Configuration Manager

The Configuration Manager lets you control some of the settings in OBO-Edit. You can bring it up as a free-floating window with [Config]->[Configuration Manager]. 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".

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. 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.

Font

• 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 font.

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 icon path>".

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).

Autosave

• 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.

Behavior

• Exclude obsolete terms from search results - OBO-Edit's default behavior is to allow obsolete terms in autocomplete lists and search results. When 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 to change.
• 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 cyclic relations 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 Adapter will 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.

Text Editing

• 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 Autocommit 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.