Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Protected Member Functions | List of all members
IdXMLFile Class Reference

Used to load and store idXML files. More...

#include <OpenMS/FORMAT/IdXMLFile.h>

Inheritance diagram for IdXMLFile:
XMLHandler XMLFile

Public Member Functions

 IdXMLFile ()
 Constructor. More...
 
void load (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
 Loads the identifications of an idXML file without identifier. More...
 
void load (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, String &document_id)
 Loads the identifications of an idXML file. More...
 
void store (String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
 Stores the data in an idXML file. More...
 
- Public Member Functions inherited from XMLFile
 XMLFile ()
 Default constructor. More...
 
 XMLFile (const String &schema_location, const String &version)
 Constructor that sets the schema location. More...
 
virtual ~XMLFile ()
 Destructor. More...
 
bool isValid (const String &filename, std::ostream &os)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Protected Member Functions

virtual void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags. More...
 
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags. More...
 
void addProteinGroups_ (MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::map< String, UInt > &accession_to_id)
 Add data from ProteinGroups to a MetaInfoInterface. More...
 
void getProteinGroups_ (std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
 Read and store ProteinGroup data. More...
 
- Protected Member Functions inherited from XMLHandler
bool equal_ (const XMLCh *a, const XMLCh *b) const
 Returns if two xerces strings are equal. More...
 
void writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
 Writes the content of MetaInfoInterface to the file. More...
 
Int asInt_ (const String &in)
 Conversion of a String to an integer value. More...
 
Int asInt_ (const XMLCh *in)
 Conversion of a Xerces string to an integer value. More...
 
UInt asUInt_ (const String &in)
 Conversion of a String to an unsigned integer value. More...
 
double asDouble_ (const String &in)
 Conversion of a String to a double value. More...
 
float asFloat_ (const String &in)
 Conversion of a String to a float value. More...
 
bool asBool_ (const String &in)
 Conversion of a string to a boolean value. More...
 
DateTime asDateTime_ (String date_string)
 Conversion of a xs:datetime string to a DataTime value. More...
 
char * attributeAsString_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a Int. More...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a double. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an StringList. More...
 
bool optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the String value if the attribute is present. More...
 
bool optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the Int value if the attribute is present. More...
 
bool optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the UInt value if the attribute is present. More...
 
bool optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the double value if the attribute is present. More...
 
bool optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the DoubleList value if the attribute is present. More...
 
bool optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the StringList value if the attribute is present. More...
 
bool optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the IntList value if the attribute is present. More...
 
char * attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a Int. More...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a double. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a StringList. More...
 
bool optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the String value if the attribute is present. More...
 
bool optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the Int value if the attribute is present. More...
 
bool optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the UInt value if the attribute is present. More...
 
bool optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the double value if the attribute is present. More...
 
bool optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the DoubleList value if the attribute is present. More...
 
bool optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the IntList value if the attribute is present. More...
 
bool optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the StringList value if the attribute is present. More...
 
SignedSize cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)
 
 XMLHandler (const String &filename, const String &version)
 Default constructor. More...
 
virtual ~XMLHandler ()
 Destructor. More...
 
void reset ()
 Release internal memory used for parsing (call. More...
 
void fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Fatal error handler. Throws a ParseError exception. More...
 
void error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Error handler for recoverable errors. More...
 
void warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Warning handler. More...
 
virtual void characters (const XMLCh *const chars, const XMLSize_t length)
 Parsing method for character data. More...
 
virtual void writeTo (std::ostream &)
 Writes the contents to a stream. More...
 
String errorString ()
 Returns the last error description. More...
 
void fatalError (const xercesc::SAXParseException &exception)
 
void error (const xercesc::SAXParseException &exception)
 
void warning (const xercesc::SAXParseException &exception)
 
- Protected Member Functions inherited from XMLFile
void parse_ (const String &filename, XMLHandler *handler)
 Parses the XML file given by filename using the handler given by handler. More...
 
void save_ (const String &filename, XMLHandler *handler) const
 Stores the contents of the XML handler given by handler in the file given by filename. More...
 
void enforceEncoding_ (const String &encoding)
 
 XMLFile ()
 Default constructor. More...
 
 XMLFile (const String &schema_location, const String &version)
 Constructor that sets the schema location. More...
 
virtual ~XMLFile ()
 Destructor. More...
 
bool isValid (const String &filename, std::ostream &os)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Protected Attributes

members for loading data
std::vector< ProteinIdentification > * prot_ids_
 Pointer to fill in protein identifications. More...
 
std::vector< PeptideIdentification > * pep_ids_
 Pointer to fill in peptide identifications. More...
 
MetaInfoInterfacelast_meta_
 Pointer to last read object with MetaInfoInterface. More...
 
std::map< String, ProteinIdentification::SearchParametersparameters_
 Search parameters map (key is the "id") More...
 
