| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
MascotXMLHandler Class Reference

Handler that is used for parsing MascotXML data. More...

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

Inheritance diagram for MascotXMLHandler:

## Public Member Functions

| MascotXMLHandler (ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
| Constructor. More...
| ~MascotXMLHandler () 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) override
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...
virtual void | writeTo (std::ostream &)
| Writes the contents to a stream. 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

## Static Public Member Functions

static std::vector< String > | splitModificationBySpecifiedAA (String mod)
| Split modification search parameter if for more than one amino acid specified e.g. Phospho (ST) More...
Static Public Member Functions inherited from XMLHandler
static String | writeXMLEscape (const String &to_escape)
| Escapes a string and returns the escaped string. More...

## Private Attributes

ProteinIdentification & | protein_identification_
| the protein identifications More...
std::vector< PeptideIdentification > & | id_data_
| the identifications (storing the peptide hits) More...
ProteinHit | actual_protein_hit_
PeptideHit | actual_peptide_hit_
PeptideEvidence | actual_peptide_evidence_
UInt | peptide_identification_index_
String | tag_
DateTime | date_
String | date_time_string_
UInt | actual_query_
ProteinIdentification::SearchParameters | search_parameters_
String | identifier_
String | actual_title_
std::map< String, std::vector< AASequence > > & | modified_peptides_
StringList | tags_open_
| tracking the current XML tree More...
String | character_buffer_
| filled by MascotXMLHandler::characters More...
String | major_version_
String | minor_version_
std::vector< String > | remove_fixed_mods_
const SpectrumMetaDataLookup & | lookup_
| Helper object for looking up RT information. More...
bool | no_rt_error_
| Error for missing RT information already reported? More...

## 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 }
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 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...

## Detailed Description

Handler that is used for parsing MascotXML data.

## Constructor & Destructor Documentation

## ◆ MascotXMLHandler()

MascotXMLHandler | ( | ProteinIdentification & | protein_identification,
|  | std::vector< PeptideIdentification > & | identifications,
|  | const String & | filename,
|  | std::map< String, std::vector< AASequence > > & | peptides,
|  | const SpectrumMetaDataLookup & | lookup
| ) |  |

Constructor.

## ◆ ~MascotXMLHandler()

~MascotXMLHandler | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ characters()

void characters | ( | const XMLCh *const | chars,
|  | const XMLSize_t |
| ) |  |

override

## ◆ endElement()

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

override

## ◆ splitModificationBySpecifiedAA()

static std::vector<String> splitModificationBySpecifiedAA | ( | String | mod | ) |

static

Split modification search parameter if for more than one amino acid specified e.g. Phospho (ST)

## ◆ startElement()

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

override

## Member Data Documentation

## ◆ actual_peptide_evidence_

PeptideEvidence actual_peptide_evidence_

private

## ◆ actual_peptide_hit_

PeptideHit actual_peptide_hit_

private

## ◆ actual_protein_hit_

ProteinHit actual_protein_hit_

private

## ◆ actual_query_

UInt actual_query_

private

## ◆ actual_title_

String actual_title_

private

## ◆ character_buffer_

String character_buffer_

private

filled by MascotXMLHandler::characters

## ◆ date_

DateTime date_

private

## ◆ date_time_string_

String date_time_string_

private

## ◆ id_data_

std::vector<PeptideIdentification>& id_data_

private

the identifications (storing the peptide hits)

## ◆ identifier_

String identifier_

private

## ◆ lookup_

const SpectrumMetaDataLookup& lookup_

private

Helper object for looking up RT information.

## ◆ major_version_

String major_version_

private

## ◆ minor_version_

String minor_version_

private

## ◆ modified_peptides_

std::map<String, std::vector<AASequence> >& modified_peptides_

private

## ◆ no_rt_error_

bool no_rt_error_

private

Error for missing RT information already reported?

## ◆ peptide_identification_index_

UInt peptide_identification_index_

private

## ◆ protein_identification_

ProteinIdentification& protein_identification_

private

the protein identifications

## ◆ remove_fixed_mods_

std::vector<String> remove_fixed_mods_

private

## ◆ search_parameters_

ProteinIdentification::SearchParameters search_parameters_

private

## ◆ tag_

String tag_

private

## ◆ tags_open_

StringList tags_open_

private

tracking the current XML tree