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OpenMS
2.5.0
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File adapter for MzIdentML files. More...
#include <OpenMS/FORMAT/MzIdentMLFile.h>
Public Member Functions | |
MzIdentMLFile () | |
Default constructor. More... | |
~MzIdentMLFile () override | |
Destructor. More... | |
void | load (const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid) |
Loads the identifications from a MzIdentML file. More... | |
void | store (const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const |
Stores the identifications in a MzIdentML file. More... | |
void | store (const String &filename, const Identification &id) const |
Stores the identifications in a MzIdentML file. More... | |
bool | isSemanticallyValid (const String &filename, StringList &errors, StringList &warnings) |
Checks if a file is valid with respect to the mapping file and the controlled vocabulary. 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... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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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 | 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) |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. 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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
File adapter for MzIdentML files.
This file adapter exposes the internal MzIdentML processing capabilities to the library. The file adapter interface is kept the same as idXML file adapter for downward capability reasons. For now, read-in will be performed with DOM write-out with STREAM
MzIdentMLFile | ( | ) |
Default constructor.
|
override |
Destructor.
bool isSemanticallyValid | ( | const String & | filename, |
StringList & | errors, | ||
StringList & | warnings | ||
) |
Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
filename | File name of the file to be checked. |
errors | Errors during the validation are returned in this output parameter. |
warnings | Warnings during the validation are returned in this output parameter. |
Exception::FileNotFound | is thrown if the file could not be opened |
void load | ( | const String & | filename, |
std::vector< ProteinIdentification > & | poid, | ||
std::vector< PeptideIdentification > & | peid | ||
) |
Loads the identifications from a MzIdentML file.
Exception::FileNotFound | is thrown if the file could not be opened |
Exception::ParseError | is thrown if an error occurs during parsing |
Referenced by TOPPViewBase::addDataFile(), and TOPPViewBase::annotateWithID().
void store | ( | const String & | filename, |
const Identification & | id | ||
) | const |
Stores the identifications in a MzIdentML file.
Exception::UnableToCreateFile | is thrown if the file could not be created |
void store | ( | const String & | filename, |
const std::vector< ProteinIdentification > & | poid, | ||
const std::vector< PeptideIdentification > & | peid | ||
) | const |
Stores the identifications in a MzIdentML file.
Exception::UnableToCreateFile | is thrown if the file could not be created |