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FeatureXMLFile.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
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34 
35 #ifndef OPENMS_FORMAT_FEATUREXMLFILE_H
36 #define OPENMS_FORMAT_FEATUREXMLFILE_H
37 
40 #include <OpenMS/FORMAT/XMLFile.h>
45 
46 #include <iosfwd>
47 
48 namespace OpenMS
49 {
61  class OPENMS_DLLAPI FeatureXMLFile :
62  protected Internal::XMLHandler,
63  public Internal::XMLFile,
64  public ProgressLogger
65  {
66 
67 public:
68 
74  ~FeatureXMLFile();
76 
83  void load(const String& filename, FeatureMap& feature_map);
84 
85  Size loadSize(const String& filename);
86 
92  void store(const String& filename, const FeatureMap& feature_map);
93 
95  FeatureFileOptions& getOptions();
96 
98  const FeatureFileOptions& getOptions() const;
99 
101  void setOptions(const FeatureFileOptions&);
102 
103 protected:
104 
105  // restore default state for next load/store operation
106  void resetMembers_();
107 
108  // Docu in base class
109  virtual void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname);
110 
111  // Docu in base class
112  virtual void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes);
113 
114  // Docu in base class
115  virtual void characters(const XMLCh* const chars, const XMLSize_t length);
116 
118  void writeFeature_(const String& filename, std::ostream& os, const Feature& feat, const String& identifier_prefix, UInt64 identifier, UInt indentation_level);
119 
121  void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
122 
123 
129  void updateCurrentFeature_(bool create);
130 
135 
146 
153 
156 
159 
162 
165 
184 
185  };
186 
187 } // namespace OpenMS
188 
189 #endif // OPENMS_FORMAT_FeatureXMLFile_H
DPosition< 2 > hull_position_
Definition: FeatureXMLFile.h:151
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
Feature * current_feature_
points to the last open tag (possibly a subordinate feature)
Definition: FeatureXMLFile.h:137
A more convenient string class.
Definition: String.h:57
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: FeatureXMLFile.h:183
A container for features.
Definition: FeatureMap.h:93
std::vector< PointType > PointArrayType
Definition: ConvexHull2D.h:77
Base class for XML handlers.
Definition: XMLHandler.h:99
Int disable_parsing_
Definition: FeatureXMLFile.h:134
bool size_only_
only parse until "count" tag is reached (used in loadSize())
Definition: FeatureXMLFile.h:143
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Search parameters of the DB search.
Definition: ProteinIdentification.h:117
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: FeatureXMLFile.h:175
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: FeatureXMLFile.h:179
Representation of a peptide hit.
Definition: PeptideHit.h:55
bool in_description_
for downward compatibility, all tags in the old description must be ignored
Definition: FeatureXMLFile.h:158
Options for loading files containing features.
Definition: FeatureFileOptions.h:47
Map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: FeatureXMLFile.h:181
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: FeatureXMLFile.h:169
An LC-MS feature.
Definition: Feature.h:70
PeptideHit pep_hit_
Temporary peptide hit.
Definition: FeatureXMLFile.h:173
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:71
Param param_
Definition: FeatureXMLFile.h:149
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:56
Management and storage of parameters / INI files.
Definition: Param.h:75
Representation of a protein hit.
Definition: ProteinHit.h:54
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: FeatureXMLFile.h:164
UInt dim_
current dimension of the feature position, quality, or convex hull point
Definition: FeatureXMLFile.h:155
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:61
Int subordinate_feature_level_
level in Feature stack during parsing
Definition: FeatureXMLFile.h:161
ProteinHit prot_hit_
Temporary protein hit.
Definition: FeatureXMLFile.h:171
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
Map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: FeatureXMLFile.h:177
FeatureMap * map_
Feature map pointer for reading.
Definition: FeatureXMLFile.h:139
int Int
Signed integer type.
Definition: Types.h:96
Size expected_size_
holds the putative size given in count
Definition: FeatureXMLFile.h:145
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: FeatureXMLFile.h:167
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
FeatureFileOptions options_
Options that can be set.
Definition: FeatureXMLFile.h:141
ConvexHull2D::PointArrayType current_chull_
Definition: FeatureXMLFile.h:150
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:19 using doxygen 1.8.9.1