35 #ifndef OPENMS_FORMAT_FEATUREXMLFILE_H
36 #define OPENMS_FORMAT_FEATUREXMLFILE_H
104 void resetMembers_();
107 virtual void endElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname);
110 virtual void startElement(
const XMLCh *
const ,
const XMLCh *
const ,
const XMLCh *
const qname,
const xercesc::Attributes & attributes);
113 virtual void characters(
const XMLCh *
const chars,
const XMLSize_t length);
116 void writeFeature_(
const String & filename, std::ostream & os,
const Feature & feat,
const String & identifier_prefix,
UInt64 identifier,
UInt indentation_level);
127 void updateCurrentFeature_(
bool create);
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 <feature> 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 "count" 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
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