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

#include <OpenMS/FORMAT/MascotRemoteQuery.h>

Inheritance diagram for MascotRemoteQuery:

Public Slots
void	run ()
Signals
void	done ()
void	loginDone ()
void	queryDone ()
Public Member Functions
void	setQuerySpectra (const String &exp)
	sets the query spectra, given in MGF file format
const QByteArray &	getMascotXMLResponse () const
	returns the Mascot XML response which contains the identifications
bool	hasError () const
	predicate which returns true if an error occurred during the query
const String &	getErrorMessage () const
	returns the error message, if hasError can be used to check whether an error has occurred
Constructors and destructors

	MascotRemoteQuery (QObject *parent=0)
	default constructor
virtual	~MascotRemoteQuery ()
	destructor
Protected Member Functions
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
Private Slots
void	timedOut ()
void	readyReadSlot (const QHttpResponseHeader &resp)
void	httpRequestFinished (int request_id, bool error)
void	httpDataReadProgress (int bytes_read, int bytes_total)
	slot connected to signal dataReadProgress of QHttp
void	httpDataSendProgress (int bytes_sent, int bytes_total)
	slot connected to signal dataSendProgress of QHttp
void	httpRequestStarted (int request_id)
	slot connected to signal requestStarted of QHttp, which indicates that the processing of request request_id has been started
void	httpStateChanged (int state)
void	httpDone (bool error)
	slot connected to signal done of QHttp
void	readResponseHeader (const QHttpResponseHeader &response_header)
	slot connect to responseHeaderRecieved, which indicates that a new response header is available
void	login ()
void	execQuery ()
void	getResults ()
void	loginSuccess ()
Private Member Functions
MascotRemoteQuery &	operator= (const MascotRemoteQuery &rhs)
	assignment operator
	MascotRemoteQuery (const MascotRemoteQuery &rhs)
	copy constructor
void	endRun_ ()
Private Attributes
String	query_spectra_
QByteArray	mascot_xml_
QHttp *	http_
QString	results_path_
QString	cookie_
String	error_message_
QTimer	timeout_
Int	to_

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!)
query_master	string	false	true, false	If this option is set to true, query peptides will be returned with non-truncated lists, however, protein references of peptides will not be correct.
max_hits	int	0	min: 0	Maximum number of hits to be exported from the server to XML (0 = AUTO)

Note:

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

Constructor & Destructor Documentation

MascotRemoteQuery ( QObject * parent = 0 )

default constructor

virtual ~MascotRemoteQuery ( ) [virtual]

destructor

MascotRemoteQuery ( const MascotRemoteQuery & rhs ) [private]

copy constructor

Member Function Documentation

void done ( ) [signal]

void endRun_ ( ) [private]

void execQuery ( ) [private, slot]

const String& getErrorMessage ( ) const

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

const QByteArray& getMascotXMLResponse ( ) const

returns the Mascot XML response which contains the identifications

void getResults ( ) [private, slot]

bool hasError ( ) const

predicate which returns true if an error occurred during the query

void httpDataReadProgress	(	int	bytes_read,
		int	bytes_total
	)			`[private, slot]`

slot connected to signal dataReadProgress of QHttp

void httpDataSendProgress	(	int	bytes_sent,
		int	bytes_total
	)			`[private, slot]`

slot connected to signal dataSendProgress of QHttp

void httpDone ( bool error ) [private, slot]

slot connected to signal done of QHttp

void httpRequestFinished	(	int	request_id,
		bool	error
	)			`[private, slot]`

slot connected to signal requestFinished of QHttp: "This signal is emitted when processing the request identified by id has finished. error is true if an error occurred during the processing; otherwise error is false"

void httpRequestStarted ( int request_id ) [private, slot]

slot connected to signal requestStarted of QHttp, which indicates that the processing of request request_id has been started

void httpStateChanged ( int state ) [private, slot]

slot connected to signal stateChanged of QHttp, which is emitted if the http state changed. See 'enum QHttp::State' of Qt docu for more info.

void login ( ) [private, slot]

void loginDone ( ) [signal]

void loginSuccess ( ) [private, slot]

MascotRemoteQuery& operator= ( const MascotRemoteQuery & rhs ) [private]

assignment operator

void queryDone ( ) [signal]

void readResponseHeader ( const QHttpResponseHeader & response_header ) [private, slot]

slot connect to responseHeaderRecieved, which indicates that a new response header is available

void readyReadSlot ( const QHttpResponseHeader & resp ) [private, slot]

void run ( ) [slot]

void setQuerySpectra ( const String & exp )

sets the query spectra, given in MGF file format

void timedOut ( ) [private, slot]

virtual void updateMembers_ ( ) [protected, virtual]

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.

Member Data Documentation

QString cookie_ [private]

String error_message_ [private]

QHttp* http_ [private]

QByteArray mascot_xml_ [private]

String query_spectra_ [private]

QString results_path_ [private]

QTimer timeout_ [private]

Int to_ [private]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1

MascotRemoteQuery Class Reference

Public Slots

Signals

Public Member Functions

Protected Member Functions

Private Slots

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation