Distiller project parameters. More...

#include <ms_distiller_data.hpp>

Inheritance diagram for ms_distiller_data:

Collaboration diagram for ms_distiller_data:

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Public Member Functions
	ms_distiller_data (const ms_distiller_data &copy)

void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	copyFrom (const ms_distiller_data *right)
	Use this member to make a copy of another instance.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

virtual ms_mascotresults_params	get_ms_mascotresults_params (const int searchIndex) const
	Return default flags and parameters for creating an ms_peptidesummary object.

virtual const ms_datfile &	getDatfile () const
	Return the Mascot data file used for the project.

virtual int	getDistillerExperimentType () const
	Return the experiment type of the project, only available from schema 1.6 onwards.

virtual std::string	getDistillerVersion () const
	Return the version number of Distiller used to generate the distiller_data xml file.

const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.

virtual const ms_fragrulesfile &	getFragRulesFile () const
	Return the fragmentation rules file used for the project.

int	getLastError () const
	Return the error description of the last error that occurred.

std::string	getLastErrorString () const
	Return the error description of the last error that occurred.

virtual int	getLoadedSearchIndex () const
	Return the index (index 1..getSearchCount) of the currently loaded search.

virtual const ms_distiller_data_quant &	getQuant (int index) const
	Return the information the selected quantitation result (index 1..getQuantCount).

virtual int	getQuantCount () const
	Return the number of quantitation results in the project.

virtual const ms_distiller_data_quant *	getQuantForSearch (const std::string &taskId) const
	Return the information the quantitation result associated with the selected search.

virtual const ms_quant_method &	getQuantMethod () const
	Return the quantitation method used for the project.

virtual const ms_distiller_data_search &	getSearch (int index) const
	Return the information the selected search (index 1..getSearchCount).

virtual int	getSearchCount () const
	Return the number of searches in the project.

bool	isValid () const
	Call this function to determine if there have been any errors.

virtual bool	loadXml (const char *xmlSchemaPath, const std::string &xmlText)
	Load Distiller data from the supplied XML text.

virtual bool	loadXmlFile (const char *xmlSchemaPath, const std::string &xmlFilename)
	Load Distiller data from the XML in the named file.

virtual bool	loadXmlStream (const char xmlSchemaPath, matrix_science::ms_input_string_stream xmlStream)
	Load Distiller data from a stream.

const ms_distiller_data &	operator= (const ms_distiller_data &copy)

Static Public Member Functions
static std::string	getDistillerProjectStreamName ()
	Return the name of the stream, within the project file, used for the Distiller project parameters.

static time_t	getDistillerResfileTimestamp ()
	Return the 'standard' Distiller results file timestamp; 2010/1/1 00:00:00.

static std::vector< std::string >	getRequiredSchemaFileNames ()
	Return a list of the filenames of the schema that will be required when loading ms_distiller_data.

Detailed Description

Distiller project parameters.

Stored in a Distiller project file (.rov) in the stream "rover_data".

Constructor & Destructor Documentation

◆ ms_distiller_data()

ms_distiller_data ( const ms_distiller_data & copy )

Parameters

copy	is the source to initialise from

Member Function Documentation

◆ appendErrors()

void appendErrors ( const ms_errors & src )

inherited

Copies all errors from another instance and appends them at the end of own list.

Parameters

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

◆ clearAllErrors()

void clearAllErrors ( )

inherited

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also: isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples: common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

◆ copyFrom() [1/2]

void copyFrom ( const ms_distiller_data * right )

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ copyFrom() [2/2]

void copyFrom ( const ms_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ get_ms_mascotresults_params()

matrix_science::ms_mascotresults_params get_ms_mascotresults_params ( const int searchIndex ) const

virtual

Return default flags and parameters for creating an ms_peptidesummary object.

Parameters

searchIndex The index number (1..n) of the search in the Distiller data.

Returns: the values and flags required to pass to the peptide summary object.

◆ getDatfile()

const matrix_science::ms_datfile & getDatfile ( ) const

virtual

Return the Mascot data file used for the project.

Returns: The server configuration's ms_datfile.

◆ getDistillerExperimentType()

int getDistillerExperimentType ( ) const

virtual

Return the experiment type of the project, only available from schema 1.6 onwards.

0 = unknown, 1 = DDA, 2 = DIA

Returns: The Distiller experiment type [default = 1]

◆ getDistillerProjectStreamName()

std::string getDistillerProjectStreamName ( )

static

Return the name of the stream, within the project file, used for the Distiller project parameters.

Returns: The name of the stream containing the Distiller project parameters.

◆ getDistillerResfileTimestamp()

time_t getDistillerResfileTimestamp ( )

static

Return the 'standard' Distiller results file timestamp; 2010/1/1 00:00:00.

The timestamp on the Distiller results file is used to determine the name of the subfolder that is used to hold the results file and peptide summary cache files. It is also stored in the results cache file to check if the results file and the cache can be used together.

Setting the last update timestamp on the results file to a fixed time means that the cache file location can be controlled and so the file re-used. This saves time when loading and can help prevent wasted disk space by duplicated files.

Returns: The 'standard' time Distiller time; 2010/1/1 00:00:00.

