OpenMS
TraMLHandler Class Reference

XML handler for TraMLFile. More...

#include <OpenMS/FORMAT/HANDLERS/TraMLHandler.h>

Inheritance diagram for TraMLHandler:
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Collaboration diagram for TraMLHandler:
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Public Types

typedef std::vector< ReactionMonitoringTransition::ProductProductListType
 
typedef std::vector< ReactionMonitoringTransition::ConfigurationConfigurationListType
 
- Public Types inherited from XMLHandler
enum  ActionMode { LOAD , STORE }
 Action to set the current mode (for error messages) More...
 
enum  LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }
 

Public Member Functions

 TraMLHandler ()=delete
 
 TraMLHandler (const TraMLHandler &rhs)=delete
 
TraMLHandleroperator= (const TraMLHandler &rhs)=delete
 
- Public Member Functions inherited from XMLHandler
 XMLHandler (const String &filename, const String &version)
 Default constructor. More...
 
 ~XMLHandler () override
 Destructor. More...
 
void reset ()
 Release internal memory used for parsing (call. More...
 
void fatalError (const xercesc::SAXParseException &exception) override
 
void error (const xercesc::SAXParseException &exception) override
 
void warning (const xercesc::SAXParseException &exception) override
 
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...
 
void characters (const XMLCh *const chars, const XMLSize_t length) override
 Parsing method for character data. More...
 
void startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
 Parsing method for opening tags. More...
 
void endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override
 Parsing method for closing tags. More...
 
virtual LOADDETAIL getLoadDetail () const
 handler which support partial loading, implement this method More...
 
virtual void setLoadDetail (const LOADDETAIL d)
 handler which support partial loading, implement this method More...
 
DataValue cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const
 Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...
 
DataValue cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
 Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...
 
void checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const
 

Constructors and destructor

const ProgressLoggerlogger_
 Progress logger. More...
 
ControlledVocabulary cv_
 Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
 
String tag_
 
TargetedExperimentexp_
 
const TargetedExperimentcexp_
 
TargetedExperiment::Publication actual_publication_
 
TargetedExperiment::Contact actual_contact_
 
TargetedExperiment::Instrument actual_instrument_
 
TargetedExperiment::Prediction actual_prediction_
 
Software actual_software_
 
TargetedExperiment::Protein actual_protein_
 
TargetedExperiment::RetentionTime actual_rt_
 
TargetedExperiment::Peptide actual_peptide_
 
TargetedExperiment::Compound actual_compound_
 
ReactionMonitoringTransition actual_transition_
 
IncludeExcludeTarget actual_target_
 
CVTermList actual_validation_
 
TargetedExperiment::Interpretation actual_interpretation_
 
std::vector< ReactionMonitoringTransition::Productactual_intermediate_products_
 
ReactionMonitoringTransition::Product actual_product_
 
ReactionMonitoringTransition::Configuration actual_configuration_
 
SourceFile actual_sourcefile_
 
 TraMLHandler (const TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a write-only handler. More...
 
 TraMLHandler (TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a read-only handler. More...
 
 ~TraMLHandler () override
 Destructor. More...
 
void endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
 
void startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
 
void characters (const XMLCh *const chars, const XMLSize_t length) override
 
void writeTo (std::ostream &os) override
 Writes the contents to a stream. More...
 
void handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const CVTerm &cv_term)
 Handles CV terms. More...
 
void handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
 Handles user terms. More...
 
void writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
 Writes user terms. More...
 
void writeUserParams_ (std::ostream &os, const std::vector< MetaInfoInterface > &meta, UInt indent) const
 
void writeCVParams_ (std::ostream &os, const CVTermList &cv_terms, UInt indent) const
 
void writeCVParams_ (std::ostream &os, const CVTermListInterface &cv_terms, UInt indent) const
 
void writeCVList_ (std::ostream &os, const std::map< String, std::vector< CVTerm >> &cv_terms, UInt indent) const
 
void writeTarget_ (std::ostream &os, const std::vector< IncludeExcludeTarget >::const_iterator &it) const
 
void writeRetentionTime_ (std::ostream &os, const TargetedExperimentHelper::RetentionTime &rt) const
 
void writeProduct_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Product >::const_iterator &prod_it) const
 
void writeConfiguration_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &cit) const
 
ControlledVocabulary::CVTerm getChildWithName_ (const String &parent_accession, const String &name) const
 Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. More...
 
static DataValue fromXSDString (const String &type, const String &value)
 Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...
 
- Protected Member Functions inherited from XMLHandler
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) const
 Conversion of a String to an integer value. More...
 
Int asInt_ (const XMLCh *in) const
 Conversion of a Xerces string to an integer value. More...
 
UInt asUInt_ (const String &in) const
 Conversion of a String to an unsigned integer value. More...
 
double asDouble_ (const String &in) const
 Conversion of a String to a double value. More...
 
float asFloat_ (const String &in) const
 Conversion of a String to a float value. More...
 
bool asBool_ (const String &in) const
 Conversion of a string to a boolean value. More...
 
DateTime asDateTime_ (String date_string) const
 Conversion of a xs:datetime string to a DateTime value. More...
 
bool equal_ (const XMLCh *a, const XMLCh *b) const
 Returns if two Xerces strings are equal. More...
 
SignedSize cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)
 
String 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...
 
