| OpenMS 2.5.0

FeatureXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
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: Marc Sturm, Chris Bielow, Clemens Groepl $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h>
38 #include <OpenMS/FORMAT/XMLFile.h>
39 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/METADATA/ProteinIdentification.h>
42 #include <OpenMS/METADATA/PeptideIdentification.h>
43 #include <OpenMS/DATASTRUCTURES/ConvexHull2D.h>
44 #include <OpenMS/DATASTRUCTURES/Param.h>
45 #include <OpenMS/DATASTRUCTURES/Map.h>
46
47 #include <iosfwd>
48
49 namespace OpenMS
50 {
51 class Feature;
52 class FeatureMap;
53
68 class OPENMS_DLLAPI FeatureXMLFile :
69 protected Internal::XMLHandler,
70 public Internal::XMLFile,
71 public ProgressLogger
72 {
73
74 public:
75
78 FeatureXMLFile();
81 ~FeatureXMLFile() override;
83
90 void load(const String& filename, FeatureMap& feature_map);
91
92 Size loadSize(const String& filename);
93
99 void store(const String& filename, const FeatureMap& feature_map);
100
102 FeatureFileOptions& getOptions();
103
105 const FeatureFileOptions& getOptions() const;
106
108 void setOptions(const FeatureFileOptions&);
109
110 protected:
111
112 // restore default state for next load/store operation
113 void resetMembers_();
114
115 // Docu in base class
116 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
117
118 // Docu in base class
119 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
120
121 // Docu in base class
122 void characters(const XMLCh* const chars, const XMLSize_t length) override;
123
125 void writeFeature_(const String& filename, std::ostream& os, const Feature& feat, const String& identifier_prefix, UInt64 identifier, UInt indentation_level);
126
128 void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
129
130
136 void updateCurrentFeature_(bool create);
137
141 Int disable_parsing_;
142
144 Feature* current_feature_;
146 FeatureMap* map_;
148 FeatureFileOptions options_;
150 bool size_only_;
152 Size expected_size_;
153
156 Param param_;
157 ConvexHull2D::PointArrayType current_chull_;
158 DPosition<2> hull_position_;
160
162 UInt dim_;
163
165 bool in_description_;
166
168 Int subordinate_feature_level_;
169
171 MetaInfoInterface* last_meta_;
172
174 ProteinIdentification prot_id_;
176 PeptideIdentification pep_id_;
178 ProteinHit prot_hit_;
180 PeptideHit pep_hit_;
182 Map<String, String> proteinid_to_accession_;
184 Map<String, Size> accession_to_id_;
186 Map<String, String> identifier_id_;
188 Map<String, String> id_identifier_;
190 ProteinIdentification::SearchParameters search_param_;
191
192 };
193
194 } // namespace OpenMS
195
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureXMLFile::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: FeatureXMLFile.h:178
OpenMS::FeatureXMLFile::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: FeatureXMLFile.h:171
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FeatureXMLFile::proteinid_to_accession_
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: FeatureXMLFile.h:182
XMLFile.h
OpenMS::ConvexHull2D::PointArrayType
std::vector< PointType > PointArrayType
Definition: ConvexHull2D.h:76
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::FeatureXMLFile::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: FeatureXMLFile.h:176
XMLHandler.h
OpenMS::FeatureXMLFile::current_feature_
Feature * current_feature_
points to the last open <feature> tag (possibly a subordinate feature)
Definition: FeatureXMLFile.h:144
OpenMS::FeatureXMLFile::hull_position_
DPosition< 2 > hull_position_
Definition: FeatureXMLFile.h:158
OpenMS::FeatureXMLFile::map_
FeatureMap * map_
Feature map pointer for reading.
Definition: FeatureXMLFile.h:146
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
OpenMS::FeatureXMLFile::param_
Param param_
Definition: FeatureXMLFile.h:156
OpenMS::FeatureXMLFile::options_
FeatureFileOptions options_
Options that can be set.
Definition: FeatureXMLFile.h:148
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::FeatureXMLFile::search_param_
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: FeatureXMLFile.h:190
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::FeatureXMLFile::dim_
UInt dim_
current dimension of the feature position, quality, or convex hull point
Definition: FeatureXMLFile.h:162
OpenMS::FeatureXMLFile::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: FeatureXMLFile.h:174
OpenMS::FeatureXMLFile::subordinate_feature_level_
Int subordinate_feature_level_
level in Feature stack during parsing
Definition: FeatureXMLFile.h:168
OpenMS::FeatureXMLFile::id_identifier_
Map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: FeatureXMLFile.h:188
OpenMS::FeatureXMLFile::in_description_
bool in_description_
for downward compatibility, all tags in the old description must be ignored
Definition: FeatureXMLFile.h:165
ProgressLogger.h
OpenMS::FeatureXMLFile::accession_to_id_
Map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: FeatureXMLFile.h:184
OpenMS::FeatureXMLFile::current_chull_
ConvexHull2D::PointArrayType current_chull_
Definition: FeatureXMLFile.h:157
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Param.h
Map.h
OpenMS::FeatureXMLFile::disable_parsing_
Int disable_parsing_
Definition: FeatureXMLFile.h:141
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::DPosition< 2 >
OpenMS::FeatureXMLFile::size_only_
bool size_only_
only parse until "count" tag is reached (used in loadSize())
Definition: FeatureXMLFile.h:150
FeatureFileOptions.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
ConvexHull2D.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
int
OpenMS::FeatureFileOptions
Options for loading files containing features.
Definition: FeatureFileOptions.h:46
OpenMS::FeatureXMLFile::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: FeatureXMLFile.h:180
OpenMS::FeatureXMLFile::identifier_id_
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: FeatureXMLFile.h:186
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::FeatureXMLFile::expected_size_
Size expected_size_
holds the putative size given in count
Definition: FeatureXMLFile.h:152