Opened 13 years ago

Closed 13 years ago

#710 closed (fixed)

Select multiple databases for Mascot search

Reported by: Fredrik Levander Owned by: olle
Milestone: Proteios SE 2.14.0 Keywords:
Cc:

Description

It should be possible to select more than one database for Mascot searches in Mascot 2.3 (this option is not available in earlier versions of Mascot). When setting up the parameters it might be difficult to check mascot version, so errors could be catched properly when trying to search with more thatn ione database in Mascot 2.2.

Change History (11)

comment:1 Changed 13 years ago by Gregory Vincic

Owner: changed from Gregory Vincic to olle

comment:2 Changed 13 years ago by olle

Status: newassigned

Ticket accepted.

comment:3 Changed 13 years ago by olle

Traceability note:

  • Support for starting Mascot searches from Proteios SE was introduced in Ticket #534 (Mascot GUI), and was updated in Ticket #623 (Multiple selections results in one job).

comment:4 Changed 13 years ago by olle

Traceability note:

  • Forms related to Mascot searches were moved into their own classes in Ticket #698 (Move forms out of the FormFactory), see change sets [3859], [3861], [3862], and [3863].

comment:5 Changed 13 years ago by olle

Design discussion.

  • Design of support for selection of more than one database for Mascot searches will be based on the design for selection of fixed and variable modifications, where already more than one item may be selected.

comment:6 Changed 13 years ago by olle

(In [3973]) Refs #710. Refs #534. Mascot search updated to support selection of more than one database:

  1. Class/file gui/form/MascotStorageForm.java in client/servlet/

updated:

  1. Public constructor MascotStorageForm(MascotParameterSet mascotParameterSet, ...)

updated to use a multiple-selection box for database selection.

  1. Class/file action/mascot/SaveMascotParameterSetStorage.java in

client/servlet/ updated:

  1. Public static valid parameter VString VMASCOT_DB updated by

increasing max character length from 32 to 255 characters, as the selection is stored as a list string, with items separated with ",".

  1. Protected method void runMe() updated by obtaining a list of

database selections and storing them as a list string.

comment:7 Changed 13 years ago by olle

Correction to commit message to change set [3973] added 2010-11-10 15:41:

  • The method that was updated in class/file action/mascot/SaveMascotParameterSetStorage.java in client/servlet/ was not protected method void runMe(), but public method MascotParameterSet fetchCurrentMascotParameterSet().

comment:8 Changed 13 years ago by olle

(In [3974]) Refs #710. Refs #534. Class/file action/mascot/SaveMascotParameterSetStorage.java in client/servlet/ updated in public method MascotParameterSet fetchCurrentMascotParameterSet() by correcting comments to refer to the currently used delimiter string "," instead of ", ".

comment:9 Changed 13 years ago by olle

(In [3978]) Refs #710. Refs #534. Class/file gui/form/MascotStorageForm.java in client/servlet/ updated:

  1. Public constructor MascotStorageForm(MascotParameterSet mascotParameterSet, ...)

updated by adding a help text to the database multiple-selection box, informing that Mascot v2.3 and up supports multiple databases, else only one.

comment:10 Changed 13 years ago by olle

Test:

  • A Mascot search was started from Proteios SE using a Mascot parameter set with two Mascot databases selected (SwissProt and yeast_SP_random). The search job finished successfully, and the result file reported that the two selected databases had been used. The test therefore passed with successful result.

comment:11 Changed 13 years ago by olle

Resolution: fixed
Status: assignedclosed

Ticket is closed as the desired functionality has been added. Should problems occur, or undesired side effects of the current solution be seen, this ticket may be reopened, or a new ticket created.

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