File adapter for MzML files. More...
#include <OpenMS/FORMAT/MzMLFile.h>
Public Member Functions | |
MzMLFile () | |
Default constructor. More... | |
~MzMLFile () | |
Destructor. More... | |
PeakFileOptions & | getOptions () |
Mutable access to the options for loading/storing. More... | |
const PeakFileOptions & | getOptions () const |
Non-mutable access to the options for loading/storing. More... | |
void | setOptions (const PeakFileOptions &) |
set options for loading/storing More... | |
template<typename MapType > | |
void | load (const String &filename, MapType &map) |
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions). More... | |
void | loadSize (const String &filename, Size &scount, Size &ccount) |
Only count he number of spectra and chromatograms from a file. More... | |
template<typename MapType > | |
void | store (const String &filename, const MapType &map) const |
Stores a map in a MzML file. More... | |
template<typename MapType > | |
void | transform (const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, bool skip_full_count=false, bool skip_first_pass=false) |
Transforms a map while loading using the supplied MSDataConsumer. More... | |
template<typename MapType > | |
void | transform (const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, MapType &map, bool skip_full_count=false, bool skip_first_pass=false) |
Transforms a map while loading using the supplied MSDataConsumer. More... | |
bool | isValid (const String &filename, std::ostream &os=std::cerr) |
Checks if a file validates against the XML schema. 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... | |
Protected Member Functions | |
template<typename MapType > | |
void | transformFirstPass_ (const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, bool skip_full_count) |
Perform first pass through the file and retrieve the meta-data to initialize the consumer. More... | |
void | safeParse_ (const String &filename, Internal::XMLHandler *handler) |
Safe parse that catches exceptions and handles them accordingly. 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 | 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) |
Private Attributes | |
PeakFileOptions | options_ |
Options for loading / storing. More... | |
String | indexed_schema_location_ |
Location of indexed mzML schema. More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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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 MzML files.
This implementation does currently not support the whole functionality of MzML.
MzMLFile | ( | ) |
Default constructor.
~MzMLFile | ( | ) |
Destructor.
PeakFileOptions& getOptions | ( | ) |
Mutable access to the options for loading/storing.
Referenced by FileHandler::loadExperiment(), SimpleSearchEngine::main_(), SwathFile::populateMetaData_(), and FileHandler::storeExperiment().
const PeakFileOptions& getOptions | ( | ) | const |
Non-mutable access to the options for loading/storing.
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 |
Checks if a file validates against the XML schema.
Exception::FileNotFound | is thrown if the file cannot be found. |
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions).
map
has to be a MSExperiment or have the same interface.
Exception::FileNotFound | is thrown if the file could not be opened |
Exception::ParseError | is thrown if an error occurs during parsing |
References MSExperiment< PeakT, ChromatogramPeakT >::reset(), DocumentIdentifier::setLoadedFilePath(), DocumentIdentifier::setLoadedFileType(), and MzMLHandler< MapType >::setOptions().
Referenced by SwathFile::doCacheFile_(), CachedSwathFileConsumer::ensureMapsAreFilled_(), FileHandler::loadExperiment(), SwathFile::loadSplit(), TOPPRNPxl::main_(), SimpleSearchEngine::main_(), and SwathFile::populateMetaData_().
Only count he number of spectra and chromatograms from a file.
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protected |
Safe parse that catches exceptions and handles them accordingly.
void setOptions | ( | const PeakFileOptions & | ) |
set options for loading/storing
Referenced by IndexedMzMLFileLoader::store().
Stores a map in a MzML file.
map
has to be a MSExperiment or have the same interface.
Exception::UnableToCreateFile | is thrown if the file could not be created |
References MzMLHandler< MapType >::setOptions().
Referenced by TOPPRNPxl::main_(), OpenSwathWorkflow::performRTNormalization(), TOPPViewBase::runTOPPTool_(), IndexedMzMLFileLoader::store(), and FileHandler::storeExperiment().
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inline |
Transforms a map while loading using the supplied MSDataConsumer.
The result will not be stored directly but is available through the events triggered by the parser and caught by the provided IMSDataConsumer object.
This function should be used if processing and storage of the result can be performed directly in the provided IMSDataConsumer object.
filename_in | Filename of input mzML file to transform |
consumer | Consumer class to operate on the input filename (implementing a transformation) |
skip_full_count | Whether to skip computing the correct number of spectra and chromatograms in the input file |
References MzMLHandler< MapType >::setMSDataConsumer(), and MzMLHandler< MapType >::setOptions().
Referenced by SwathFile::doCacheFile_(), and SwathFile::loadMzML().
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inline |
Transforms a map while loading using the supplied MSDataConsumer.
The result will be stored in the provided map.
This function should be used if a specific pre-processing should be applied to the data before storing them in a map (e.g. if data-reduction should be applied to the data before loading all data into memory).
filename_in | Filename of input mzML file to transform |
consumer | Consumer class to operate on the input filename (implementing a transformation) |
map | Map to store the resulting spectra and chromatograms |
skip_full_count | Whether to skip computing the correct number of spectra and chromatograms in the input file |
References PeakFileOptions::setAlwaysAppendData(), MzMLHandler< MapType >::setMSDataConsumer(), and MzMLHandler< MapType >::setOptions().
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inlineprotected |
Perform first pass through the file and retrieve the meta-data to initialize the consumer.
References MzMLHandler< MapType >::getCounts(), IMSDataConsumer< MapType >::setExpectedSize(), IMSDataConsumer< MapType >::setExperimentalSettings(), PeakFileOptions::setMetadataOnly(), MzMLHandler< MapType >::setOptions(), and PeakFileOptions::setSizeOnly().
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private |
Location of indexed mzML schema.
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private |
Options for loading / storing.
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11 |