OBO-Edit 2.0 beta release notes: Difference between revisions

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<h1>Release notes for OBO-Edit2 betas</h1>
[[Category:OBO-Edit]]
<h3>Release Name: 2.000-beta25</h3>
<h3>Release Name: 2.000-beta25</h3>
<b>Notes:</b>
<b>Notes:</b>
Line 16: Line 16:


<h3>Release Name: 2.000-beta24</h3>
<h3>Release Name: 2.000-beta24</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* (See beta23 release notes for many other changes)
* (See beta23 release notes for many other changes)
* Fixed bug where menus would not appear (SF 1845378)
* Fixed bug where menus would not appear (SF 1845378)
* Removed option to create a desktop link from installer (SF 1845378)
* Removed option to create a desktop link from installer (SF 1845378)
<h3>Release Name: 2.000-beta23</h3>
<h3>Release Name: 2.000-beta23</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added framework to attach help topics to components. If a component has a help
Added framework to attach help topics to components. If a component has a help
  topic attached, a little question mark button appears in the title bar. When
          topic attached, a little question mark button appears in the title bar. When
  the button is clicked, help for that component is displayed.
          the button is clicked, help for that component is displayed.
* Text edits no longer lost when a new search item is selected (SF 1844991)
Text edits no longer lost when a new search item is selected (SF 1844991)
* Fixed numerous bugs in custom verification checks
Fixed numerous bugs in custom verification checks
* Fixed bug where Graph Editor would not properly display explanations for some
Fixed bug where Graph Editor would not properly display explanations for some
  links (thanks to Chris for fixing this)
          links (thanks to Chris for fixing this)
* Fixed bug where the save dialog would appear when there were fatal errors in the
Fixed bug where the save dialog would appear when there were fatal errors in the
  ontology (all the more ironic because it appeared after a message explaining that you
          ontology (all the more ironic because it appeared after a message explaining that you
  will not be allowed to save until these errors are fixed)
          will not be allowed to save until these errors are fixed)
* Redundant and implied links once again have a distinctive appearance - you will need
Redundant and implied links once again have a distinctive appearance - you will need
  to delete ~/.oboeditbeta/filter_prefs.xml to get the new default settings (SF 1844745)
          to delete ~/.oboeditbeta/filter_prefs.xml to get the new default settings (SF 1844745)
* Many changes to text editor quickfix system (SF 1844885):
Many changes to text editor quickfix system (SF 1844885):
  * Added quickfix for &quot;no punctuation at end of sentence&quot; error
          * Added quickfix for &quot;no punctuation at end of sentence&quot; error
  * Added quickfix for &quot;non-url characters in dbxref&quot; error
          * Added quickfix for &quot;non-url characters in dbxref&quot; error
  * In text editor panes, errors are highlighted in red. Errors that can be quickfixed
          * In text editor panes, errors are highlighted in red. Errors that can be quickfixed
    are also underlined.
            are also underlined.
  * In list editors (like the dbxref editor or the synonym editor), items that contain
          * In list editors (like the dbxref editor or the synonym editor), items that contain
    errors are listed in red. Items that can be quickfixed display a quickfix icon
            errors are listed in red. Items that can be quickfixed display a quickfix icon
    next to them. Quickfixes can be applied by right-clicking an item and selecting
            next to them. Quickfixes can be applied by right-clicking an item and selecting
    a fix from the menu.
            a fix from the menu.
  * Quickfixes are now available in the synonym text text editor.
          * Quickfixes are now available in the synonym text text editor.
<h3>Release Name: 2.000-beta22</h3>
<h3>Release Name: 2.000-beta22</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Global renderers are now used to display search results
Global renderers are now used to display search results
* Fixed problem where live verification data would not be updated properly when
Fixed problem where live verification data would not be updated properly when
  definition dbxref problems have been fixed (SF 1844213)
          definition dbxref problems have been fixed (SF 1844213)
* The big, distracting text editor error message panel has been removed. Now
The big, distracting text editor error message panel has been removed. Now
  error messages appear in the text editor's title bar. Mousing over the title
          error messages appear in the text editor's title bar. Mousing over the title
  bar will display a tooltip listing the errors.
          bar will display a tooltip listing the errors.
* Remove redundant links problem (SF 1844193) and associated reasoned link
Remove redundant links problem (SF 1844193) and associated reasoned link
  deletion bugs are fixed.  
          deletion bugs are fixed.
