&
               charge_ == rhs.charge_ &&
               charge_set_ == rhs.charge_set_;
      }

      void setChargeState(int charge)
      {
        charge_ = charge;
        charge_set_ = true;
      }

      bool hasCharge() const
      {
        return charge_set_;
      }

      int getChargeState() const
      {
        OPENMS_PRECONDITION(charge_set_, "Cannot return charge which was never set")
        return charge_;
      }

      void setDriftTime(double dt)
      {
        drift_time_ = dt;
      }

      double getDriftTime() const
      {
        return drift_time_;
      }


      bool hasRetentionTime() const
      {
        return (!rts.empty() && rts[0].isRTset());
      }

      double getRetentionTime() const
      {
        if (!hasRetentionTime())
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
              "No retention time information available");
        }
        return rts[0].getRT();
      }

      RetentionTime::RTType getRetentionTimeType() const
      {
        if (!hasRetentionTime())
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
              "No retention time information available");
        }
        return rts[0].retention_time_type;
      }

      RetentionTime::RTUnit getRetentionTimeUnit() const
      {
        if (!hasRetentionTime())
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
              "No retention time information available");
        }
        return rts[0].retention_time_unit;
      }

      String id;
      std::vector<RetentionTime> rts;

protected:
      int charge_;
      bool charge_set_;
      double drift_time_;

    };

    class OPENMS_DLLAPI Compound :
      public PeptideCompound
    {
public:

      Compound() :
        theoretical_mass(0.0)
      {
      }

      Compound(const Compound & rhs) :
        PeptideCompound(rhs),
        molecular_formula(rhs.molecular_formula),
        smiles_string(rhs.smiles_string),
        theoretical_mass(rhs.theoretical_mass)
      {
      }

      Compound & operator=(const Compound & rhs)
      {
        if (this != &rhs)
        {
          PeptideCompound::operator=(rhs);
          molecular_formula = rhs.molecular_formula;
          smiles_string = rhs.smiles_string;
          theoretical_mass = rhs.theoretical_mass;
        }
        return *this;
      }

      bool operator==(const Compound & rhs) const
      {
        return PeptideCompound::operator==(rhs) &&
               molecular_formula == rhs.molecular_formula &&
               smiles_string == rhs.smiles_string &&
               theoretical_mass == rhs.theoretical_mass;
      }

      String molecular_formula;
      String smiles_string;
      double theoretical_mass;

protected:

    };

    class OPENMS_DLLAPI Peptide :
      public PeptideCompound
    {
public:

      struct Modification :
        public CVTermListInterface
      {
        double avg_mass_delta;
        double mono_mass_delta;
        Int32 location;
        Int32 unimod_id;

        Modification() :
          CVTermListInterface(),
          location(-1),
          unimod_id(-1)
        {
        }

      };

      Peptide() :
        PeptideCompound()
      {
      }

      Peptide(const Peptide & rhs) :
        PeptideCompound(rhs),
        protein_refs(rhs.protein_refs),
        evidence(rhs.evidence),
        sequence(rhs.sequence),
        mods(rhs.mods),
        peptide_group_label_(rhs.peptide_group_label_)
      {
      }

      Peptide & operator=(const Peptide & rhs)
      {
        if (this != &rhs)
        {
          PeptideCompound::operator=(rhs);
          protein_refs = rhs.protein_refs;
          evidence = rhs.evidence;
          sequence = rhs.sequence;
          mods = rhs.mods;
          peptide_group_label_ = rhs.peptide_group_label_;
        }
        return *this;
      }

      bool operator==(const Peptide & rhs) const
      {
        return PeptideCompound::operator==(rhs) &&
               protein_refs == rhs.protein_refs &&
               evidence == rhs.evidence &&
               sequence == rhs.sequence &&
               mods == rhs.mods &&
               peptide_group_label_ == rhs.peptide_group_label_;
      }

      void setPeptideGroupLabel(const String & label)
      {
        peptide_group_label_ = label;
      }

      String getPeptideGroupLabel() const
      {
        return peptide_group_label_;
      }

      std::vector<String> protein_refs;
      CVTermList evidence;
      String sequence;
      std::vector<Modification> mods;

protected:
      String peptide_group_label_;
    };

    struct OPENMS_DLLAPI Contact :
      public CVTermList
    {
      Contact() :
        CVTermList()
      {
      }

      String id;

      bool operator==(const Contact & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               id == rhs.id;
      }

      Contact & operator=(const Contact & rhs)
      {
        if (&rhs != this)
        {
          CVTermList::operator=(rhs);
          id = rhs.id;
        }
        return *this;
      }

    };

    struct OPENMS_DLLAPI Publication :
      public CVTermList
    {
      Publication() :
        CVTermList()
      {
      }

      String id;

      bool operator==(const Publication & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               id == rhs.id;
      }

      Publication & operator=(const Publication & rhs)
      {
        if (&rhs != this)
        {
          CVTermList::operator=(rhs);
          id = rhs.id;
        }
        return *this;
      }

    };

    struct OPENMS_DLLAPI Instrument :
      public CVTermList
    {
      Instrument() :
        CVTermList()
      {
      }

      String id;

      bool operator==(const Instrument & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               id == rhs.id;
      }

      Instrument & operator=(const Instrument & rhs)
      {
        if (&rhs != this)
        {
          CVTermList::operator=(rhs);
          id = rhs.id;
        }
        return *this;
      }

    };

    struct OPENMS_DLLAPI Prediction :
      public CVTermList
    {
      Prediction() :
        CVTermList()
      {
      }

