Class which handles the communication between OpenMS and the Mascot server. More...

#include <OpenMS/FORMAT/MascotRemoteQuery.h>

Inheritance diagram for MascotRemoteQuery:

Collaboration diagram for MascotRemoteQuery:

Constructors and destructors
QNetworkAccessManager *	manager_

String	query_spectra_

QByteArray	mascot_xml_

QByteArray	mascot_decoy_xml_

QString	cookie_

String	error_message_

QTimer	timeout_

String	search_identifier_

String	server_path_
	Path on mascot server. More...

String	host_name_
	Hostname of the mascot server. More...

bool	requires_login_
	Login required. More...

bool	use_ssl_
	Use SSL connection. More...

String	boundary_
	boundary string that will be embedded into the HTTP requests More...

Int	to_
	Timeout after these many seconds. More...

bool	export_decoys_ = false

	MascotRemoteQuery (QObject *parent=0)
	default constructor More...

	~MascotRemoteQuery () override
	destructor More...

void	setQuerySpectra (const String &exp)
	sets the query spectra, given in MGF file format More...

const QByteArray &	getMascotXMLResponse () const
	returns the Mascot XML response which contains the identifications More...

bool	hasError () const
	predicate which returns true if an error occurred during the query More...

const String &	getErrorMessage () const
	returns the error message, if hasError can be used to check whether an error has occurred More...

String	getSearchIdentifier () const
	returns the search number More...

void	setExportDecoys (const bool b)
	request export of decoy summary and decoys (note: internal decoy search must be enabled in the MGF file passed to mascot) More...

const QByteArray &	getMascotXMLDecoyResponse () const
	returns the Mascot XML response which contains the decoy identifications (note: setExportDecoys must be set to true, otherwise result will be empty) More...

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	run ()

void	timedOut () const
	slot connected to QTimer (timeout_) More...

void	readResponse (QNetworkReply *reply)
	slot connected to the QNetworkAccessManager::finished signal More...

void	downloadProgress (qint64 bytes_read, qint64 bytes_total)
	slot connected to signal downloadProgress More...

void	uploadProgress (qint64 bytes_read, qint64 bytes_total)
	slot connected to signal uploadProgress More...

void	followRedirect (QNetworkReply *reply)
	slot connected to signal gotRedirect More...

void	gotRedirect (QNetworkReply *reply)
	signal when class got a redirect More...

void	done ()
	signal when class is done and results can be collected More...

void	login ()
	login to Mascot server More...

void	execQuery ()
	execute query (upload file) More...

void	getResults (QString results_path)
	download result file More...

MascotRemoteQuery &	operator= (const MascotRemoteQuery &rhs)
	assignment operator More...

	MascotRemoteQuery (const MascotRemoteQuery &rhs)
	copy constructor More...

void	endRun_ ()
	finish a run and emit "done" More...

void	removeHostName_ (QString &url)
	Remove host name information from an url, e.g., "http://www.google.de/search" -> "search". More...

QUrl	buildUrl_ (std::string path)
	helper function to build URL More...

void	logHeader_ (const QNetworkRequest header, const String &what)
	Write HTTP header to error stream (for debugging) More...

void	logHeader_ (const QNetworkReply *header, const String &what)
	Write HTTP header to error stream (for debugging) More...

String	getSearchIdentifierFromFilePath (const String &path) const

void	readResponseHeader (const QNetworkReply *reply)
	parse new response header More...

Additional Inherited Members
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Class which handles the communication between OpenMS and the Mascot server.

This class provides a communication interface which is able to query the Mascot server and reports the identifications provided be the Mascot server

Parameters of this class are:

Name	Type	Default	Restrictions	Description
hostname	string			Address of the host where Mascot listens, e.g. 'mascot-server' or '127.0.0.1'
host_port	int	80	min: 0	Port where the Mascot server listens, 80 should be a good guess
server_path	string	mascot		Path on the server where Mascot server listens, 'mascot' should be a good guess
timeout	int	1500	min: 0	Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps. Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!
boundary	string	GZWgAaYKjHFeUaLOLEIOMq		Boundary for the MIME section
use_proxy	string	false	true, false	Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'
proxy_host	string			Host where the proxy server runs on
proxy_port	int	0	min: 0	Port where the proxy server listens
proxy_username	string			Login name for the proxy server, if needed
proxy_password	string			Login password for the proxy server, if needed
login	string	false	true, false	Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then.
username	string			Name of the user if login is used (Mascot security must be enabled!)
password	string			Password of the user if login is used (Mascot security must be enabled!)
use_ssl	string	false	true, false	Flag indicating whether you want to send requests to an HTTPS server or not (HTTP). Requires OpenSSL to be installed (see openssl.org)
export_params	string	_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0		Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script). Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides.
skip_export	string	false	true, false	For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results. The output file produced by MascotAdapterOnline will contain only the Mascot search number.
batch_size	int	50000	min: 0	Number of spectra processed in one batch by Mascot (default 50000)

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ MascotRemoteQuery() [1/2]

MascotRemoteQuery ( QObject * parent = 0 )

default constructor

◆ ~MascotRemoteQuery()

~MascotRemoteQuery ( )

override

destructor

◆ MascotRemoteQuery() [2/2]

MascotRemoteQuery ( const MascotRemoteQuery & rhs )

private

copy constructor

Member Function Documentation

◆ buildUrl_()