* Platform independent launcher bug fixed (SF 1843989)
Platform independent launcher bug fixed (SF 1843989)
* Log files are being generated correctly again (SF 1844183)
Log files are being generated correctly again (SF 1844183)
* Garbage tabs no longer appear if OBO-Edit is shut down with search results
Garbage tabs no longer appear if OBO-Edit is shut down with search results
  still visible (SF 1844184)
          still visible (SF 1844184)
* Fixed disappearing global/local selection mode buttons (SF 1838678)
Fixed disappearing global/local selection mode buttons (SF 1838678)
* Added new log messages to aid in diagnosis of rogue popup menu problem
Added new log messages to aid in diagnosis of rogue popup menu problem
  (SF 1839411)
          (SF 1839411)
* Fixed problem where list editors (like the synonym editor) could cause
Fixed problem where list editors (like the synonym editor) could cause
  unexpected changes if the selection changed while the editor panel was
          unexpected changes if the selection changed while the editor panel was
  still open (SF 1837056)
          still open (SF 1837056)
 
 
<h3>Release Name: 2.000-beta21</h3>
<h3>Release Name: 2.000-beta21</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Fixed bug where synonym dbxrefs would be lost on synonym edit (SF 1843460)
Fixed bug where synonym dbxrefs would be lost on synonym edit (SF 1843460)
* Added editor for synonym dbxrefs
Added editor for synonym dbxrefs
* Dbxref listing is now always the same size in synonym editor (SF 1843405)
Dbxref listing is now always the same size in synonym editor (SF 1843405)
* Live error highlighting in the text editor now works properly
Live error highlighting in the text editor now works properly
* All TableList editors (like the dbxref editors and the synonym editor) now commit their changes the minute they are unfocused, which should make them easier to use
All TableList editors (like the dbxref editors and the synonym editor) now commit their changes
    the minute they are unfocused, which should make them easier to use
<h3>Release Name: 2.000-beta20</h3>
<h3>Release Name: 2.000-beta20</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added customizable heat maps
Added customizable heat maps
* Right-clicking a component's title bar allows you to change the title
Right-clicking a component's title bar allows you to change the title
* Search control now remembers last settings
Search control now remembers last settings
* Search results text is now customizable in search control settings
Search results text is now customizable in search control settings
* Added new Icons &amp; Colors tab in configuration manager (SF 1838664)
Added new Icons &amp; Colors tab in configuration manager (SF 1838664)
* Added icons for OBO-Edit application and installer
Added icons for OBO-Edit application and installer
* The Mac OS &quot;Quit&quot; and &quot;About&quot; menus are now properly handled
The Mac OS &quot;Quit&quot; and &quot;About&quot; menus are now properly handled
  by OBO-Edit
          by OBO-Edit
* Text edits now autocommit if another edit occurs (for example,
Text edits now autocommit if another edit occurs (for example,
  if you have pending text edits and you create a new term, your text
          if you have pending text edits and you create a new term, your text
  edits are no longer lost)
          edits are no longer lost)
* Changed Parent Editor appearance to make things fit on the screen
Changed Parent Editor appearance to make things fit on the screen
  better
          better
* Fixed unhandled exceptions when clicking &quot;classes&quot;, &quot;properties&quot;,
Fixed unhandled exceptions when clicking &quot;classes&quot;, &quot;properties&quot;,
  etc (SF 1840390)
          etc (SF 1840390)
* Fixed undo/redo failures (SF 1839564, SF 1839564)
Fixed undo/redo failures (SF 1839564, SF 1839564)
* Fixed shortcut key bugs (SF 1838830, SF 1836524)
Fixed shortcut key bugs (SF 1838830, SF 1836524)
* Fixed bug where &quot;&lt;new term&gt;&quot; did not appear correctly after new
Fixed bug where &quot;&lt;new term&gt;&quot; did not appear correctly after new
  terms were created (SF 1838829)
          terms were created (SF 1838829)
* Made &quot;working&quot; popup look a little better (SF 1838787)
Made &quot;working&quot; popup look a little better (SF 1838787)
* Fixed bug where search results disappeared between layout switches
Fixed bug where search results disappeared between layout switches
  (SF 1838784)
          (SF 1838784)
* Fixed bug where panels would not update correctly after new ontology load
Fixed bug where panels would not update correctly after new ontology load
  (SF 1838764), and for good measure fixed some other screen update bugs in
          (SF 1838764), and for good measure fixed some other screen update bugs in
  the graph editor, including bugs that left stray arrows floating around
          the graph editor, including bugs that left stray arrows floating around
* Fixed graphical artifacts and switched-around button behaviors in
Fixed graphical artifacts and switched-around button behaviors in
  term change tracker (SF 1838679)
          term change tracker (SF 1838679)
* Fixed problem where a change in the autocommit setting did not cause
Fixed problem where a change in the autocommit setting did not cause
  &quot;commit&quot; and &quot;revert&quot; buttons to immediately appear (SF 1838673)
          &quot;commit&quot; and &quot;revert&quot; buttons to immediately appear (SF 1838673)
* Fixed parent editor drag and drop button (SF 1838669)
Fixed parent editor drag and drop button (SF 1838669)
* Fixed bug where namespace changes would not be saved (SF 1838656)
Fixed bug where namespace changes would not be saved (SF 1838656)
* Fixed icon browsing problem (SF 1838651)
Fixed icon browsing problem (SF 1838651)
* Fixed bug where OBO-Edit would not display installer-generated
Fixed bug where OBO-Edit would not display installer-generated
