OpenMS  3.0.0
ToolDescription.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 2002-2022.
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: Chris Bielow $
32 // $Authors: Chris Bielow, Mathias Walzer $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
40 
41 #include <OpenMS/OpenMSConfig.h>
42 
43 #include <map>
44 
45 namespace OpenMS
46 {
47  namespace Internal
48  {
53  struct FileMapping
54  {
57  // thus: move location -> target
58 
60  FileMapping() = default;
61 
63  FileMapping(const FileMapping& other) = default;
64 
66  FileMapping& operator=(const FileMapping& rhs) = default;
67  };
68 
73  struct MappingParam
74  {
75  std::map<Int, String> mapping;
76  std::vector<FileMapping> pre_moves;
77  std::vector<FileMapping> post_moves;
78 
80  MappingParam() = default;
81 
83  MappingParam(const MappingParam& other) = default;
84 
86  MappingParam& operator=(const MappingParam& other) = default;
87  };
88 
96  struct OPENMS_DLLAPI ToolDescriptionInternal
97  {
98  bool is_internal = false;
102 
104  ToolDescriptionInternal() = default;
105 
107  ToolDescriptionInternal(const bool p_is_internal, const String& p_name, const String& p_category, const StringList& p_types);
108 
110  ToolDescriptionInternal(const String& p_name, const StringList& p_types);
111 
113  ToolDescriptionInternal& operator=(const ToolDescriptionInternal& rhs) = default;
114 
115  bool operator==(const ToolDescriptionInternal& rhs) const;
116 
117  bool operator<(const ToolDescriptionInternal& rhs) const;
118  };
119 
120  struct OPENMS_DLLAPI ToolExternalDetails
121  {
131  };
132 
136  struct OPENMS_DLLAPI ToolDescription :
138  {
140  std::vector<ToolExternalDetails> external_details;
141 
143  ToolDescription() = default;
144 
146  ToolDescription(const ToolDescription& other) = default;
147 
149  ToolDescription(const String& p_name, const String& p_category, const StringList& p_types = StringList());
150 
152  ToolDescription& operator=(const ToolDescription& rhs) = default;
153 
154  void addExternalType(const String& type, const ToolExternalDetails& details);
155 
156  void append(const ToolDescription& other);
157  };
158  } // namespace Internal
159 } // namespace OPENMS
OpenMS::Internal::MappingParam::operator=
MappingParam & operator=(const MappingParam &other)=default
Copy assignment.
OpenMS::Internal::ToolExternalDetails::param
Param param
Definition: ToolDescription.h:130
OpenMS::Internal::FileMapping::operator=
FileMapping & operator=(const FileMapping &rhs)=default
Copy assignment.
OpenMS::Internal::ToolExternalDetails
Definition: ToolDescription.h:120
OpenMS::Internal::MappingParam::pre_moves
std::vector< FileMapping > pre_moves
Definition: ToolDescription.h:76
OpenMS::Internal::FileMapping
Maps input/output files to filenames for the external program.
Definition: ToolDescription.h:53
OpenMS::Internal::FileMapping::FileMapping
FileMapping()=default
Default constructor.
OpenMS::Internal::ToolDescriptionInternal::types
StringList types
-types of the tool (if any, e.g. ['centroided','wavelet'])
Definition: ToolDescription.h:101
OpenMS::Internal::ToolExternalDetails::text_fail
String text_fail
Definition: ToolDescription.h:123
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::ToolDescriptionInternal
ToolDescription Class.
Definition: ToolDescription.h:96
OpenMS::Internal::MappingParam
Filename mappings for all input/output files.
Definition: ToolDescription.h:73
OpenMS::Internal::ToolExternalDetails::path
String path
filename to external tool
Definition: ToolDescription.h:127
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::Internal::ToolDescriptionInternal::name
String name
Definition: ToolDescription.h:99
ListUtils.h
OpenMS::Internal::FileMapping::location
String location
a regex/macro mix; to be expanded by tool;
Definition: ToolDescription.h:55
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::MappingParam::MappingParam
MappingParam()=default
Default constructor.
OpenMS::Internal::ToolExternalDetails::text_finish
String text_finish
Definition: ToolDescription.h:124
OpenMS::Internal::ToolDescription::external_details
std::vector< ToolExternalDetails > external_details
additional details for external tools (one entry for each 'type')
Definition: ToolDescription.h:140
OpenMS::Internal::FileMapping::target
String target
TOPP parameter that determines the desired name.
Definition: ToolDescription.h:56
OpenMS::Internal::ToolDescriptionInternal::category
String category
Definition: ToolDescription.h:100
OpenMS::Internal::ToolExternalDetails::tr_table
MappingParam tr_table
Definition: ToolDescription.h:129
Param.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::StringConversions::append
void append(const T &i, String &target)
Definition: StringConversions.h:118
OpenMS::Internal::MappingParam::mapping
std::map< Int, String > mapping
Definition: ToolDescription.h:75
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::Internal::ToolDescription
Definition: ToolDescription.h:136
String.h
OpenMS::Internal::ToolExternalDetails::commandline
String commandline
Definition: ToolDescription.h:126
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::Internal::ToolExternalDetails::text_startup
String text_startup
Definition: ToolDescription.h:122
OpenMS::Internal::ToolExternalDetails::working_directory
String working_directory
folder where the command will be executed from
Definition: ToolDescription.h:128
OpenMS::Internal::ToolExternalDetails::category
String category
Definition: ToolDescription.h:125
OpenMS::Internal::MappingParam::post_moves
std::vector< FileMapping > post_moves
Definition: ToolDescription.h:77