Used to load Mascot PepXML files. More...
#include <OpenMS/FORMAT/PepXMLFileMascot.h>
Public Member Functions | |
PepXMLFileMascot () | |
Constructor. More... | |
void | load (const String &filename, std::map< String, std::vector< AASequence > > &peptides) |
Loads peptide sequences with modifications out of a PepXML file. More... | |
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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 | |
virtual void | endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname) |
Parsing method for closing tags. More... | |
virtual void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) |
Parsing method for opening tags. More... | |
void | matchModification_ (double mass, String &modification_description) |
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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 DataTime value. More... | |
char * | 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... | |
char * | 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... | |
virtual | ~XMLHandler () |
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... | |
virtual void | characters (const XMLCh *const chars, const XMLSize_t length) |
Parsing method for character data. More... | |
virtual void | writeTo (std::ostream &) |
Writes the contents to a stream. More... | |
String | errorString () |
Returns the last error description. More... | |
void | fatalError (const xercesc::SAXParseException &exception) |
void | error (const xercesc::SAXParseException &exception) |
void | warning (const xercesc::SAXParseException &exception) |
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void | parse_ (const String &filename, XMLHandler *handler) |
Parses the XML file given by filename 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... | |
Protected Attributes | |
members for loading data | |
String | actual_title_ |
Pointer to fill in protein identifications. More... | |
String | actual_sequence_ |
The sequence of the actual peptide hit. More... | |
std::vector< std::pair< String, UInt > > | actual_modifications_ |
The modifications of the actual peptide hit (position is 1-based) More... | |
std::map< String, std::vector < AASequence > > * | peptides_ |
The peptides together with the spectrum title. More... | |
std::vector< AASequence > | actual_aa_sequences_ |
stores the actual peptide sequences More... | |
std::vector< String > | fixed_modifications_ |
stores the fixed residue modifications More... | |
std::vector< std::pair< String, double > > | variable_modifications_ |
stores the variable residue modifications More... | |
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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... | |
std::vector< std::vector < String > > | cv_terms_ |
Array of CV term lists (one sublist denotes one term and it's children) More... | |
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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... | |
Additional Inherited Members | |
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enum | ActionMode { LOAD, STORE } |
Action to set the current mode (for error messages) More... | |
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static String | writeXMLEscape (const String &to_escape) |
Escapes a string and returns the escaped string. More... | |
Used to load Mascot PepXML files.
A schema for this format can be found at http://www.matrixscience.com/xmlns/schema/pepXML_v18/pepXML_v18.xsd.
PepXMLFileMascot | ( | ) |
Constructor.
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protectedvirtual |
Parsing method for closing tags.
Reimplemented from XMLHandler.
void load | ( | const String & | filename, |
std::map< String, std::vector< AASequence > > & | peptides | ||
) |
Loads peptide sequences with modifications out of a PepXML file.
Exception::FileNotFound | is thrown if the file could not be opened |
Exception::ParseError | is thrown if an error occurs during parsing |
|
protectedvirtual |
Parsing method for opening tags.
Reimplemented from XMLHandler.
|
protected |
stores the actual peptide sequences
The modifications of the actual peptide hit (position is 1-based)
|
protected |
The sequence of the actual peptide hit.
|
protected |
Pointer to fill in protein identifications.
The title of the actual spectrum
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protected |
stores the fixed residue modifications
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protected |
The peptides together with the spectrum title.
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:47 using doxygen 1.8.5 |