  memory settings on Mac OS (SF 1838648)
          memory settings on Mac OS (SF 1838648)
* Installer now WILL create a desktop icon if you ask it to (SF 1838648)
Installer now WILL create a desktop icon if you ask it to (SF 1838648)
* If there are unsaved changes to an ontology, a special message appears
If there are unsaved changes to an ontology, a special message appears
  in the quit confirmation dialog (SF 1838644) (note that this message
          in the quit confirmation dialog (SF 1838644) (note that this message
  will appear whether or not you have &quot;confirm on exit&quot; checked, on the
          will appear whether or not you have &quot;confirm on exit&quot; checked, on the
  theory that anyone would want to know about this potential disaster)
          theory that anyone would want to know about this potential disaster)
* Fixed spurious &quot;unsaved changes&quot; message (SF 1837005)
Fixed spurious &quot;unsaved changes&quot; message (SF 1837005)
* It is now possible to re-select already selected search results
It is now possible to re-select already selected search results
  (SF 1836549)
          (SF 1836549)
<h3>Release Name: 2.000-beta19</h3>
<h3>Release Name: 2.000-beta19</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added Import... to the file menu
Added Import... to the file menu
* Added Fix ids... to the file menu
Added Fix ids... to the file menu
* Added a verification system check for bad ids. The id fix options are all
Added a verification system check for bad ids. The id fix options are all
  available as quickfixes
          available as quickfixes
* Added a new system for installing custom graph decorators
Added a new system for installing custom graph decorators
<h3>Release Name: 2.000-beta18</h3>
<h3>Release Name: 2.000-beta18</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Fixed OBO 1.2 save bug (SF 1827542)
Fixed OBO 1.2 save bug (SF 1827542)
* Fixed bugs when saving filtered files with range &amp; domain defined
Fixed bugs when saving filtered files with range &amp; domain defined
* Changed method of starting load/save operations
Changed method of starting load/save operations
<h3>Release Name: 2.000-beta17</h3>
<h3>Release Name: 2.000-beta17</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added new rendering system
Added new rendering system
* Added Image Display Component
Added Image Display Component
* Added Configurable Message Component
Added Configurable Message Component
* You can now autotype individual words in an autocomplete box using Ctrl+Space (on any platform) or Command+Shift+Space (on macs only) or Ctrl+Shift+Space (on non-mac-platforms only)
You can now autotype individual words in an autocomplete box using Ctrl+Space (on any platform)
* Fixed problem where arrowheads would drift around while scrolling the ontology
    or Command+Shift+Space (on macs only)
  editor panel
    or Ctrl+Shift+Space (on non-mac-platforms only)
* Changed wording of &quot;load&quot; menu item to Load Ontologies (SF 1826388)
Fixed problem where arrowheads would drift around while scrolling the ontology editor panel
* Changed default ordering of data adapters to something sensible (SF 1826388)
Changed wording of &quot;load&quot; menu item to Load Ontologies (SF 1826388)
* Added clearer error messages when a file of the wrong type is loaded by
Changed default ordering of data adapters to something sensible (SF 1826388)
  the serial adapter (SF 1826388)
Added clearer error messages when a file of the wrong type is loaded by
* Fixed broken autocomplete in Cross Products panel (SF 1825311)
          the serial adapter (SF 1826388)
* Fixed bugs in list editors (SF 1824736 + others)
Fixed broken autocomplete in Cross Products panel (SF 1825311)
* Fixed &quot;change relationship type&quot; bug (SF 1824731)
Fixed bugs in list editors (SF 1824736 + others)
* Disabled autopanning in the graph editor (SF 1820642)
Fixed &quot;change relationship type&quot; bug (SF 1824731)
* Fixed &quot;multiple globe icons&quot; problem (SF 1820621 &amp; 1820134)
Disabled autopanning in the graph editor (SF 1820642)
* Fixed graph dag viewer problems (SF 1820621)
Fixed &quot;multiple globe icons&quot; problem (SF 1820621 &amp; 1820134)
Fixed graph dag viewer problems (SF 1820621)
 
<h3>Release Name: 2.000-beta16</h3>
<h3>Release Name: 2.000-beta16</h3>
<b>Notes:</b>
<b>Notes:</b>
Line 173: Line 167:


<b>Changes:</b>
<b>Changes:</b>
* Added lots o' hotkeys, see release notes on sourceforge
Added lots o' hotkeys, see release notes on sourceforge
* Reworded obsolete warning message (SF 1810837)
Reworded obsolete warning message (SF 1810837)
* Fixed bugs in ancestor &amp; descendant searching (SF 1811624)
Fixed bugs in ancestor &amp; descendant searching (SF 1811624)
* Fixed commit keyboard shortcut (SF 1811771)
Fixed commit keyboard shortcut (SF 1811771)
* Fixed save bug (SF 1811658)
Fixed save bug (SF 1811658)
* Added ability to expand the full path to a term in the Graph Editor
Added ability to expand the full path to a term in the Graph Editor
  (this can be disabled in the configuration screen) (SF 1811581)
          (this can be disabled in the configuration screen) (SF 1811581)
* When multiple child terms are added, they are assigned to the parent namespace
When multiple child terms are added, they are assigned to the parent namespace
  (SF 1814547)
          (SF 1814547)
* Default id rule is no longer broken (SF 1811685)
Default id rule is no longer broken (SF 1811685)
* Text edit hotkey now works (SF 1811771)
Text edit hotkey now works (SF 1811771)
* Fixed problem where table lists in the text editor did not autocommit
Fixed problem where table lists in the text editor did not autocommit
  pending edits when their values are requested. This manifested as bugs
          pending edits when their values are requested. This manifested as bugs
  in the dbxref and synonym editing lists (SF 1814568).
