The Configuration Manager lets you control some of the settings in OBO-Edit.
You can bring it up as a free-floating window with
If you prefer it to be docked into the main OBO-Edit window, you can use the
little downward-curving arrow to dock it.
When you are done adjusting your configuration options, click the
"Save Configuration" button to accept your changes and update the
display. There are several different configuration tabs. The first tab
is "User Settings".
- Configuration directory -
Displays the path to the OS-appropriate directory that contains your personal OBO-Edit
configuration info. This field is not editable; it is for
informational purposes only. You can mouse-select the directory path and copy it to your
clipboard to paste elsewhere, if you want.
- Log file - The text output from OBO-Edit is saved in
this file in your configuration directory. It can be useful for debugging.
This field is not editable, but can be copied and pasted elsewhere.
- OBO-Edit memory allocation (requires restart) -
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 make OBO-Edit less likely to run out of memory and
crash, but will also lessen the amount of memory available to
other programs and may cause OBO-Edit to run slower on some platforms. Unless
you have a 64-bit JVM, Java limits the maximum memory allocation to 1860M
(1024M on Windows machines).
Mac users, please see this information about
memory allocation on MacOSX.
Changing the memory configuration without the configuration manager:
The configuration manager limits the maximum memory you can set depending on the
version of Java you have installed, the available memory, and the operating
system. If you want to set a higher memory allocation and you know your
computer can handle it (for example, if you have a 64-bit-capable Mac and OBO-Edit is refusing to let you
set a memory allocation higher than 1860M), you can edit the OBO-Edit.vmoptions file in the folder
where OBO-Edit is installed.
After an OBO-Edit restart (on MacOS two restarts are required) the new
memory setting will be used.
WARNING: Setting an invalid or too large amount of memory will prevent
OBO-Edit from starting.
- User name - The user name OBO-Edit should use when
saving your edits. This
information is used in the "saved-by" header field when using the OBO adapter.
- 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" shows the alphabet in the selected
Icons and Colors
Changing 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 an existing 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 white text.
To edit an existing relationship type icon association, select a
relationship type from the list. The icon association editor will appear:
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. (Note: it takes a few seconds for OBO-Edit to find
and display all the built-in icons.) The "Icon URL" box will get filled in automatically
when you choose one of the icons.
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 temporary id "UNKNOWN" and the icon path "<new
To change the link color for a relationship, click the button below "Link
color" that says the color name (e.g., "blue (click to modify)").
Changing link color
Below the "Browse" buttons is the text "Link color" and the name of the color (e.g., "blue").
Click on the color name to pop up a color chooser and select a new color for links
of that particular relationship type.
As when you select a new icon, the OBO-Edit
display will not automatically refresh. You will see the new link color when you do
something that changes the display (e.g., click open a node).
- Enable autosave - If this box is checked, OBO-Edit will
automatically save backup copies of your work. Your edited ontology will be saved periodically in the autosave file
path (see next item). The default is for autosave
to be enabled; you can turn this off if you prefer.
- Directory for autosave -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.
- Exclude obsolete terms from search results - OBO-Edit's
default behavior is to allow obsolete terms in autocomplete lists and search
you start typing in a search or filter box, a dropdown list of term names
appears, including terms (or relations) that include the text you've typed
so far. By default, this list includes terms that have been marked as
obsolete. If you prefer to exclude obsolete terms from these dropdown lists
and also from search results, check this checkbox.
The downside is that the searches will take slightly longer
(because OBO-Edit has to do extra work, checking each term to see
whether it's obsolete or not).
Note that if you change this option in the
configuration manager, you must quit and restart OBO-Edit for the behavior
- 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 Tree Editor. Enabling this feature will make OBO-Edit run slightly slower
on older machines.
- 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
for more information about what constitutes a cycle.
- 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.
- Only one Ontology Tree Editor at a time can be in global mode - If this box is checked,
then only one Ontology Tree Editor can be in global selection mode at a
given time. Any other Ontology Tree Editors will automatically be put into
local selection mode.
- 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
issue a warning when saving with no definition file.
- Confirm on exit- If this
box is checked, OBO-Edit will ask for confirmation before exiting.
- Autocommit 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
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 (except in dbxrefs) - 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. Also be aware that some other
applications may not accept extended characters.
- 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.