MultiplexDeltaMassesGenerator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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.
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//    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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexDeltaMasses.h>
 
#include <vector>
#include <algorithm>
#include <iosfwd>
 
 
namespace OpenMS
{
  class OPENMS_DLLAPI MultiplexDeltaMassesGenerator :
    public DefaultParamHandler
  {
    public:
 
    struct OPENMS_DLLAPI Label
    {
      String short_name;
      String long_name;
      String description;
      double delta_mass;
      
      Label(String sn, String ln, String d, double dm);
    };
   
    MultiplexDeltaMassesGenerator();
    
    MultiplexDeltaMassesGenerator(String labels, int missed_cleavages, std::map<String,double> label_mass_shift);
     
    void generateKnockoutDeltaMasses();
 
    void printSamplesLabelsList(std::ostream &stream) const;
    
    void printDeltaMassesList(std::ostream &stream) const;
    
    std::vector<MultiplexDeltaMasses> getDeltaMassesList();
    
    const std::vector<MultiplexDeltaMasses>& getDeltaMassesList() const;
    
    std::vector<std::vector<String> > getSamplesLabelsList();
    
    const std::vector<std::vector<String> >& getSamplesLabelsList() const;
    
    String getLabelShort(const String& label);
    
    String getLabelLong(const String& label);
    
    MultiplexDeltaMasses::LabelSet extractLabelSet(const AASequence& sequence);
    
    private:
   
    String labels_;
    
    std::vector<String> labels_list_;
    
    std::vector<std::vector<String> > samples_labels_;
    
    int missed_cleavages_;
 
    std::vector<MultiplexDeltaMasses> delta_masses_list_;
      
    std::vector<Label> label_master_list_;
    
    std::map<String, double> label_delta_mass_;
    
    std::map<String, String> label_short_long_;
    
    std::map<String, String> label_long_short_;
    
    void fillLabelMasterList_();
 };
  
}