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DAG-Edit 1.411 available (lots of fixes/new features)

John Day-Richter john.richter at aya.yale.edu
Tue Mar 2 10:49:20 PST 2004


DAG-Edit 1.411 is now available from:

http://sourceforge.net/projects/geneontology

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 
	   information.

	* 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 
	  					load/save errors.
		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

Enjoy!

	-John


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