          in the dbxref and synonym editing lists (SF 1814568).
* Added add/remove buttons to renderer lists in Global Filter Manager
Added add/remove buttons to renderer lists in Global Filter Manager
* Load/save error details are once again displayed
Load/save error details are once again displayed
* Created image saving plugin
Created image saving plugin
* No more flickers of movement in graph no-animations mode
No more flickers of movement in graph no-animations mode
* Added option to hide &quot;Search results&quot; prefix for search results (SF 1816398)
Added option to hide &quot;Search results&quot; prefix for search results (SF 1816398)
<h3>Release Name: a></h3>
<h3>Release Name: a></h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added ability to remove consider/replaced-by terms with the right-click &quot;delete&quot; option
Added ability to remove consider/replaced-by terms with the right-click &quot;delete&quot; option
* Added in-panel &quot;popup-window&quot; that appears when a parent/child expansion control
Added in-panel &quot;popup-window&quot; that appears when a parent/child expansion control
  is clicked in the graph editor
          is clicked in the graph editor
* Disabled default spell checking when saving
Disabled default spell checking when saving
* Fixed icon configuration bugs
Fixed icon configuration bugs
* Fixed text editor bugs
Fixed text editor bugs
* Fixed drag and drop bugs
Fixed drag and drop bugs
* Fixed autocommit bugs
Fixed autocommit bugs
* Fixed right-click editing menu bugs
Fixed right-click editing menu bugs
* Fixed expanding children when right-clicking in graph editor
Fixed expanding children when right-clicking in graph editor
<h3>Release Name: 2.000-beta14</h3>
<h3>Release Name: 2.000-beta14</h3>
<b>Notes:</b>
<b>Changes:</b>
<b>Changes:</b>
* Fixed Save As lockups
Fixed Save As lockups
* Fixed autocomplete bugs
Fixed autocomplete bugs
* Changed autocomplete box in search control to initiate a search if enter is
Changed autocomplete box in search control to initiate a search if enter is
  pressed when the autocomplete popup is hidden
          pressed when the autocomplete popup is hidden
* Added lightbulb tooltips in new search controls
Added lightbulb tooltips in new search controls
* Graph editor tooltips are no longer animated in no-animations mode
Graph editor tooltips are no longer animated in no-animations mode
* Fixed bugs in reasoning over intersections with sub-properties
Fixed bugs in reasoning over intersections with sub-properties
* Graph editor now only pans to a newly selected node if it is not currently on
Graph editor now only pans to a newly selected node if it is not currently on the screen
  the screen
Fixed bug where OBO-Edit would not exit properly if closed from the window controls
* Fixed bug where OBO-Edit would not exit properly if closed from the window
Added possible fixes for Windows XP problems - if problems persist, try the
  controls
          command-line switch -J-DuseModalProgressMonitors=false to disable a potentially
* Added possible fixes for Windows XP problems - if problems persist, try the
          problematic feature on Windows
  command-line switch -J-DuseModalProgressMonitors=false to disable a potentially
Improved animation disabling code
  problematic feature on Windows
Animations can now be disabled in the graph dag viewer
* Improved animation disabling code
Added unicode character searching
* Animations can now be disabled in the graph dag viewer
Progress windows now automatically choose the correct size
* Added unicode character searching
Added better progress bar updating for long-running tasks
* Progress windows now automatically choose the correct size
Added support for plugins
* Added better progress bar updating for long-running tasks
* Added support for plugins
<h3>Release Name: 2.000-beta13</h3>
<h3>Release Name: 2.000-beta13</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Faster graph relayout
Faster graph relayout
* Changed expand/collapse graph editor controls
Changed expand/collapse graph editor controls
* Graph editor node boxes are now sized to just fit the node label
Graph editor node boxes are now sized to just fit the node label
* Link lines in graph editor will no longer appear above term boxes
Link lines in graph editor will no longer appear above term boxes
* Changed default font size to 12 point
Changed default font size to 12 point
* Fixed bugs in reloading saved renderers
