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Public Member Functions | Static Public Member Functions

ms_distiller_data Class Reference
[Quantitation analysis for Mascot Server and Distiller]

Distiller project parameters. More...

#include <ms_distiller_data.hpp>

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List of all members.

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 const ms_datfilegetDatfile () const
 Return the Mascot data file used for the project.
const ms_errsgetErrorHandler () const
 Retrive the error object using this function to get access to all errors and error parameters.
virtual const ms_fragrulesfilegetFragRulesFile () 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_methodgetQuantMethod () 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_dataoperator= (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 ( const ms_distiller_data copy )
Parameters:
copyis the source to initialise from

Member Function Documentation

void appendErrors ( const ms_errors src ) [inherited]

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

Parameters:
srcThe object to copy the errors across from. See Maintaining object references: two rules of thumb.
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.
void copyFrom ( const ms_errors right ) [inherited]

Use this member to make a copy of another instance.

Parameters:
rightis the source to initialise from
void copyFrom ( const ms_distiller_data right )

Use this member to make a copy of another instance.

Parameters:
rightis the source to initialise from
const matrix_science::ms_datfile & getDatfile (  ) const [virtual]

Return the Mascot data file used for the project.

Returns:
The server configuration's ms_datfile.
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.
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.
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.
const matrix_science::ms_fragrulesfile & getFragRulesFile (  ) const [virtual]

Return the fragmentation rules file used for the project.

Returns:
The server configuration's ms_fragrulesfile.
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.

Reimplemented in ms_mascotresfile.

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()

Reimplemented in ms_mascotresfile.

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.
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.
const matrix_science::ms_distiller_data_quant & getQuant ( int  index ) const [virtual]

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

Parameters:
indexAn index (1..getQuantCount()) into the quantitation results int the project.
Returns:
The selected quantitation result.
int getQuantCount (  ) const [virtual]

Return the number of quantitation results in the project.

Returns:
The number of quantitation results in the project file.
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:
taskIdThe task identifier of the Mascot search.
Returns:
The search's quantitation result.
const matrix_science::ms_quant_method & getQuantMethod (  ) const [virtual]

Return the quantitation method used for the project.

Returns:
The quantitation method used.
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
const matrix_science::ms_distiller_data_search & getSearch ( int  index ) const [virtual]

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

Parameters:
indexAn index (1..getSearchCount()) into the search results int the project.
Returns:
The selected search.
int getSearchCount (  ) const [virtual]

Return the number of searches in the project.

Returns:
The number of searches in the project file.
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 is 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, resfile_summary.cpp, and tools_aahelper.cpp.
bool loadXml ( const char *  xmlSchemaPath,
const std::string &  xmlText 
) [virtual]

Load Distiller data from the supplied XML text.

Parameters:
xmlSchemaPathThe folder where the quantitation XML schema files (XSD) can be found.
xmlTextThe XML data to load.
Returns:
True if the XML file was parsed and loaded successfully.
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:
xmlSchemaPathThe folder where the quantitation XML schema files (XSD) can be found.
xmlFilenameThe path and filename of the XML file to load.
Returns:
True if the XML file was parsed and loaded successfully.
bool loadXmlStream ( const char *  xmlSchemaPath,
matrix_science::ms_input_string_stream *  xmlStream 
) [virtual]

Load Distiller data from a stream.

Parameters:
xmlSchemaPathThe path to the location of the XML schema (XSD) files.
xmlStreamThe stream interface offering the data.
Returns:
True if the data was parsed and loaded successfully.
const ms_distiller_data & operator= ( const ms_distiller_data copy )
Parameters:
copyis the source to initialise from
Returns:
reference to the current object

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:52