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DAG-Edit 1.411 available (lots of fixes/new features)
john.richter at aya.yale.edu
Tue Mar 2 10:49:20 PST 2004
DAG-Edit 1.411 is now available from:
If you don't want to read the rest of this email, I strongly suggest you look
over the DAG-Edit user's guide to learn about the new DAG-Edit features
(especially the sections: "Meet the Term Editor Panel", "Searching and
Filtering", "Deleting, Obsoleting, and Destroying Terms", and "Working with
Namespaces", and "Editing Term Text").
This version contains a ton of bug fixes and new features, including:
* View locking - It is now possible to select a term and choose "lock view"
from the popup menu. No matter what you do, the screen will not scroll away
from the locked term.
* Selection scrolling - Pressing the ] key will automatically scroll to the
next selected term. Pressing [ scrolls to the previous term.
* Search improvements - Basic/Advanced search modes, improved searching/
selection speed, the ability to choose which terms to search, and a search
history capability have been added.
* The DESTROY capability - Users may now permanently destroy a term in
DAG-Edit. When a term is destroyed, it is wiped off the face of the earth
forever, never to appear again, not even in the obsolete set. Obsolete
terms and relationship types can be destroyed as well. (Note that
destroying terms can cause unpleasant, irreversable side effects that
future generations of curators will have to deal with. See the sidebar in
"Deleting, Obsoleting and Destroying Terms" in the user's guide for more
* A new era in relationships - It is now possible to mark a term relationship
(or its inverse) as "necessarily true". Term relationships can also be
assigned namespaces for users who need to store a collection of term
relationships in an external obo file.
* Centralized namespace management - Namespaces are now managed through the
Namespace Manager Plugin.
* Mac OS X improvements - On Mac OS X, the popup menu will now only appear as
the result of a Command-click (this should finally, permanently solve the
problems with Control-clicking on the Macintosh). Also, buttons and drop
down boxes no longer have stupid looking blue borders on Mac OS.
* Keyboard improvements - There are now visual cues to show which DAG-Edit
editor panel is receiving keyboard input. Also, a shortcut key (control
+enter) has been added for committing term text edit changes.
* More integrity checks - DAG-Edit now issues a warning if you are about to
commit a term with the name <new term> or <new ontology>, or if the term
contains synonyms named <new synonym> or dbxrefs named <new dbxref>
* Improvements to text editing - Secondary ids are no longer editable, and
the term namespace can be set on the text editor screen.
* Better memory usage - When DAG-Edit's memory is getting full, it will now
throw away performance enhancing memory caches. This should help with
out-of-memory problems on some platforms.
* History saves - You may now save the results of the Term Change Tracker
Plugin to a file.
* Tons of bug fixes:
OBO Adapter: fixed gui bugs, added progress bars, fixed
Flat File Adapter: fixed definition export bug.
Interface: Fixed bad labels in Category Manager plugin,
fixed term editor panel resizing bug,
fixed bug in synonym dbxref editor,
fixed bad filter save icon on macs.
Shell scripts: fixed minor bugs in obo2flat, flat2obo launcher
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