OpenMS  3.0.0
FeatureXMLHandler.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.h>
45 
46 #include <iosfwd>
47 #include <map>
48 
49 namespace OpenMS
50 {
51  class Feature;
52  class FeatureMap;
53 
54  namespace Internal
55  {
56 
71  class OPENMS_DLLAPI FeatureXMLHandler :
72  public Internal::XMLHandler,
73  public ProgressLogger
74  {
75 
76 public:
77 
80  FeatureXMLHandler(FeatureMap& map, const String& filename);
82  FeatureXMLHandler(const FeatureMap& map, const String& filename);
84  ~FeatureXMLHandler() override;
86 
87 
89  void writeTo(std::ostream& os) override;
90 
92  FeatureFileOptions& getOptions();
93 
95  const FeatureFileOptions& getOptions() const;
96 
98  void setOptions(const FeatureFileOptions&);
99 
100  void setSizeOnly(const bool size_only)
101  {
102  size_only_ = size_only;
103  }
104 
105  Size getSize() const
106  {
107  return expected_size_;
108  }
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 
135  void updateCurrentFeature_(bool create);
136 
141 
154 
161 
164 
167 
170 
173 
183  std::map<String, String> proteinid_to_accession_;
185  std::map<String, Size> accession_to_id_;
187  std::map<String, String> identifier_id_;
189  std::map<String, String> id_identifier_;
192 
193  };
194 
195 } // namespace Internal
196 } // namespace OpenMS
197 
OpenMS::Internal::FeatureXMLHandler::current_chull_
ConvexHull2D::PointArrayType current_chull_
Definition: FeatureXMLHandler.h:158
XMLFile.h
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::Internal::FeatureXMLHandler::size_only_
bool size_only_
only parse until "count" tag is reached (used in loadSize())
Definition: FeatureXMLHandler.h:151
OpenMS::FeatureFileOptions
Options for loading files containing features.
Definition: FeatureFileOptions.h:46
OpenMS::Internal::FeatureXMLHandler::id_identifier_
std::map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: FeatureXMLHandler.h:189
OpenMS::Internal::FeatureXMLHandler::map_
FeatureMap * map_
Feature map pointer for writing.
Definition: FeatureXMLHandler.h:145
OpenMS::Internal::FeatureXMLHandler::setSizeOnly
void setSizeOnly(const bool size_only)
Definition: FeatureXMLHandler.h:100
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::Internal::FeatureXMLHandler::param_
Param param_
Definition: FeatureXMLHandler.h:157
OpenMS::Internal::FeatureXMLHandler::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: FeatureXMLHandler.h:175
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::FeatureXMLHandler::disable_parsing_
Int disable_parsing_
Definition: FeatureXMLHandler.h:140
OpenMS::Internal::FeatureXMLHandler::search_param_
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: FeatureXMLHandler.h:191
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Internal::FeatureXMLHandler::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: FeatureXMLHandler.h:179
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::Internal::FeatureXMLHandler::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: FeatureXMLHandler.h:172
OpenMS::Internal::FeatureXMLHandler
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLHandler.h:71
XMLHandler.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::Internal::FeatureXMLHandler::cmap_
const FeatureMap * cmap_
Feature map pointer for reading.
Definition: FeatureXMLHandler.h:147
OpenMS::ConvexHull2D::PointArrayType
std::vector< PointType > PointArrayType
Definition: ConvexHull2D.h:76
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::Internal::FeatureXMLHandler::expected_size_
Size expected_size_
holds the putative size given in count
Definition: FeatureXMLHandler.h:153
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
ConvexHull2D.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
ProteinIdentification.h
Param.h
OpenMS::Internal::FeatureXMLHandler::identifier_id_
std::map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: FeatureXMLHandler.h:187
OpenMS::Internal::FeatureXMLHandler::hull_position_
DPosition< 2 > hull_position_
Definition: FeatureXMLHandler.h:159
OpenMS::DPosition< 2 >
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::FeatureXMLHandler::proteinid_to_accession_
std::map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: FeatureXMLHandler.h:183
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::Internal::FeatureXMLHandler::subordinate_feature_level_
Int subordinate_feature_level_
level in Feature stack during parsing
Definition: FeatureXMLHandler.h:169
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::Internal::FeatureXMLHandler::options_
FeatureFileOptions options_
Options that can be set.
Definition: FeatureXMLHandler.h:149
OpenMS::Internal::FeatureXMLHandler::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: FeatureXMLHandler.h:181
OpenMS::Internal::FeatureXMLHandler::in_description_
bool in_description_
for downward compatibility, all tags in the old description must be ignored
Definition: FeatureXMLHandler.h:166
OpenMS::Internal::FeatureXMLHandler::accession_to_id_
std::map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: FeatureXMLHandler.h:185
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
FeatureFileOptions.h
OpenMS::Internal::FeatureXMLHandler::current_feature_
Feature * current_feature_
points to the last open <feature> tag (possibly a subordinate feature)
Definition: FeatureXMLHandler.h:143
PeptideIdentification.h
OpenMS::Internal::FeatureXMLHandler::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: FeatureXMLHandler.h:177
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::Internal::FeatureXMLHandler::getSize
Size getSize() const
Definition: FeatureXMLHandler.h:105
OpenMS::Internal::FeatureXMLHandler::dim_
UInt dim_
current dimension of the feature position, quality, or convex hull point
Definition: FeatureXMLHandler.h:163
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55