◆ getDistillerVersion()

std::string getDistillerVersion ( ) const

virtual

Return the version number of Distiller used to generate the distiller_data xml file.

Returns: The Distiller version number.

◆ getErrorHandler()

const ms_errs * getErrorHandler ( ) const

inherited

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns: Constant pointer to the error handler

See also: isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, and http_helper_getstring.cpp.

◆ getFragRulesFile()

const matrix_science::ms_fragrulesfile & getFragRulesFile ( ) const

virtual

Return the fragmentation rules file used for the project.

Returns: The server configuration's ms_fragrulesfile.

◆ getLastError()

int getLastError ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also: isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns: the error number of the last error, or 0 if there have been no errors.

◆ getLastErrorString()

std::string getLastErrorString ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns: Most recent error, warning, information or debug message

See Error Handling.

See also: isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

◆ getLoadedSearchIndex()

int getLoadedSearchIndex ( ) const

virtual

Return the index (index 1..getSearchCount) of the currently loaded search.

Returns: The current search index, or zero if no search is currently selected.

◆ getQuant()

const matrix_science::ms_distiller_data_quant & getQuant ( int index ) const

virtual

Return the information the selected quantitation result (index 1..getQuantCount).

Parameters

index An index (1..getQuantCount()) into the quantitation results int the project.

Returns: The selected quantitation result.

◆ getQuantCount()

int getQuantCount ( ) const

virtual

Return the number of quantitation results in the project.

Returns: The number of quantitation results in the project file.

◆ getQuantForSearch()

const matrix_science::ms_distiller_data_quant * getQuantForSearch ( const std::string & taskId ) const

virtual

Return the information the quantitation result associated with the selected search.

Parameters

taskId The task identifier of the Mascot search.

Returns: The search's quantitation result.

◆ getQuantMethod()

const matrix_science::ms_quant_method & getQuantMethod ( ) const

virtual

Return the quantitation method used for the project.

Returns: The quantitation method used.

◆ getRequiredSchemaFileNames()

std::vector< std::string > getRequiredSchemaFileNames ( )

static

Return a list of the filenames of the schema that will be required when loading ms_distiller_data.

This function can be used for checking that the required schema files are present before an error is raised.

Returns: a list of the filenames of the schema that will be required when loading ms_distiller_data, ms_distiller_master_project and ms_distiller_search_status_list from xml / project files

◆ getSearch()

const matrix_science::ms_distiller_data_search & getSearch ( int index ) const

virtual

Return the information the selected search (index 1..getSearchCount).

Parameters

index An index (1..getSearchCount()) into the search results int the project.

Returns: The selected search.

◆ getSearchCount()

int getSearchCount ( ) const

virtual

Return the number of searches in the project.

Returns: The number of searches in the project file.

◆ isValid()

bool isValid ( ) const

inherited

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns: True if no fatal error occured

See also: getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

◆ loadXml()

bool loadXml	(	const char *	xmlSchemaPath,
		const std::string &	xmlText
	)

virtual

Load Distiller data from the supplied XML text.

Parameters

xmlSchemaPath	The folder where the quantitation XML schema files (XSD) can be found.
xmlText	The XML data to load.

Returns: True if the XML file was parsed and loaded successfully.

◆ loadXmlFile()

bool loadXmlFile	(	const char *	xmlSchemaPath,
		const std::string &	xmlFilename
	)

virtual

Load Distiller data from the XML in the named file.

If the schema path contains spaces, it should be prefixed with "file:///" and the spaces should be replaced with "%20"

Parameters

xmlSchemaPath	The folder where the quantitation XML schema files (XSD) can be found.
xmlFilename	The path and filename of the XML file to load.

Returns: True if the XML file was parsed and loaded successfully.

◆ loadXmlStream()

bool loadXmlStream	(	const char *	xmlSchemaPath,
		matrix_science::ms_input_string_stream *	xmlStream
	)

virtual

Load Distiller data from a stream.

Parameters

xmlSchemaPath	The path to the location of the XML schema (XSD) files.
xmlStream	The stream interface offering the data.

Returns: True if the data was parsed and loaded successfully.

◆ operator=()

const ms_distiller_data & operator= ( const ms_distiller_data & copy )

Parameters

copy	is the source to initialise from

Returns: reference to the current object

The documentation for this class was generated from the following files:

ms_distiller_data.hpp
ms_distiller_data.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_distiller_data()

Member Function Documentation

◆ appendErrors()

◆ clearAllErrors()

◆ copyFrom() [1/2]

◆ copyFrom() [2/2]

◆ get_ms_mascotresults_params()

◆ getDatfile()

◆ getDistillerExperimentType()

◆ getDistillerProjectStreamName()

◆ getDistillerResfileTimestamp()

◆ getDistillerVersion()

◆ getErrorHandler()

◆ getFragRulesFile()

◆ getLastError()

◆ getLastErrorString()

◆ getLoadedSearchIndex()

◆ getQuant()

◆ getQuantCount()

◆ getQuantForSearch()

◆ getQuantMethod()

◆ getRequiredSchemaFileNames()

◆ getSearch()

◆ getSearchCount()

◆ isValid()

◆ loadXml()

◆ loadXmlFile()

◆ loadXmlStream()

◆ operator=()