QUrl buildUrl_ ( std::string path )

private

helper function to build URL

◆ done

void done ( )

signal

signal when class is done and results can be collected

◆ downloadProgress

void downloadProgress	(	qint64	bytes_read,
		qint64	bytes_total
	)

privateslot

slot connected to signal downloadProgress

◆ endRun_()

void endRun_ ( )

private

finish a run and emit "done"

◆ execQuery()

void execQuery ( )

private

execute query (upload file)

◆ followRedirect

void followRedirect ( QNetworkReply * reply )

privateslot

slot connected to signal gotRedirect

◆ getErrorMessage()

const String& getErrorMessage ( ) const

returns the error message, if hasError can be used to check whether an error has occurred

◆ getMascotXMLDecoyResponse()

const QByteArray& getMascotXMLDecoyResponse ( ) const

returns the Mascot XML response which contains the decoy identifications (note: setExportDecoys must be set to true, otherwise result will be empty)

◆ getMascotXMLResponse()

const QByteArray& getMascotXMLResponse ( ) const

returns the Mascot XML response which contains the identifications

◆ getResults()

void getResults ( QString results_path )

private

download result file

◆ getSearchIdentifier()

String getSearchIdentifier ( ) const

returns the search number

◆ getSearchIdentifierFromFilePath()

String getSearchIdentifierFromFilePath ( const String & path ) const

private

◆ gotRedirect

void gotRedirect ( QNetworkReply * reply )

signal

signal when class got a redirect

◆ hasError()

bool hasError ( ) const

predicate which returns true if an error occurred during the query

◆ logHeader_() [1/2]

void logHeader_	(	const QNetworkReply *	header,
		const String &	what
	)

private

Write HTTP header to error stream (for debugging)

◆ logHeader_() [2/2]

void logHeader_	(	const QNetworkRequest	header,
		const String &	what
	)

private

Write HTTP header to error stream (for debugging)

◆ login()

void login ( )

private

login to Mascot server

◆ operator=()

MascotRemoteQuery& operator= ( const MascotRemoteQuery & rhs )

private

assignment operator

◆ readResponse

void readResponse ( QNetworkReply * reply )

privateslot

slot connected to the QNetworkAccessManager::finished signal

◆ readResponseHeader()

void readResponseHeader ( const QNetworkReply * reply )

private

parse new response header

◆ removeHostName_()

void removeHostName_ ( QString & url )

private

Remove host name information from an url, e.g., "http://www.google.de/search" -> "search".

Parameters

The	url that will be manipulated.

◆ run

void run ( )

slot

◆ setExportDecoys()

void setExportDecoys ( const bool b )

request export of decoy summary and decoys (note: internal decoy search must be enabled in the MGF file passed to mascot)

◆ setQuerySpectra()

void setQuerySpectra ( const String & exp )

sets the query spectra, given in MGF file format

◆ timedOut

void timedOut ( ) const

privateslot

slot connected to QTimer (timeout_)

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

◆ uploadProgress

void uploadProgress	(	qint64	bytes_read,
		qint64	bytes_total
	)

privateslot

slot connected to signal uploadProgress

Member Data Documentation

◆ boundary_

String boundary_

private

boundary string that will be embedded into the HTTP requests

◆ cookie_

QString cookie_

private

◆ error_message_

String error_message_

private

◆ export_decoys_

bool export_decoys_ = false

private

◆ host_name_

String host_name_

private

Hostname of the mascot server.

◆ manager_

QNetworkAccessManager* manager_

private

◆ mascot_decoy_xml_

QByteArray mascot_decoy_xml_

private

◆ mascot_xml_

QByteArray mascot_xml_

private

◆ query_spectra_

String query_spectra_

private

◆ requires_login_

bool requires_login_

private

Login required.

◆ search_identifier_

String search_identifier_

private

◆ server_path_

String server_path_

private

Path on mascot server.

◆ timeout_

QTimer timeout_

private

◆ to_

Int to_

private

Timeout after these many seconds.

◆ use_ssl_

bool use_ssl_

private

Use SSL connection.

Constructors and destructors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MascotRemoteQuery() [1/2]

◆ ~MascotRemoteQuery()

◆ MascotRemoteQuery() [2/2]

Member Function Documentation

◆ buildUrl_()

◆ done

◆ downloadProgress

◆ endRun_()

◆ execQuery()

◆ followRedirect

◆ getErrorMessage()

◆ getMascotXMLDecoyResponse()

◆ getMascotXMLResponse()

◆ getResults()

◆ getSearchIdentifier()

◆ getSearchIdentifierFromFilePath()

◆ gotRedirect

◆ hasError()

◆ logHeader_() [1/2]

◆ logHeader_() [2/2]

◆ login()

◆ operator=()

◆ readResponse

◆ readResponseHeader()

◆ removeHostName_()

◆ run

◆ setExportDecoys()

◆ setQuerySpectra()

◆ timedOut

◆ updateMembers_()

◆ uploadProgress

Member Data Documentation

◆ boundary_

◆ cookie_

◆ error_message_

◆ export_decoys_

◆ host_name_

◆ manager_

◆ mascot_decoy_xml_

◆ mascot_xml_

◆ query_spectra_

◆ requires_login_

◆ search_identifier_

◆ server_path_

◆ timeout_

◆ to_

◆ use_ssl_