OpenMS
RTAlignment.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Juliane Schmachtenberg, Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/QC/QCBase.h>
12 
13 namespace OpenMS
14 {
15  class FeatureMap;
16  class PeptideIdentification;
17  class TransformationDescription;
18 
27  class OPENMS_DLLAPI RTAlignment : public QCBase
28  {
29  public:
31  RTAlignment() = default;
32 
34  virtual ~RTAlignment() = default;
35 
43  void compute(FeatureMap& fm, const TransformationDescription& trafo) const;
44 
52  void compute(std::vector<PeptideIdentification>& ids, const TransformationDescription& trafo) const;
53 
55  const String& getName() const override;
56 
58  Status requirements() const override;
59 
60  private:
62  const String name_ = "RTAlignment";
63  };
64 } // namespace OpenMS
A container for features.
Definition: FeatureMap.h:80
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:28
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:29
Take the original retention time before map alignment and use the alignment's trafoXML for calculatio...
Definition: RTAlignment.h:28
void compute(std::vector< PeptideIdentification > &ids, const TransformationDescription &trafo) const
Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all Pep...
void compute(FeatureMap &fm, const TransformationDescription &trafo) const
Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all Pep...
const String & getName() const override
returns the name of the metric
Status requirements() const override
define the required input file: featureXML before map alignment (=POSTFDRFEAT), trafoXML after map al...
RTAlignment()=default
Constructor.
virtual ~RTAlignment()=default
Destructor.
A more convenient string class.
Definition: String.h:34
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:37
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22