OpenMS  2.8.0
ToolDescription.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow, Mathias Walzer $
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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 
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 
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
Management and storage of parameters / INI files.
Definition: Param.h:70
A more convenient string class.
Definition: String.h:60
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
String commandline
Definition: ToolDescription.h:126
String text_startup
Definition: ToolDescription.h:122
String category
Definition: ToolDescription.h:125
String text_finish
Definition: ToolDescription.h:124
String text_fail
Definition: ToolDescription.h:123
String working_directory
folder where the command will be executed from
Definition: ToolDescription.h:128
Param param
Definition: ToolDescription.h:130
String path
filename to external tool
Definition: ToolDescription.h:127
MappingParam tr_table
Definition: ToolDescription.h:129
Definition: ToolDescription.h:121
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Maps input/output files to filenames for the external program.
Definition: ToolDescription.h:54
FileMapping(const FileMapping &other)=default
Copy constructor.
String location
a regex/macro mix; to be expanded by tool;
Definition: ToolDescription.h:55
String target
TOPP parameter that determines the desired name.
Definition: ToolDescription.h:56
FileMapping()=default
Default constructor.
FileMapping & operator=(const FileMapping &rhs)=default
Copy assignment.
Filename mappings for all input/output files.
Definition: ToolDescription.h:74
MappingParam & operator=(const MappingParam &other)=default
Copy assignment.
std::vector< FileMapping > post_moves
Definition: ToolDescription.h:77
MappingParam(const MappingParam &other)=default
Copy constructor.
std::map< Int, String > mapping
Definition: ToolDescription.h:75
MappingParam()=default
Default constructor.
std::vector< FileMapping > pre_moves
Definition: ToolDescription.h:76
ToolDescription Class.
Definition: ToolDescription.h:97
ToolDescriptionInternal()=default
default C'Tor
String category
Definition: ToolDescription.h:100
ToolDescriptionInternal & operator=(const ToolDescriptionInternal &rhs)=default
Copy assignment.
bool operator<(const ToolDescriptionInternal &rhs) const
StringList types
-types of the tool (if any, e.g. ['centroided','wavelet'])
Definition: ToolDescription.h:101
String name
Definition: ToolDescription.h:99
ToolDescriptionInternal(const String &p_name, const StringList &p_types)
short C'Tor
ToolDescriptionInternal(const bool p_is_internal, const String &p_name, const String &p_category, const StringList &p_types)
C'Tor with arguments.
bool operator==(const ToolDescriptionInternal &rhs) const
Definition: ToolDescription.h:138
ToolDescription()=default
default CTor
ToolDescription & operator=(const ToolDescription &rhs)=default
Copy assignment.
void append(const ToolDescription &other)
std::vector< ToolExternalDetails > external_details
additional details for external tools (one entry for each 'type')
Definition: ToolDescription.h:140
void addExternalType(const String &type, const ToolExternalDetails &details)
ToolDescription(const String &p_name, const String &p_category, const StringList &p_types=StringList())
C'Tor for internal TOPP tools.
ToolDescription(const ToolDescription &other)=default
Copy C'Tor.