MascotRemoteQuery Class Reference

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	gotRedirect (const QHttpResponseHeader &resp)

Public Member Functions
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...
Int	getSearchNumber () const
	returns the search number More...
Constructors and destructors
	MascotRemoteQuery (QObject *parent=0)
	default constructor More...
virtual	~MascotRemoteQuery ()
	destructor More...
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...

Protected Member Functions
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

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 More...
void	httpDataSendProgress (int bytes_sent, int bytes_total)
	slot connected to signal dataSendProgress of QHttp More...
void	httpRequestStarted (int request_id)
	slot connected to signal requestStarted of QHttp, which indicates that the processing of request request_id has been started More...
void	httpStateChanged (int state)
void	httpDone (bool error)
	slot connected to signal done of QHttp More...
void	readResponseHeader (const QHttpResponseHeader &response_header)
	slot connect to responseHeaderRecieved, which indicates that a new response header is available More...
void	login ()
void	execQuery ()
void	getResults (QString results_path)
void	followRedirect (const QHttpResponseHeader &resp)

Private Member Functions
MascotRemoteQuery &	operator= (const MascotRemoteQuery &rhs)
	assignment operator More...
	MascotRemoteQuery (const MascotRemoteQuery &rhs)
	copy constructor More...
void	endRun_ ()
void	logHeader_ (const QHttpHeader &header, const String &what)
	Write HTTP header to error stream (for debugging) More...
void	removeHostName_ (QString &url)
	Remove host name information from an url, e.g., "http://www.google.de/search" -> "search". More...
Int	getSearchNumberFromFilePath_ (const String &path) const

Private Attributes
String	query_spectra_
QByteArray	mascot_xml_
QHttp *	http_
QString	cookie_
String	error_message_
QTimer	timeout_
Int	to_
Int	search_number_
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...

Additional Inherited Members
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 wether the server uses HTTPS or not.
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.

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()

virtual ~MascotRemoteQuery ( )

virtual

destructor

MascotRemoteQuery() [2/2]

MascotRemoteQuery ( const MascotRemoteQuery &  rhs )

private

copy constructor

Member Function Documentation

done

void done ( )

signal

endRun_()

void endRun_ ( )

private

execQuery

void execQuery ( )

privateslot

followRedirect

void followRedirect ( const QHttpResponseHeader &  resp )

privateslot

getErrorMessage()

const String& getErrorMessage

(

)

const

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

getMascotXMLResponse()

const QByteArray& getMascotXMLResponse

(

)

const

returns the Mascot XML response which contains the identifications

getResults

void getResults ( QString  results_path )

privateslot

getSearchNumber()

Int getSearchNumber

(

)

const

returns the search number

getSearchNumberFromFilePath_()

Int getSearchNumberFromFilePath_ ( const String &  path ) const

private

gotRedirect

void gotRedirect ( const QHttpResponseHeader &  resp )

signal

hasError()

bool hasError

(

)

const

predicate which returns true if an error occurred during the query

httpDataReadProgress

void httpDataReadProgress ( int  bytes_read, int  bytes_total  )

privateslot

slot connected to signal dataReadProgress of QHttp

httpDataSendProgress

void httpDataSendProgress ( int  bytes_sent, int  bytes_total  )

privateslot

slot connected to signal dataSendProgress of QHttp

httpDone

void httpDone ( bool  error )

privateslot

slot connected to signal done of QHttp

httpRequestFinished

void httpRequestFinished ( int  request_id, bool  error  )

privateslot

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"

httpRequestStarted

void httpRequestStarted ( int  request_id )

privateslot

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

httpStateChanged

void httpStateChanged ( int  state )

privateslot

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.

logHeader_()

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

private

Write HTTP header to error stream (for debugging)

login

void login ( )

privateslot

operator=()

MascotRemoteQuery& operator= ( const MascotRemoteQuery &  rhs )

private

assignment operator

readResponseHeader

void readResponseHeader ( const QHttpResponseHeader &  response_header )

privateslot

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

readyReadSlot

void readyReadSlot ( const QHttpResponseHeader &  resp )

privateslot

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

setQuerySpectra()

void setQuerySpectra

(

const String &

exp

)

sets the query spectra, given in MGF file format

timedOut

void timedOut ( )

privateslot

updateMembers_()

virtual void updateMembers_ ( )

protectedvirtual

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

boundary_

String boundary_

private

boundary string that will be embedded into the HTTP requests

cookie_

QString cookie_

private

error_message_

String error_message_

private

host_name_

String host_name_

private

Hostname of the mascot server.

http_

QHttp* http_

private

mascot_xml_

QByteArray mascot_xml_

private

query_spectra_

String query_spectra_

private

requires_login_

bool requires_login_

private

Login required.

search_number_

Int search_number_

private

server_path_

String server_path_

private

Path on mascot server.

timeout_

QTimer timeout_

private

to_

Int to_

private

use_ssl_

bool use_ssl_

private

Use SSL connection.