      String software_ref;
      String contact_ref;

      bool operator==(const Prediction & rhs) const
      {
        return CVTermList::operator==(rhs) &&
               contact_ref == rhs.contact_ref &&
               software_ref == rhs.software_ref;
      }

      Prediction & operator=(const Prediction & rhs)
      {
        if (&rhs != this)
        {
          CVTermList::operator=(rhs);
          software_ref = rhs.software_ref;
          contact_ref = rhs.contact_ref;
        }
        return *this;
      }

    };

    struct OPENMS_DLLAPI Interpretation :
      public CVTermListInterface
    {

      /*
      enum ResidueType
      {
        Full = 0,       // with N-terminus and C-terminus
        Internal,       // internal, without any termini
        NTerminal,      // only N-terminus
        CTerminal,      // only C-terminus
        AIon,           // MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond
        BIon,           // MS:1001224 N-terminus up to the peptide bond
        CIon,           // MS:1001231 N-terminus up to the amide/C-alpha bond
        XIon,           // MS:1001228 amide/C-alpha bond up to the C-terminus
        YIon,           // MS:1001220 peptide bond up to the C-terminus
        ZIon,           // MS:1001230 C-alpha/carbonyl carbon bond
        Precursor,      // MS:1001523 Precursor ion
        BIonMinusH20,   // MS:1001222 b ion without water
        YIonMinusH20,   // MS:1001223 y ion without water
        BIonMinusNH3,   // MS:1001232 b ion without ammonia
        YIonMinusNH3,   // MS:1001233 y ion without ammonia
        NonIdentified,  // MS:1001240 Non-identified ion
        Unannotated,    // no stored annotation
        SizeOfResidueType
      };
      */

      typedef Residue::ResidueType IonType; // Interpretation IonType

      unsigned char ordinal; // MS:1000903 (product ion series ordinal)
      unsigned char rank; // MS:1000926 (product interpretation rank)
      IonType iontype; // which type of ion (b/y/z/ ...), see Residue::ResidueType

      // Constructor
      Interpretation() :
        CVTermListInterface(),
        ordinal(0),
        rank(0),
        iontype(Residue::Unannotated) // Unannotated does not imply any MS OBO term
      {
      }

      // Copy constructor
      Interpretation(const Interpretation & rhs) :
        CVTermListInterface(rhs),
        ordinal(rhs.ordinal),
        rank(rhs.rank),
        iontype(rhs.iontype)
      {
      }

      bool operator==(const Interpretation & rhs) const
      {
        return CVTermListInterface::operator==(rhs) &&
               ordinal == rhs.ordinal &&
               rank == rhs.rank &&
               iontype == rhs.iontype;
      }

      Interpretation & operator=(const Interpretation & rhs)
      {
        if (&rhs != this)
        {
          CVTermListInterface::operator=(rhs);
          ordinal = rhs.ordinal;
          rank = rhs.rank;
          iontype = rhs.iontype;
        }
        return *this;
      }

      bool operator!=(const Interpretation & rhs) const
      {
        return !(operator==(rhs));
      }

    };

    struct OPENMS_DLLAPI TraMLProduct :
      public CVTermListInterface
    {
      TraMLProduct() :
        CVTermListInterface(),
        charge_(0),
        charge_set_(false),
        mz_(0)
      {
      }

      bool operator==(const TraMLProduct & rhs) const
      {
        return CVTermListInterface::operator==(rhs) &&
               charge_ == rhs.charge_ &&
               charge_set_ == rhs.charge_set_ &&
               mz_ == rhs.mz_ &&
               configuration_list_ == rhs.configuration_list_ &&
               interpretation_list_ == rhs.interpretation_list_;
      }

      TraMLProduct & operator=(const TraMLProduct & rhs)
      {
        if (&rhs != this)
        {
          CVTermListInterface::operator=(rhs);
          charge_ = rhs.charge_;
          charge_set_ = rhs.charge_set_;
          mz_ = rhs.mz_;
          configuration_list_ = rhs.configuration_list_;
          interpretation_list_ = rhs.interpretation_list_;
        }
        return *this;
      }

      void setChargeState(int charge)
      {
        charge_ = charge;
        charge_set_ = true;
      }

      bool hasCharge() const
      {
        return charge_set_;
      }

      int getChargeState() const
      {
        OPENMS_PRECONDITION(charge_set_, "Cannot return charge which was never set")
        return charge_;
      }

      double getMZ() const
      {
        return mz_;
      }

      void setMZ(double mz)
      {
        mz_ = mz;
      }

      const std::vector<Configuration> & getConfigurationList() const
      {
        return configuration_list_;
      }

      void addConfiguration(const Configuration configuration)
      {
        return configuration_list_.push_back(configuration);
      }

      const std::vector<Interpretation> & getInterpretationList() const
      {
        return interpretation_list_;
      }

      void addInterpretation(const Interpretation interpretation)
      {
        return interpretation_list_.push_back(interpretation);
      }

      void resetInterpretations()
      {
        return interpretation_list_.clear();
      }

private:
      int charge_;
      bool charge_set_;
      double mz_;
      std::vector<Configuration> configuration_list_;
      std::vector<Interpretation> interpretation_list_;

    };

    OPENMS_DLLAPI OpenMS::AASequence getAASequence(const Peptide& peptide);

    OPENMS_DLLAPI void setModification(int location, int max_size, String modification, OpenMS::AASequence & aas);

  }

} // namespace OpenMS