35 #ifndef OPENMS_FORMAT_FEATUREXMLFILE_H
36 #define OPENMS_FORMAT_FEATUREXMLFILE_H
106 void resetMembers_();
109 virtual void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname);
112 virtual void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes);
115 virtual void characters(
const XMLCh*
const chars,
const XMLSize_t length);
118 void writeFeature_(
const String& filename, std::ostream& os,
const Feature& feat,
const String& identifier_prefix,
UInt64 identifier,
UInt indentation_level);
129 void updateCurrentFeature_(
bool create);
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 <feature> 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
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
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