Fixed bugs in reloading saved renderers
* User-added links are no longer trimmed by the reasoner
User-added links are no longer trimmed by the reasoner
<h3>Release Name: 2.000-beta12</h3>
<h3>Release Name: 2.000-beta12</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Fixed bugs where sometimes screen would go blank when showing a new component
Fixed bugs where sometimes screen would go blank when showing a new component
* Big reasoner speedups
Big reasoner speedups
* BIG editing speedups
BIG editing speedups
* New search interface
New search interface
* Updated filtering interface in most places (old filtering system is still in
Updated filtering interface in most places (old filtering system is still in use for filtered saves)
  use for filtered saves)
Graph Editor now supports filtering (but not rendering)
* Graph Editor now supports filtering (but not rendering)
<h3>Release Name: 2.000-beta11</h3>
<h3>Release Name: 2.000-beta11</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Fixed bugs in obo2obo
Fixed bugs in obo2obo
* Fixed bug in dbxref checking that greatly increases speed of verification checks
Fixed bug in dbxref checking that greatly increases speed of verification checks
* Fixed bug where links don't work properly in verification results page
Fixed bug where links don't work properly in verification results page
* Dbxref verification no longer reports % as a non-dbxref character
Dbxref verification no longer reports % as a non-dbxref character
* Added resizable graph overview panel to the graph editor
Added resizable graph overview panel to the graph editor
* Added &quot;Remove redundant links...&quot; menu item
Added &quot;Remove redundant links...&quot; menu item
* Fixed bug where panning the graph editor would cause view to jump wildly
Fixed bug where panning the graph editor would cause view to jump wildly
* Dbxref library buttons now work
Dbxref library buttons now work
* Fixed bug where dag graph view would be disconnected if there were many is_a
Fixed bug where dag graph view would be disconnected if there were many is_a
  links between the selected term and the first non-is_a link in a transitive
          links between the selected term and the first non-is_a link in a transitive path
  path
Graph editor now does text wrapping
* Graph editor now does text wrapping
OBO-Edit no longer applies font changes to menus - instead it uses the system
* OBO-Edit no longer applies font changes to menus - instead it uses the system
          default. This should allow better integration with a given platform's look and feel
  default. This should allow better integration with a given platform's look and feel  
<h3>Release Name: 2.000-beta10</h3>
<h3>Release Name: 2.000-beta10</h3>
<b>Notes:</b>
<b>Changes:</b>
<b>Changes:</b>
* Improved Graph DAG Viewer display
Improved Graph DAG Viewer display
* Fixed bugs in search panel selection that would make it impossible to select search
Fixed bugs in search panel selection that would make it impossible to select search
  results if many intersection definitions were loaded
          results if many intersection definitions were loaded
* Dangling relationship types are now supported
Dangling relationship types are now supported
* Fixed bugs in displaying dangling references in the intersection editor
Fixed bugs in displaying dangling references in the intersection editor
* Changed implementation of links in OBO-Edit so that most link objects should use
Changed implementation of links in OBO-Edit so that most link objects should use
  about half the space they used to use (this is significant, particularly when the
          about half the space they used to use (this is significant, particularly when the
  reasoner is running, because there are *far* more links than terms)
          reasoner is running, because there are *far* more links than terms)
* Fixed reasoner bugs that would manifest with certain kinds of redundant links
Fixed reasoner bugs that would manifest with certain kinds of redundant links
* Improved support for reading in links implied by an external reasoner
Improved support for reading in links implied by an external reasoner
* Platform independent OBO-Edit launcher now reads memory settings correctly
Platform independent OBO-Edit launcher now reads memory settings correctly
* Font changes update immediately. No need to restart!
Font changes update immediately. No need to restart!
