| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
TraMLHandler Class Reference

XML handler for TraMLFile. More...

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

Inheritance diagram for TraMLHandler:

## Public Types

typedef std::vector< ReactionMonitoringTransition::Product > | ProductListType
typedef std::vector< ReactionMonitoringTransition::Configuration > | ConfigurationListType
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

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...
Constructors and destructor
| 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...
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 (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...
String | errorString ()
| Returns the last error description. 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...
void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids)
void | fatalError (const xercesc::SAXParseException &exception) override
void | error (const xercesc::SAXParseException &exception) override
void | warning (const xercesc::SAXParseException &exception) override

## Protected Member Functions

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
template<typename CVTList >
void | writeCVParams_ (std::ostream &os, const CVTList &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...
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 DateTime value. More...
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...
SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)

## Protected Attributes

const ProgressLogger & | logger_
| Progress logger. More...
ControlledVocabulary | cv_
| Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
String | tag_
TargetedExperiment * | exp_
const TargetedExperiment * | cexp_
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::Product > | actual_intermediate_products_
ReactionMonitoringTransition::Product | actual_product_
ReactionMonitoringTransition::Configuration | actual_configuration_
SourceFile | actual_sourcefile_
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< String > | open_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...

## Private Member Functions

| TraMLHandler ()
| Helper method that writes a source file. More...
| TraMLHandler (const TraMLHandler &rhs)
TraMLHandler & | operator= (const TraMLHandler &rhs)

## 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...

## Detailed Description

XML handler for TraMLFile.

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

## Member Typedef Documentation

## ◆ ConfigurationListType

typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType

## ◆ ProductListType

typedef std::vector<ReactionMonitoringTransition::Product> ProductListType

## Constructor & Destructor Documentation

## ◆ TraMLHandler() [1/4]

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

Constructor for a write-only handler.

## ◆ TraMLHandler() [2/4]

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

Constructor for a read-only handler.

## ◆ ~TraMLHandler()

~TraMLHandler | ( |  | ) |

override

Destructor.

## ◆ TraMLHandler() [3/4]

TraMLHandler | ( |  | ) |

private

Helper method that writes a source file.

## ◆ TraMLHandler() [4/4]

TraMLHandler | ( | const TraMLHandler & | rhs | ) |

private

## 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 | ) |

private

## ◆ 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

## ◆ writeCVParams_()

void writeCVParams_ | ( | std::ostream & | os,
|  | const CVTList & | cv_terms,
|  | UInt | indent
| ) |  | const

inline 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 & |  | ) |

override virtual

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