| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
OMSSAXMLFile Class Reference
Format » File IO

Used to load OMSSAXML files. More...

`#include <OpenMS/FORMAT/OMSSAXMLFile.h>`

Inheritance diagram for OMSSAXMLFile:

## Public Member Functions

| OMSSAXMLFile ()
| Default constructor. More...
| ~OMSSAXMLFile () override
| Destructor. More...
void | load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
| loads data from a OMSSAXML file More...
void | setModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
| sets the valid modifications 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 String & | getVersion () const
| return the version of the schema More...

## Protected 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) override
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)
| 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
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 | parseBuffer_ (const std::string &buffer, XMLHandler *handler)
| Parses the in-memory buffer given by `buffer` 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 String & | getVersion () const
| return the version of the schema More...

## Private Member Functions

| OMSSAXMLFile (const OMSSAXMLFile &rhs)
OMSSAXMLFile & | operator= (const OMSSAXMLFile &rhs)
void | readMappingFile_ ()
| reads the mapping file needed for modifications More...

## Private Attributes

std::vector< PeptideIdentification > * | peptide_identifications_
| the identifications (storing the peptide hits) More...
ProteinHit | actual_protein_hit_
PeptideHit | actual_peptide_hit_
PeptideEvidence | actual_peptide_evidence_
std::vector< PeptideEvidence > | actual_peptide_evidences_
PeptideIdentification | actual_peptide_id_
ProteinIdentification | actual_protein_id_
String | tag_
UInt | actual_mod_site_
| site of the actual modification (simple position in the peptide) More...
String | actual_mod_type_
| type of the modification More...
std::vector< std::pair< UInt, String > > | modifications_
| modifications of the peptide defined by site and type More...
bool | load_proteins_
| should protein hits be read from the file? More...
bool | load_empty_hits_
| should empty peptide identifications be loaded or skipped? More...
Map< UInt, std::vector< const ResidueModification * > > | mods_map_
| modifications mapping file from OMSSA mod num to UniMod accession More...
Map< String, UInt > | mods_to_num_
| modification mapping reverse, from the modification to the mod_num More...
ModificationDefinitionsSet | mod_def_set_
| modification definitions set of the search, needed to annotate fixed modifications More...

## Additional Inherited Members

Protected 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 Protected Member Functions inherited from XMLHandler
static String | writeXMLEscape (const String &to_escape)
| Escapes a string and returns the escaped string. 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< 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...
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...

## Detailed Description

Used to load OMSSAXML files.

This class is used to load documents that implement the schema of OMSSAXML files.

## Constructor & Destructor Documentation

## ◆ OMSSAXMLFile() [1/2]

OMSSAXMLFile | ( |  | ) |

Default constructor.

## ◆ ~OMSSAXMLFile()

~OMSSAXMLFile | ( |  | ) |

override

Destructor.

## ◆ OMSSAXMLFile() [2/2]

OMSSAXMLFile | ( | const OMSSAXMLFile & | rhs | ) |

private

## Member Function Documentation

## ◆ characters()

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

override protected

## ◆ endElement()

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

override protected

## ◆ operator=()

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

private

## ◆ readMappingFile_()

void readMappingFile_ | ( |  | ) |

private

reads the mapping file needed for modifications

## ◆ setModificationDefinitionsSet()

void setModificationDefinitionsSet | ( | const ModificationDefinitionsSet & | rhs | ) |

sets the valid modifications

## ◆ startElement()

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

override protected

## Member Data Documentation

## ◆ actual_mod_site_

UInt actual_mod_site_

private

site of the actual modification (simple position in the peptide)

## ◆ actual_mod_type_

String actual_mod_type_

private

type of the modification

## ◆ actual_peptide_evidence_

PeptideEvidence actual_peptide_evidence_

private

## ◆ actual_peptide_evidences_

std::vector<PeptideEvidence> actual_peptide_evidences_

private

## ◆ actual_peptide_hit_

PeptideHit actual_peptide_hit_

private

## ◆ actual_peptide_id_

PeptideIdentification actual_peptide_id_

private

## ◆ actual_protein_hit_

ProteinHit actual_protein_hit_

private

## ◆ actual_protein_id_

ProteinIdentification actual_protein_id_

private

## ◆ load_empty_hits_

bool load_empty_hits_

private

should empty peptide identifications be loaded or skipped?

## ◆ load_proteins_

bool load_proteins_

private

should protein hits be read from the file?

## ◆ mod_def_set_

ModificationDefinitionsSet mod_def_set_

private

modification definitions set of the search, needed to annotate fixed modifications

## ◆ modifications_

std::vector<std::pair<UInt, String> > modifications_

private

modifications of the peptide defined by site and type

## ◆ mods_map_

Map<UInt, std::vector<const ResidueModification*> > mods_map_

private

modifications mapping file from OMSSA mod num to UniMod accession

## ◆ mods_to_num_

Map<String, UInt> mods_to_num_

private

modification mapping reverse, from the modification to the mod_num

## ◆ peptide_identifications_

std::vector<PeptideIdentification>* peptide_identifications_

private

the identifications (storing the peptide hits)

## ◆ tag_

String tag_

private