* Fixed inconsistencies in typeface, background colors and button colors
Fixed inconsistencies in typeface, background colors and button colors
<h3>Release Name: 2.000-beta9</h3>
<h3>Release Name: 2.000-beta9</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added scale bar to graph editor
Added scale bar to graph editor
* Changed the way toolbar is added to the graph editor to save space
Changed the way toolbar is added to the graph editor to save space
<h3>Release Name: 2.00-beta8</h3>
<h3>Release Name: 2.00-beta8</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Fixed bugs in implied link expansion menu
Fixed bugs in implied link expansion menu
* Fixed search bugs
Fixed search bugs
* Fixed bug where Configuration Manager settings were lost
Fixed bug where Configuration Manager settings were lost
* Greatly sped up save of Configuration Manager settings
Greatly sped up save of Configuration Manager settings
* Individual component settings now save properly
Individual component settings now save properly
* Added OWL URL reader adapter
Added OWL URL reader adapter
<h3>Release Name: 2.000-beta7</h3>
<h3>Release Name: 2.000-beta7</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Beta versions now write settings to the .oboeditbeta directory
Beta versions now write settings to the .oboeditbeta directory
<h3>Release Name: 2.000-beta6</h3>
<h3>Release Name: 2.000-beta6</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* obomerge now properly merges consider and replaced_by tags
obomerge now properly merges consider and replaced_by tags
* New memory settings screen in installers
New memory settings screen in installers
<h3>Release Name: a></h3>
<h3>Release Name: a></h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
* Added global selection controls to component title bars
Added global selection controls to component title bars
* Added filter control button to component title bars
Added filter control button to component title bars
* Reinstated autosave; autosave files are now in OBO format
Reinstated autosave; autosave files are now in OBO format
* Disabling graph editor animations now disables tooltip popup animations as well
Disabling graph editor animations now disables tooltip popup animations as well
* Added ability to right-click highlighted errors in text editor and choose a
Added ability to right-click highlighted errors in text editor and choose a
  quick fix from the popup menu
          quick fix from the popup menu
* obo2obo now supports dangling links in loaded-in files
  obo2obo now supports dangling links in loaded-in files
<h3>Release Name: 2.000-beta4</h3>
<h3>Release Name: 2.000-beta4</h3>
<b>Notes:</b>
<b>Notes:</b>
Line 332: Line 309:
* Autocommit mode is always on
* Autocommit mode is always on
<b>Changes:</b>
<b>Changes:</b>
* Fixed search
Fixed search
* Changed to IDW docking framework
Changed to IDW docking framework
* Changed the way automatic error reporting works
Changed the way automatic error reporting works
* Changed synonym editor to list-based editor
Changed synonym editor to list-based editor
* Enabled basic perspective switching in the text editor
Enabled basic perspective switching in the text editor
* Added quick configuration buttons to docking headers
Added quick configuration buttons to docking headers
<h3>Release Name: 2.000-beta3</h3>
<h3>Release Name: 2.000-beta3</h3>
<b>Notes:</b>


<b>Changes:</b>
<b>Changes:</b>
Line 350: Line 326:
   * Text-edit error checking is disabled
   * Text-edit error checking is disabled
   * Some quick-fixes are not available
   * Some quick-fixes are not available
   * The automatic error loader will occassionally report a non-existent error, usually one about definitions with no dbxrefs, even though they're there
   * The automatic error loader will occassionally report a non-existent error, usually one about definitions with no dbxrefs,
        even though they're there
   * The user's guide is totally out of date
   * The user's guide is totally out of date
<b>Changes:</b>
<b>Changes:</b>
* Fixed some problems in graph-based editing
Fixed some problems in graph-based editing
* Added the javadocking system
Added the javadocking system
* Added some spellcheck features
Added some spellcheck features
* Added dynamic error checking displays
Added dynamic error checking displays
* The settings directory can now be specified with the &quot;-Dprefsdir=&quot; option
The settings directory can now be specified with the &quot;-Dprefsdir=&quot; option
<h3>Release Name: 2.000-beta1</h3>
<h3>Release Name: 2.000-beta1</h3>
<b>Notes:</b>
<b>Notes:</b>
This is the first beta release of OBO-Edit 2.0. It's going to be buggier than you're used to in an OBO-Edit release, but we need user feedback on the new graph editor.
This is the first beta release of OBO-Edit 2.0. It's going to be buggier than you're used to in an OBO-Edit release, but we need user feedback on the new graph editor.
<b>Changes:</b>
<h3>Release Name: a></h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where &quot;on reasoner&quot; checks always ran at load,
  even if the reasoner was not enabled.
* Fixed bug where the reasoner drew many incorrect disjoint_from inferences
* Fixed bug where disjointness verification check would double-report errors
* Made default size of OBO advanced configuration screen much larger, and
  rearranged components to make better use of available space
* Fixed bug in relative path resolution of OBO &quot;import&quot; tags
<h3>Release Name: 1.100-beta24</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where various user-defined check attributes would not load
* Fixed bug where only the first non-fatal warning would display when saving
* Fixed bug where user-defined checks could not be deleted
<h3>Release Name: 1.100-beta23</h3>
<b>Notes:</b>
<b>Changes:</b>
* User-defined verification checks now load properly when OBO-Edit is restarted
<h3>Release Name: 1.100-beta22</h3>
<b>Notes:</b>
<b>Changes:</b>
* Added diagnostic messages to help track down a rarely seen Category Manager
  load/save bug
* Changed compilation settings to add greater usefulness to stderr output
* Fixed reasoner bug caused by incomplete transitivity rules
* Verification plugin no longer shows hyperlinks in situations where clicking the
  link would have no effect
* Fixed bug where beta21 required Java 1.5 instead of Java 1.4
* Fixed reasoner bug that caused obo2obo to fail when using reasoner
<h3>Release Name: 1.100-beta21</h3>
<b>Notes:</b>
<b>Changes:</b>
* A warning will appear if the screen is locked around a non-visible path
* A progress bar now pops up while the reasoner is working.
