OpenMS
ExperimentalDesignFile.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Lukas Zimmermann $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 #include <map>
40 #include <set>
41 
42 namespace OpenMS
43 {
44  class ExperimentalDesign;
45  class TextFile;
52  class OPENMS_DLLAPI ExperimentalDesignFile
53  {
54  public:
55 
57  static ExperimentalDesign load(const String& tsv_file, bool require_spectra_files);
58 
60  static ExperimentalDesign load(const TextFile& text_file, const bool require_spectra_file, String filename);
61 
62  private:
63  static bool isOneTableFile_(const TextFile& text_file);
64  static ExperimentalDesign parseOneTableFile_(const TextFile& text_file, const String& tsv_file, bool require_spectra_file);
65  static ExperimentalDesign parseTwoTableFile_(const TextFile& text_file, const String& tsv_file, bool require_spectra_file);
68  static void parseHeader_(
69  const StringList &header,
70  const String &filename,
71  std::map <String, Size> &column_map,
72  const std::set <String> &required,
73  const std::set <String> &optional,
74  bool allow_other_header);
75 
77  static void parseErrorIf_(const bool test, const String &filename, const String &message);
78  };
79 }
80 
Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported for...
Definition: ExperimentalDesignFile.h:53
static ExperimentalDesign load(const String &tsv_file, bool require_spectra_files)
Loads an experimental design from a tabular separated file.
static ExperimentalDesign load(const TextFile &text_file, const bool require_spectra_file, String filename)
Loads an experimental design from an already loaded or generated, tabular file.
static void parseHeader_(const StringList &header, const String &filename, std::map< String, Size > &column_map, const std::set< String > &required, const std::set< String > &optional, bool allow_other_header)
static void parseErrorIf_(const bool test, const String &filename, const String &message)
static ExperimentalDesign parseTwoTableFile_(const TextFile &text_file, const String &tsv_file, bool require_spectra_file)
static bool isOneTableFile_(const TextFile &text_file)
static ExperimentalDesign parseOneTableFile_(const TextFile &text_file, const String &tsv_file, bool require_spectra_file)
Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesi...
Definition: ExperimentalDesign.h:245
A more convenient string class.
Definition: String.h:60
This class provides some basic file handling methods for text files.
Definition: TextFile.h:47
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
bool test
Status of the current subsection.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48