The Configuration Plugin
The Configuration Plugin contains all the configuration
options in OBO-Edit. Open the Configuration Plugin by selecting it from the
"Plugins" menu:

The "Save Configuration" button accepts any changes and
updates the display. There are several tabs of configuration info. The first tab is "General
GUI".
General GUI Options
Relationship Type Icons
These controls allow a custom icon to be specified for a relationship type.
This does not create new relationship types! It just associates an icon
with a relationship type.
Note that relationship types don't need a custom icon. If no icon is specified, OBO-Edit will display the default icon, consisting of a black rectangle containing the relationship type id in black text.
To edit an existing relationship type icon association, left-click the
association to edit it. The icon association editor will appear:

Enter the id of the relationship type to associate into the "Relationship
type" box. Type a file location or URL for an image file to use as an icon into
the "Icon URL" box. To pick an image file from the local disk, press the "Browse
files" button. To use one of OBO-Edit's built-in icons, press the "Browse
built-in icons" button.
To delete a relationship type icon association, left-click the association
and press the "Del" button.
To add a new relationship type icon association, press the "Add" button. A
new association will be created with the id "UNKNOWN" and the icon path "<new
icon path>".
Runtime display options
- Case sensitive term sorting - If this box is checked, the case of a term name will be
taken into account when sorting terms. Lower case letters will appear before
upper case letters.
- Show terms ids as tool tips in term panels - If this box
is checked, the id of a term will appear if the mouse hovers over a term in
the ontology editor panel
. Enabling this feature will make OBO-Edit run slightly slower
on older machines.
- Confirm on exit- If this
box is checked, OBO-Edit will ask for confirmation before exiting.
Startup Options
These are options that do not take effect until OBO-Edit is restarted.
- OBO-Edit memory allocation - The text box specifies the amount of memory that should
be allocated to OBO-Edit. The value is given as an integer followed by the
letter M, indicating the number of megabytes of memory that should be
allocated. A high value will prevent OBO-Edit from running out of memory and
crashing, but higher values will lessen the amount of memory available to
other programs and may cause OBO-Edit to run slower on some platforms.
- Default font - These controls specify the font OBO-Edit
should use when displaying buttons, labels, dropdown menus, etc. The first
dropdown specifies the font family name, the second specifies the font size,
and the third specifies the font style (normal, italic, bold or bold-italic).
The "Font preview" label below will display the example text in the selected
font.
Paths & Autosave

Paths
- Config file -
Displays the path to the ".oboedit" directory that contains all of OBO-Edit's
configuration info. This field is not editable; it provides information alone.
- History file - The location of the history configuration
file that contains data adapter configuration info, including save profiles.
This location can be changed if the user wishes.
Autosave Options
- Enable autosave - If this box is checked, autosave will
be enabled. The ontology will be saved periodically in serial format.
- Autosave file path - This field specifies a directory where autosave
files will be stored.
- Do autosave every - This field specifies the number of minutes between autosaves
- Autosave files expire in - The number of days old an
autosave file must be before it is automatically deleted.
Behavior

- Allow new cycles to be created - If this box is checked, OBO-Edit will allow cycles to be
created. If it is not checked, OBO-Edit will refuse to allow new cycles to be
made. Only enable this option if an ontology requires cycles. Most do not. See
cyclic relations
for more information about what constitutes a cycle.
- Warn before final delete - If this box is checked, OBO-Edit displays a warning before
the last instance of a term is deleted and the term becomes obsolete.
- Warn before discarding definitions on save - If this box
is checked, the old GO Flat File
Adapter will
issue a warning when saving with no definition file.
- Use advanced root detection - If this box is selected,
OBO-Edit will use advanced root detection. Normally, OBO-Edit treats a term as
a root if it has no parents. If advanced root detection is enabled, terms with
no transitive parents are treated as roots.
User Settings
User Info
- User name - The user name OBO-Edit should use. This
information is used in the "saved-by" header field when using the OBO adapter.
- Full name - The
user's full name. This information is not currently used.
- Email address - The user's email address. This
information is not currently used.
Text Editing
This section controls text-editing behaviors in
OBO-Edit.
- Auto commit text edits - If this box
is checked, OBO-Edit commits text edits as soon as a new term is selected or
the ontology is saved. The user does not have to explicitly commit text edits
by pressing a "commit" button.
- Warn before discarding text edits - If Auto
commit text edits is not selected, this box is enabled. In manual
commit mode, the user must press a "commit" button to make text edits
permanent. If a user selects a new term without committing their text edits,
the edits are lost. If this box is checked, the user will see a warning if
uncommitted text edits are about to be discarded.
- Allow extended characters - If this box is selected,
extended (non-ASCII) characters are allowed in term names, synonyms,
definitions, etc. Note that this does not guarantee that non-ascii characters
will actually be written out to disk. Some data adapters (like the OBO
Adapter) currently do not allow extended characters under any circumstances.
- Use Personal Definition - If this box is selected, a user
may specify a default definition and dbxrefs that will automatically be used
when a new term is created.s
Display Layout
This section controls the layout of the main OBO-Edit user interface. Users
can create a custom layout using a special XML format. Components and plugins
can be arranged however a user wants:
The large text box contains the XML code for the layout. See Customizing the Interface to
learn how to specify a custom layout.
The xml editor does some syntax highlighting, automatic
text generating and auto-indenting. The line number and column number
of the current cursor position are displayed in a label below the xml editor. If
there is an error in the layout, an error message will appear beneath the xml
editor when the "Save Configuration" button is pressed.
To automatically indent the XML code, press the
"Auto-Indent XML" button.
The "Import XML File..." button loads an XML layout file from a local disk.
The "Export XML File..." button saves the current layout to a file. These
buttons allow users to share useful layouts with other users.
To return to
the default OBO-Edit layout, press the "Load default layout" button.