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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>
43 
44 #include <iostream>
45 
46 namespace OpenMS
47 {
59  class OPENMS_DLLAPI FeatureXMLFile :
60  protected Internal::XMLHandler,
61  public Internal::XMLFile,
62  public ProgressLogger
63  {
64 
65 public:
66 
72  ~FeatureXMLFile();
74 
81  void load(const String & filename, FeatureMap<> & feature_map);
82 
83  Size loadSize(const String & filename);
84 
90  void store(const String & filename, const FeatureMap<> & feature_map);
91 
93  FeatureFileOptions & getOptions();
94 
96  const FeatureFileOptions & getOptions() const;
97 
99  void setOptions(const FeatureFileOptions &);
100 
101 protected:
102 
103  // restore default state for next load/store operation
104  void resetMembers_();
105 
106  // Docu in base class
107  virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
108 
109  // Docu in base class
110  virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
111 
112  // Docu in base class
113  virtual void characters(const XMLCh * const chars, const XMLSize_t length);
114 
116  void writeFeature_(const String & filename, std::ostream & os, const Feature & feat, const String & identifier_prefix, UInt64 identifier, UInt indentation_level);
117 
119  void writePeptideIdentification_(const String & filename, std::ostream & os, const PeptideIdentification & id, const String & tag_name, UInt indentation_level);
120 
121 
127  void updateCurrentFeature_(bool create);
128 
133 
144 
152 
155 
158 
161 
164 
183 
184  };
185 
186 } // namespace OpenMS
187 
188 #endif // OPENMS_FORMAT_FeatureXMLFile_H
DPosition< 2 > hull_position_
Definition: FeatureXMLFile.h:150
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
Feature * current_feature_
points to the last open &lt;feature&gt; tag (possibly a subordinate feature)
Definition: FeatureXMLFile.h:135
A more convenient string class.
Definition: String.h:56
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: FeatureXMLFile.h:182
std::vector< PointType > PointArrayType
Definition: ConvexHull2D.h:79
Base class for XML handlers.
Definition: XMLHandler.h:89
Int disable_parsing_
Definition: FeatureXMLFile.h:132
bool size_only_
only parse until &quot;count&quot; tag is reached (used in loadSize())
Definition: FeatureXMLFile.h:141
Search parameters of the DB search.
Definition: ProteinIdentification.h:115
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: FeatureXMLFile.h:174
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: FeatureXMLFile.h:178
Representation of a peptide hit.
Definition: PeptideHit.h:54
bool in_description_
for downward compatibility, all tags in the old description must be ignored
Definition: FeatureXMLFile.h:157
ModelDescription< 2 > model_desc_
Definition: FeatureXMLFile.h:147
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:180
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: FeatureXMLFile.h:168
An LC-MS feature.
Definition: Feature.h:66
PeptideHit pep_hit_
Temporary peptide hit.
Definition: FeatureXMLFile.h:172
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:75
Param param_
Definition: FeatureXMLFile.h:148
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Management and storage of parameters / INI files.
Definition: Param.h:69
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:163
FeatureMap< Feature > * map_
Feature map pointer for reading.
Definition: FeatureXMLFile.h:137
UInt dim_
current dimension of the feature position, quality, or convex hull point
Definition: FeatureXMLFile.h:154
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:59
Int subordinate_feature_level_
level in Feature stack during parsing
Definition: FeatureXMLFile.h:160
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
ProteinHit prot_hit_
Temporary protein hit.
Definition: FeatureXMLFile.h:170
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:51
Map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: FeatureXMLFile.h:176
int Int
Signed integer type.
Definition: Types.h:100
Size expected_size_
holds the putative size given in count
Definition: FeatureXMLFile.h:143
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: FeatureXMLFile.h:166
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
FeatureFileOptions options_
Options that can be set.
Definition: FeatureXMLFile.h:139
ConvexHull2D::PointArrayType current_chull_
Definition: FeatureXMLFile.h:149
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:14 using doxygen 1.8.5