* Fixed broken load history browse button.
* Fixed DAG Viewer slow update (at least in some circumstances)
* Fixed problem where filtering seemed to always be strict (which was actually
  caused by an underlying bug that was probably effecting the display in other ways)
* Fixed bugs in history system
* Removed the sub-selection control and added buttons so the sub-selection can be
  controlled via the ontology editor panel
<h3>Release Name: 1.100-beta20</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed dangling propertyValue bug
* Fixed bug where non-transitive paths were displayed in the DAG Viewer even
  when the &quot;Show non-transitive paths&quot; setting was disabled
* Fixed bug where only obsolete search results could be selected
* Layout editor now provides useful error messages when too many subtags are added
  to a tag that normally only allows one subtag
<h3>Release Name: 1.100-beta19</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed a number of reasoner bugs
* Fixed problems with DAG Viewer performance
* Fixed DAG Viewer problems in cyclic ontologies
* Fixed link filter editor bugs
* Fixed bug in synonym category manager
* Fixed bug in 'write id rules' control in OBO file save gui
<h3>Release Name: 1.100-beta18</h3>
<b>Notes:</b>
<b>Changes:</b>
* Eliminated save bottlenecks and other performance problems introduced by new
  datamodels
* Fixed errors in filtered reasoner behavior introduced by datamodel improvements
* Fixed null pointer exceptions when running &quot;obodiff -t xml&quot;
* Fixed bad error location reporting from OBO adapter when loading files that use
  the import statement
<h3>Release Name: 1.100-beta17</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where OBO-Edit put in line feed characters in Windows
* Fixed DAG Viewer bugs
* Added more detail to search summary line in filter editor
* Fixed bugs when using the Root search aspect to filter
* Crippled reasoner code so that the OBO-Edit gui freezes while the ontology is being
  re-reasoned. This sucks, but it's better than the current behavior where
  users see the ontology being taken apart and reassembled by the reasoner in real
  time (which leads to all kinds of strange graphical artifacts)
* Fixed spurious &quot;uncommitted text edits&quot; messages from terms that have cross-product
  definitions AND explicit assertions of the cross product links
* 100-fold speedup when the &quot;flower button&quot; (actually called the reasoned
  prefilter button) is used
* Reduced lag between when a term is selected and when it appears in the text
  editor by around 75%
* Fixed bug where ontologies with dbxref descriptions that contain commas
  cannot be saved
<h3>Release Name: 1.100-beta16</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed constant exception popup caused by a verification configuration file that refers to non-existant checks
<h3>Release Name: a></h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where obomerge would unobsolete some terms
* Fixed bug where obomerge would create duplicate synonyms
* Fixed constant NullPointException messages from the Verification Plugin
* Updated documentation
<h3>Release Name: 1.100-beta14</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed giant Configuration Panel bug
* Fixed bugs that occured when loading plugins with external libraries
* Unsealed org.geneontology.oboedit.plugin package (which was creating problems when
  loading external plugins)
* OBO-Edit can finally load extended characters again
* Removed harmless startup NullPointerException messages
* Added obomerge to platform independent version
* Finished documentation (I think)
<h3>Release Name: 1.100-beta13</h3>
<b>Notes:</b>
Additional Files:
* questionplugin.jar
Say hello to the first external OBO-Edit Plugin! This is the Question Plugin. When a term is selected, the Question Plugin displays a list of (possibly) interesting questions about the term, and the answers to those questions.
Currently all answers consist of a structured list of term names. If a term name is clicked, it will become selected in the main gui.
To get more info about how a question is being answered, mouseover the question text.
To install this plugin, place questionplugin.jar in the extensions subdirectory of your OBO-Edit installation directory.
* oboedit.jar
The recently added oboedit.jar file is a patch to fix an obomerge bug where instead of writing the merge results to disk it would just write out one of the original files in 1.2 format.
To install:
* Shut down OBO-Edit
* Copying the oboedit.jar file into the runtime/ subdirectory of your OBO-Edit installation
It's installed!
<b>Changes:</b>
* Changed the implementation of sets in the OBO-Edit datamodels. This will
  lead to negligibly slower performance (I would be stunned if it were a &gt; 5%
  performance hit) but dramatically reduced memory usage (OBO-Edit will use
  50-80% less memory with most ontologies). Many thanks to
  Mark Gibson and his profiling tools for pointing out the bad memory use.
