85 void load(
const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
96 void load(
const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids,
String& document_id);
105 void store(
const String& filename,
const std::vector<ProteinIdentification>& protein_ids,
const std::vector<PeptideIdentification>& peptide_ids,
const String& document_id =
"");
110 void endElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname)
override;
113 void startElement(
const XMLCh*
const ,
const XMLCh*
const ,
const XMLCh*
const qname,
const xercesc::Attributes& attributes)
override;
118 void addProteinGroups_(
MetaInfoInterface& meta,
const std::vector<ProteinIdentification::ProteinGroup>& groups,
122 void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups,
const String& group_name);
128 static std::ostream& createFlankingAAXMLString_(
const std::vector<PeptideEvidence> & pes, std::ostream& os);
134 static std::ostream& createPositionXMLString_(
const std::vector<PeptideEvidence> & pes, std::ostream& os);
140 static void writeFragmentAnnotations_(
const String & tag_name, std::ostream & os,
141 const std::vector<PeptideHit::PeakAnnotation>& annotations,
UInt indent);
146 static void parseFragmentAnnotation_(
const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
151 std::vector<ProteinIdentification>* prot_ids_;
158 std::map<String, ProteinIdentification::SearchParameters>
parameters_;
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:174
std::unordered_map< std::string, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:176
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:210
Base class for XML handlers.
Definition: XMLHandler.h:151
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Temporary analysis result instance.
Definition: IdXMLFile.h:172
Used to load and store idXML files.
Definition: IdXMLFile.h:63
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:168
Representation of a protein hit.
Definition: ProteinHit.h:57
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:180
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
String * document_id_
Document identifier.
Definition: IdXMLFile.h:178
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:154
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:169
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:158
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:166
Representation of a peptide hit.
Definition: PeptideHit.h:54
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
String id_
Temporary id.
Definition: IdXMLFile.h:162
A more convenient string class.
Definition: String.h:58
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:160
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:156
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:170
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:164
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46