| OpenMS 2.5.0

ToolDescription.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow, Mathias Walzer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/Param.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39
40 #include <OpenMS/OpenMSConfig.h>
41
42 #include <map>
43
44 namespace OpenMS
45 {
46
47 namespace Internal
48 {
53 struct FileMapping
54 {
55 String location;
56 String target;
57 // thus: move location -> target
58
59 FileMapping& operator=(const FileMapping& rhs);
60 };
61
66 struct MappingParam
67 {
68 std::map<Int, String> mapping;
69 std::vector<FileMapping> pre_moves;
70 std::vector<FileMapping> post_moves;
71
72 OPENMS_DLLAPI MappingParam& operator=(const MappingParam& rhs);
73
74 };
75
83 struct OPENMS_DLLAPI ToolDescriptionInternal
84 {
85 bool is_internal;
86 String name;
87 String category;
88 StringList types;
89
91 ToolDescriptionInternal();
92
94 ToolDescriptionInternal(const bool p_is_internal, const String& p_name, const String& p_category, const StringList& p_types);
95
97 ToolDescriptionInternal(const String& p_name, const StringList& p_types);
98
99 ToolDescriptionInternal& operator=(const ToolDescriptionInternal& rhs);
100
101 bool operator==(const ToolDescriptionInternal& rhs) const;
102
103 bool operator<(const ToolDescriptionInternal& rhs) const;
104 };
105
106 struct OPENMS_DLLAPI ToolExternalDetails
107 {
108 String text_startup;
109 String text_fail;
110 String text_finish;
111 String category;
112 String commandline;
113 String path;
114 String working_directory;
115 MappingParam tr_table;
116 Param param;
117 };
118
122 struct OPENMS_DLLAPI ToolDescription :
123 ToolDescriptionInternal
124 {
126 std::vector<ToolExternalDetails> external_details;
127
129 ToolDescription();
130
132 ToolDescription(const String& p_name, const String& p_category, const StringList& p_types = StringList());
133
134 void addExternalType(const String& type, const ToolExternalDetails& details);
135
136 void append(const ToolDescription& other);
137
138 ToolDescription& operator=(const ToolDescription& rhs);
139 };
140
141 } // namespace Internal
142
143 } // namespace OPENMS
144
OpenMS::Internal::ToolExternalDetails
Definition: ToolDescription.h:106
OpenMS::Internal::ToolExternalDetails::tr_table
MappingParam tr_table
Definition: ToolDescription.h:115
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::Internal::ToolExternalDetails::text_finish
String text_finish
Definition: ToolDescription.h:110
OpenMS::Internal::ToolDescriptionInternal::name
String name
Definition: ToolDescription.h:86
OpenMS::Internal::ToolExternalDetails::text_startup
String text_startup
Definition: ToolDescription.h:108
OpenMS::Internal::ToolExternalDetails::commandline
String commandline
Definition: ToolDescription.h:112
OpenMS::Internal::FileMapping
Maps input/output files to filenames for the external program.
Definition: ToolDescription.h:53
OpenMS::Internal::ToolDescriptionInternal::types
StringList types
-types of the tool (if any, e.g. [&#39;centroided&#39;,&#39;wavelet&#39;])
Definition: ToolDescription.h:88
OpenMS::Internal::FileMapping::operator=
FileMapping & operator=(const FileMapping &rhs)
OpenMS::Internal::ToolDescriptionInternal::is_internal
bool is_internal
Definition: ToolDescription.h:85
OpenMS::Internal::MappingParam::operator=
MappingParam & operator=(const MappingParam &rhs)
String.h
OpenMS::StringConversions::append
void append(const T &i, String &target)
Definition: StringUtils.h:77
OpenMS::Internal::ToolExternalDetails::text_fail
String text_fail
Definition: ToolDescription.h:109
OpenMS::Internal::ToolDescriptionInternal
ToolDescription Class.
Definition: ToolDescription.h:83
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Internal::ToolDescriptionInternal::category
String category
Definition: ToolDescription.h:87
Param.h
OpenMS::Internal::FileMapping::target
String target
TOPP parameter that determines the desired name.
Definition: ToolDescription.h:56
OpenMS::Internal::MappingParam::post_moves
std::vector< FileMapping > post_moves
Definition: ToolDescription.h:70
OpenMS::Internal::ToolDescription
Definition: ToolDescription.h:122
OpenMS::Internal::MappingParam
Filename mappings for all input/output files.
Definition: ToolDescription.h:66
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Internal::FileMapping::location
String location
a regex/macro mix; to be expanded by tool;
Definition: ToolDescription.h:55
OpenMS::Internal::ToolDescription::external_details
std::vector< ToolExternalDetails > external_details
additional details for external tools (one entry for each &#39;type&#39;)
Definition: ToolDescription.h:126
OpenMS::Internal::ToolExternalDetails::working_directory
String working_directory
folder where the command will be executed from
Definition: ToolDescription.h:114
OpenMS::Internal::MappingParam::mapping
std::map< Int, String > mapping
Definition: ToolDescription.h:68
OpenMS::Internal::MappingParam::pre_moves
std::vector< FileMapping > pre_moves
Definition: ToolDescription.h:69
OpenMS::Internal::ToolExternalDetails::param
Param param
Definition: ToolDescription.h:116
OpenMS::Internal::ToolExternalDetails::path
String path
filename to external tool
Definition: ToolDescription.h:113
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::Internal::ToolExternalDetails::category
String category
Definition: ToolDescription.h:111