Opening Preferences window
Preferences are the way to set up parameters that apply to the entire program, independently of the project.
To open the Preferences window, select Preferences from the Help menu. This opens a standard preferences window. On the left side, there are different preference categories and sub-categories. Some of them belong to the plug-ins of which BiSSAP is composed. You can change these settings, but this is not recommended.
The following settings for BiSSAP operations are described below:
- general BiSSAP preferences
- countries
- languages
- taxonomy
If using Mac OS X, open Preferences from the BiSSAP menu or press Command-, (i.e. Command plus comma).
Preferences
General preferences
Import directory
The directory to which the file selection dialog points when it is opened during an import/load operation. This value is updated each time a sequence is loaded.
Output directory
The directory to which the file selection dialog points when it is opened during an export/generate operation. This value is updated each time a sequence is generated.
Default verify directory
You can set a directory on which Automatic Batch Verification is performed. When you press Alt-V, BiSSAP performs Batch Verification on all the files in this directory.
If this directory is not set, Automatic Batch Verification is not possible and BiSSAP reports a problem.
Maximum number of sequences
This is the highest number of sequences that can be displayed in the Sequence Browser. For practical reasons, the value should be less then 500. If you choose a greater value, performance can become unacceptable. You should adapt this value to your style of working with BiSSAP.
For more information on the Sequence Browser, see here.
Countries
In many places where you have to select the country, BiSSAP lets you do so by choosing from a box. Scrolling down through a list of all the countries is not always practical, however. You will typically use only a handful of them. This option makes it possible to customise the Countries box so that only the countries you need are displayed.
Please note that you have to restart to activate this option.
Languages
As in the case of countries, applicants typically use only a few of the languages routinely. This option allows you to restrict as required the number of languages visible in the language boxes.
Taxonomy
BiSSAP uses the NCBI's taxonomy, which is divided into several groups (dictionaries) like scientific name or user defined. BiSSAP allows you to set the taxonomy dictionaries used in the sequences and features.
Use scientific names wherever possible. If you enter a name that does not exist in the database, the program asks you if you want to define a new name. If you confirm that this is so, a new name is added to the database as a user defined name. Extreme caution is advised when using this feature. It can lead to the generation of incorrect yet verified sequence listing files.
If you change this setting or introduce a new name into the database, you do so at your own responsibility.
Please note that you have to restart to activate the changes.