OpenMS
2.4.0
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Class which handles the communication between OpenMS and the Mascot server. More...
#include <OpenMS/FORMAT/MascotRemoteQuery.h>
Public Slots | |
void | run () |
Signals | |
void | gotRedirect (QNetworkReply *reply) |
signal when class got a redirect More... | |
void | done () |
signal when class is done and results can be collected More... | |
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... | |
String | getSearchIdentifier () 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 ¶m) |
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 () |
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... | |
Private Member Functions | |
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... | |
Private Attributes | |
QNetworkAccessManager * | manager_ |
String | query_spectra_ |
QByteArray | mascot_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... | |
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... | |
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 |
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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. |
MascotRemoteQuery | ( | QObject * | parent = 0 | ) |
default constructor
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destructor
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private |
copy constructor
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helper function to build URL
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signal |
signal when class is done and results can be collected
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privateslot |
slot connected to signal downloadProgress
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private |
finish a run and emit "done"
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private |
execute query (upload file)
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privateslot |
slot connected to signal gotRedirect
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
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private |
download result file
String getSearchIdentifier | ( | ) | const |
returns the search number
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signal |
signal when class got a redirect
bool hasError | ( | ) | const |
predicate which returns true if an error occurred during the query
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private |
Write HTTP header to error stream (for debugging)
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Write HTTP header to error stream (for debugging)
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login to Mascot server
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assignment operator
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privateslot |
slot connected to the QNetworkAccessManager::finished signal
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parse new response header
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Remove host name information from an url, e.g., "http://www.google.de/search" -> "search".
The | url that will be manipulated. |
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void setQuerySpectra | ( | const String & | exp | ) |
sets the query spectra, given in MGF file format
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privateslot |
slot connected to QTimer (timeout_)
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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.
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privateslot |
slot connected to signal uploadProgress
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boundary string that will be embedded into the HTTP requests
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Hostname of the mascot server.
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Login required.
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Path on mascot server.
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Timeout after these many seconds.
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Use SSL connection.