ProteinIdentification::SearchParameters param_
 Temporary search parameters variable. More...
 
String id_
 Temporary id. More...
 
ProteinIdentification prot_id_
 Temporary protein ProteinIdentification. More...
 
PeptideIdentification pep_id_
 Temporary peptide ProteinIdentification. More...
 
ProteinHit prot_hit_
 Temporary protein hit. More...
 
PeptideHit pep_hit_
 Temporary peptide hit. More...
 
std::vector< PeptideEvidencepeptide_evidences_
 Temporary peptide evidences. More...
 
std::map< String, Stringproteinid_to_accession_
 Map from protein id to accession. More...
 
Stringdocument_id_
 Document identifier. More...
 
bool prot_id_in_run_
 true if a prot id is contained in the current run More...
 
- Protected Attributes inherited from XMLHandler
String error_message_
 Error message of the last error. More...
 
String file_
 File name. More...
 
String version_
 Schema version. More...
 
StringManager sm_
 Helper class for string conversion. More...
 
std::vector< Stringopen_tags_
 Stack of open XML tags. More...
 
std::vector< std::vector< String > > cv_terms_
 Array of CV term lists (one sublist denotes one term and it's children) More...
 
- Protected Attributes inherited from XMLFile
String schema_location_
 XML schema file location. More...
 
String schema_version_
 Version string. More...
 
String enforced_encoding_
 Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
 

Additional Inherited Members

- Protected Types inherited from XMLHandler
enum  ActionMode { LOAD, STORE }
 Action to set the current mode (for error messages) More...
 
- Static Protected Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. More...
 

Detailed Description

Used to load and store idXML files.

This class is used to load and store documents that implement the schema of idXML files.

A documented schema for this format can be found at http://open-ms.sourceforge.net/schemas/.

One file can contain several ProteinIdentification runs. Each run consists of peptide hits stored in PeptideIdentification and (optional) protein hits stored in Identification. Peptide and protein hits are connected via a string identifier. We use the search engine and the date as identifier.

Note
This format will eventually be replaced by the HUPO-PSI (mzIdentML and mzQuantML)) AnalysisXML formats!

Constructor & Destructor Documentation

IdXMLFile ( )

Constructor.

Member Function Documentation

void addProteinGroups_ ( MetaInfoInterface meta,
const std::vector< ProteinIdentification::ProteinGroup > &  groups,
const String group_name,
const std::map< String, UInt > &  accession_to_id 
)
protected

Add data from ProteinGroups to a MetaInfoInterface.

virtual void endElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname 
)
protectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

void getProteinGroups_ ( std::vector< ProteinIdentification::ProteinGroup > &  groups,
const String group_name 
)
protected

Read and store ProteinGroup data.

void load ( const String filename,
std::vector< ProteinIdentification > &  protein_ids,
std::vector< PeptideIdentification > &  peptide_ids 
)

Loads the identifications of an idXML file without identifier.

The information is read in and the information is stored in the corresponding variables

Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::annotateWithID(), IDEvaluationBase::loadCurve(), and TOPPRNPxl::main_().

void load ( const String filename,
std::vector< ProteinIdentification > &  protein_ids,
std::vector< PeptideIdentification > &  peptide_ids,
String document_id 
)

Loads the identifications of an idXML file.

The information is read in and the information is stored in the corresponding variables

Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing
virtual void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname,
const xercesc::Attributes &  attrs 
)
protectedvirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

void store ( String  filename,
const std::vector< ProteinIdentification > &  protein_ids,
const std::vector< PeptideIdentification > &  peptide_ids,
const String document_id = "" 
)

Stores the data in an idXML file.

The data is read in and stored in the file 'filename'.

Exceptions
Exception::UnableToCreateFileis thrown if the file could not be created

Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::main_().

Member Data Documentation

String* document_id_
protected

Document identifier.

String id_
protected

Temporary id.

MetaInfoInterface* last_meta_
protected

Pointer to last read object with MetaInfoInterface.

Temporary search parameters variable.

std::map<String, ProteinIdentification::SearchParameters> parameters_
protected

Search parameters map (key is the "id")

PeptideHit pep_hit_
protected

Temporary peptide hit.

PeptideIdentification pep_id_
protected

Temporary peptide ProteinIdentification.

std::vector<PeptideIdentification>* pep_ids_
protected

Pointer to fill in peptide identifications.

std::vector<PeptideEvidence> peptide_evidences_
protected

Temporary peptide evidences.

ProteinHit prot_hit_
protected

Temporary protein hit.

ProteinIdentification prot_id_
protected

Temporary protein ProteinIdentification.

bool prot_id_in_run_
protected

true if a prot id is contained in the current run

std::vector<ProteinIdentification>* prot_ids_
protected

Pointer to fill in protein identifications.

std::map<String, String> proteinid_to_accession_
protected

Map from protein id to accession.


OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:38 using doxygen 1.8.9.1