| OpenMS 2.5.0

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

XML handler for MzQuantMLFile. More...

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

Inheritance diagram for MzQuantMLHandler:

## 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
| MzQuantMLHandler (const MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
| Constructor for a write-only handler. More...
| MzQuantMLHandler (MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
| Constructor for a read-only handler. More...
| ~MzQuantMLHandler () 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 String &accession, const String &name, const String &value, const xercesc::Attributes &attributes, const String &cv_ref, const String &unit_accession="")
| 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 | writeCVParams_ (String &s, const Map< String, std::vector< CVTerm > > &, UInt indent)
| Write CV term. More...
void | writeUserParams_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent)
| Writes user terms. More...
void | writeUserParams_ (String &s, const MetaInfoInterface &meta, UInt indent)
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...
void | writeFeature_ (String &feature_xml, const std::vector< FeatureMap > &fm, UInt indentation_level)
| Helper method that writes the featuremaps. 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 (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo) More...
String | tag_
MSQuantifications * | msq_
const MSQuantifications * | cmsq_
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

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

## Private Attributes

std::map< String, std::vector< ExperimentalSettings > > | current_files_
| 1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings More...
String | current_id_
String | current_cf_id_
Size | current_count_
std::vector< MetaInfo > | up_stack_
std::vector< CVTerm > | cvp_stack_
MSQuantifications::Assay | current_assay_
std::multimap< String, String > | cm_cf_ids_
std::map< String, String > | f_cf_ids_
std::map< String, ConsensusFeature > | cf_cf_obj_
std::map< String, FeatureHandle > | f_f_obj_
std::map< String, ConsensusFeature::Ratio > | r_rtemp_
std::map< String, String > | numden_r_ids_
std::map< String, ConsensusFeature::Ratio > | r_r_obj_
std::map< String, Software > | current_sws_
std::map< int, DataProcessing > | current_orderedps_
std::pair< int, DataProcessing > | current_dp_
std::set< DataProcessing::ProcessingAction > | current_pas_
std::vector< String > | current_col_types_
std::vector< double > | current_dm_values_
std::vector< double > | current_row_

## Additional Inherited Members

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 }
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 MzQuantMLFile.

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

## Constructor & Destructor Documentation

## ◆ MzQuantMLHandler() [1/4]

MzQuantMLHandler | ( | const MSQuantifications & | msq,
|  | const String & | filename,
|  | const String & | version,
|  | const ProgressLogger & | logger
| ) |  |

Constructor for a write-only handler.

## ◆ MzQuantMLHandler() [2/4]

MzQuantMLHandler | ( | MSQuantifications & | msq,
|  | const String & | filename,
|  | const String & | version,
|  | const ProgressLogger & | logger
| ) |  |

Constructor for a read-only handler.

## ◆ ~MzQuantMLHandler()

~MzQuantMLHandler | ( |  | ) |

override

Destructor.

## ◆ MzQuantMLHandler() [3/4]

MzQuantMLHandler | ( |  | ) |

private

Helper method that writes a source file.

## ◆ MzQuantMLHandler() [4/4]

MzQuantMLHandler | ( | const MzQuantMLHandler & | 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 String & | accession,
|  | const String & | name,
|  | const String & | value,
|  | const xercesc::Attributes & | attributes,
|  | const String & | cv_ref,
|  | const String & | unit_accession = `""`
| ) |  |

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=()

MzQuantMLHandler& operator= | ( | const MzQuantMLHandler & | rhs | ) |

private

## ◆ startElement()

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

override

## ◆ writeCVParams_()

void writeCVParams_ | ( | String & | s,
|  | const Map< String, std::vector< CVTerm > > & | ,
|  | UInt | indent
| ) |  |

protected

Write CV term.

## ◆ writeFeature_()

void writeFeature_ | ( | String & | feature_xml,
|  | const std::vector< FeatureMap > & | fm,
|  | UInt | indentation_level
| ) |  |

protected

Helper method that writes the featuremaps.

## ◆ writeTo()

void writeTo | ( | std::ostream & |  | ) |

override virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

## ◆ writeUserParams_() [1/2]

void writeUserParams_ | ( | std::ostream & | os,
|  | const MetaInfoInterface & | meta,
|  | UInt | indent
| ) |  |

protected

Writes user terms.

## ◆ writeUserParams_() [2/2]

void writeUserParams_ | ( | String & | s,
|  | const MetaInfoInterface & | meta,
|  | UInt | indent
| ) |  |

protected

## Member Data Documentation

## ◆ cf_cf_obj_

std::map<String, ConsensusFeature> cf_cf_obj_

private

## ◆ cm_cf_ids_

std::multimap<String, String> cm_cf_ids_

private

## ◆ cmsq_

const MSQuantifications* cmsq_

protected

## ◆ current_assay_

MSQuantifications::Assay current_assay_

private

## ◆ current_cf_id_

String current_cf_id_

private

## ◆ current_col_types_

std::vector<String> current_col_types_

private

## ◆ current_count_

Size current_count_

private

## ◆ current_dm_values_

std::vector<double> current_dm_values_

private

## ◆ current_dp_

std::pair<int, DataProcessing> current_dp_

private

## ◆ current_files_

std::map<String, std::vector<ExperimentalSettings> > current_files_

private

1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings

## ◆ current_id_

String current_id_

private

## ◆ current_orderedps_

std::map<int, DataProcessing> current_orderedps_

private

## ◆ current_pas_

std::set<DataProcessing::ProcessingAction> current_pas_

private

## ◆ current_row_

std::vector<double> current_row_

private

## ◆ current_sws_

std::map<String, Software> current_sws_

private

## ◆ cv_

ControlledVocabulary cv_

protected

Controlled vocabulary (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo)

## ◆ cvp_stack_

std::vector<CVTerm> cvp_stack_

private

## ◆ f_cf_ids_

std::map<String, String> f_cf_ids_

private

## ◆ f_f_obj_

std::map<String, FeatureHandle> f_f_obj_

private

## ◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

## ◆ msq_

MSQuantifications* msq_

protected

## ◆ numden_r_ids_

std::map<String, String> numden_r_ids_

private

## ◆ r_r_obj_

std::map<String, ConsensusFeature::Ratio> r_r_obj_

private

## ◆ r_rtemp_

std::map<String, ConsensusFeature::Ratio> r_rtemp_

private

## ◆ tag_

String tag_

protected

## ◆ up_stack_

std::vector<MetaInfo> up_stack_

private