String 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...
 
- Protected Attributes inherited from XMLHandler
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...
 
LOADDETAIL load_detail_
 parse only until total number of scans and chroms have been determined from attributes More...
 
std::vector< std::vector< String > > cv_terms_
 Array of CV term lists (one sublist denotes one term and it's children) More...
 

Detailed Description

XML handler for TraMLFile.

Note
Do not use this class. It is only needed in TraMLFile.

Member Typedef Documentation

◆ ConfigurationListType

◆ ProductListType

Constructor & Destructor Documentation

◆ TraMLHandler() [1/4]

TraMLHandler ( )
delete

◆ TraMLHandler() [2/4]

TraMLHandler ( const TraMLHandler rhs)
delete

◆ TraMLHandler() [3/4]

TraMLHandler ( const TargetedExperiment exp,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a write-only handler.

◆ TraMLHandler() [4/4]

TraMLHandler ( TargetedExperiment exp,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a read-only handler.

◆ ~TraMLHandler()

~TraMLHandler ( )
override

Destructor.

Member Function Documentation

◆ characters()

void characters ( const XMLCh *const  chars,
const XMLSize_t  length 
)
override

◆ endElement()

void endElement ( const XMLCh * const  ,
const XMLCh * const  ,
const XMLCh *const  qname 
)
override

◆ getChildWithName_()

ControlledVocabulary::CVTerm getChildWithName_ ( const String parent_accession,
const String name 
) const
protected

Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.

◆ handleCVParam_()

void handleCVParam_ ( const String parent_parent_tag,
const String parent_tag,
const CVTerm cv_term 
)
protected

Handles CV terms.

◆ handleUserParam_()

void handleUserParam_ ( const String parent_parent_tag,
const String parent_tag,
const String name,
const String type,
const String value 
)
protected

Handles user terms.

◆ operator=()

TraMLHandler& operator= ( const TraMLHandler rhs)
delete

◆ startElement()

void startElement ( const XMLCh * const  ,
const XMLCh * const  ,
const XMLCh *const  qname,
const xercesc::Attributes &  attributes 
)
override

◆ writeConfiguration_()

void writeConfiguration_ ( std::ostream &  os,
const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &  cit 
) const
protected

◆ writeCVList_()

void writeCVList_ ( std::ostream &  os,
const std::map< String, std::vector< CVTerm >> &  cv_terms,
UInt  indent 
) const
protected

◆ writeCVParams_() [1/2]

void writeCVParams_ ( std::ostream &  os,
const CVTermList cv_terms,
UInt  indent 
) const
protected

◆ writeCVParams_() [2/2]

void writeCVParams_ ( std::ostream &  os,
const CVTermListInterface cv_terms,
UInt  indent 
) const
protected

◆ writeProduct_()

void writeProduct_ ( std::ostream &  os,
const std::vector< ReactionMonitoringTransition::Product >::const_iterator &  prod_it 
) const
protected

◆ writeRetentionTime_()

void writeRetentionTime_ ( std::ostream &  os,
const TargetedExperimentHelper::RetentionTime rt 
) const
protected

◆ writeTarget_()

void writeTarget_ ( std::ostream &  os,
const std::vector< IncludeExcludeTarget >::const_iterator &  it 
) const
protected

◆ writeTo()

void writeTo ( std::ostream &  )
overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParam_()

void writeUserParam_ ( std::ostream &  os,
const MetaInfoInterface meta,
UInt  indent 
) const
protected

Writes user terms.

◆ writeUserParams_()

void writeUserParams_ ( std::ostream &  os,
const std::vector< MetaInfoInterface > &  meta,
UInt  indent 
) const
protected

Member Data Documentation

◆ actual_compound_

TargetedExperiment::Compound actual_compound_
protected

◆ actual_configuration_

ReactionMonitoringTransition::Configuration actual_configuration_
protected

◆ actual_contact_

TargetedExperiment::Contact actual_contact_
protected

◆ actual_instrument_

TargetedExperiment::Instrument actual_instrument_
protected

◆ actual_intermediate_products_

std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_
protected

◆ actual_interpretation_

TargetedExperiment::Interpretation actual_interpretation_
protected

◆ actual_peptide_

TargetedExperiment::Peptide actual_peptide_
protected

◆ actual_prediction_

TargetedExperiment::Prediction actual_prediction_
protected

◆ actual_product_

ReactionMonitoringTransition::Product actual_product_
protected

◆ actual_protein_

TargetedExperiment::Protein actual_protein_
protected

◆ actual_publication_

TargetedExperiment::Publication actual_publication_
protected

◆ actual_rt_

TargetedExperiment::RetentionTime actual_rt_
protected

◆ actual_software_

Software actual_software_
protected

◆ actual_sourcefile_

SourceFile actual_sourcefile_
protected

◆ actual_target_

IncludeExcludeTarget actual_target_
protected

◆ actual_transition_

ReactionMonitoringTransition actual_transition_
protected

◆ actual_validation_

CVTermList actual_validation_
protected

◆ cexp_

const TargetedExperiment* cexp_
protected

◆ cv_

ControlledVocabulary cv_
protected

Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)

◆ exp_

TargetedExperiment* exp_
protected

◆ logger_

const ProgressLogger& logger_
protected

Progress logger.

◆ tag_

String tag_
protected