* Fixed problems with right-click menu when there is no selection
* Fixed unhandled exception when changing the relationship type of a link and
  an ancestor link at the same time
* Fixed bug where no warning would pop up when OBO-Edit ran out of ids
* Fixed autocommit bugs that appeared after the autocommit settings had been
  changed
* Fixed bug where asterisk did not appear on cross-product tab for terms that
  had cross products defined
* Fixed bug where dbxrefs containing a # would be marked as containing non-URI
  characters
* Fixed bug where some verification checks would be run on text edit even if
  the user had disabled them
* The plugin system can now load external libraries
* Completed documentation for the verification plugin
<h3>Release Name: 1.100-beta12</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where last item in an OBO file would not have its namespace loaded
  correctly if it used the default ontology namespace
* Fixed StackOverflowError when filtering ancestors in an ontology with cycles
* Fixed obo2obo bugs
* Fixed problem reading OBO files with curly braces in term names
* Graph viewer plugin now wraps long term names on spaces, tabs, underscores,
  dashes and commas
* Fixed bad automatic sizing of definition dbxref control
* Added Quick Fix for verification warning about multiple spaces in a row
* Improved messages for verification warnings about multiple spaces in a row and
  missing spaces around periods.
* Fixed bugs where quick fixes that modified the ontology would not work in
  autocommit mode
* Improved documentation
<h3>Release Name: 1.000-beta11</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed lost genus info
* Fixed major new bugs in filter editor
* Fixed bugs when starting OBO-Edit with no exiting configuration data
* If id generation rules were loaded from a file, OBO-Edit now saves those
  rules by default
<h3>Release Name: 1.100-beta10</h3>
<b>Notes:</b>
<b>Changes:</b>
* Bug fixes
* Added quick-fix items to verification system
* Added lots of quick fixes
* Fixed bug where synonym categories with bad ids could be saved
* Fixed bug where primary selector would be deselected when the configuration changed
* Fixed user's guide search problems
* Created local filtering checkbox in Graph Viewer
* Mac installer can now create aliases
<h3>Release Name: 1.100-beta9</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug in text verifications that would cause verification step
  to crash in some circumstances.
* Improved information given in unhandled exception message
* Fixed bad reasoner link trimming behavior
* Fixed bugs in memory setting updates from installer
* Fixed Mac OS launcher bugs
* Added script launching to obo2obo
<h3>Release Name: 1.100-beta8</h3>
<b>Notes:</b>
<b>Changes:</b>
* Rebuilt platform independent launchers to use the same vm options passing
  as the installer-built launchers
* Fixed bug when loading an obo file with an exclamation point inside of quotes
* Fixed bugs in writing memory settings to .vmoptions and Info.plist files
* Added popup message for out of memory errors
* Fixed bugs in import code
* Documentation improvements
<h3>Release Name: 1.100-beta7</h3>
<b>Notes:</b>
<b>Changes:</b>
* Added hidden -fixdbxrefs parameter to obo2obo
* Added &quot;Always save properties&quot; mode to OBO advanced save
* Changed default layout
* Added &quot;Use default layout&quot; button to layout editor
* Documentation updates
<h3>Release Name: 1.100-beta6</h3>
<b>Notes:</b>
<b>Changes:</b>
* Bug fixes
* Added support for saving reasoned links to disk in obo2obo
* Added support for realizing implied links as real links in OBO adapter
* Added clash detection/repair in obomerge
* Documentation improvements
<h3>Release Name: a></h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed problem where FindPanel forgets settings on exit
* Sorted properties in CopyAction, MoveAction and TypeChangeAction menus
* Rebuilt installers
<h3>Release Name: 1.100-beta4</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed OBOMerge problems
* Fixed problems when deleting newly created, unmodified dbxrefs
* Fixed launcher problems
* Fixed bug where dbxrefs from the DbxrefPlugin would disappear
  from the definition refs editor when the edit button was pressed
* Improved descriptions in OBODiff for several types of history items
<h3>Release Name: 1.100-beta3-rebuild</h3>
<b>Notes:</b>
Rebuilt installers for beta3 to try to fix widespread installation problems.
<b>Changes:</b>
<h3>Release Name: 1.100-beta3</h3>
<b>Notes:</b>
<b>Changes:</b>
* Added &quot;Root&quot; aspect to search aspects
* Added verification system
* Added pre-trim type filters to save
* Added root detection algorithm to save
* OBO-Edit chooses much better default selection paths when a search
  result is selected
* Non-transitive links are now hidden by default
* Added isa complete filter
* Added transitivity, cyclicity, symmetry controls for properties
<h3>Release Name: 1.100-beta2</h3>
<b>Notes:</b>
<b>Changes:</b>
* Added &quot;Root&quot; aspect to search aspects
* Added verification system
* Added pre-trim type filters to save
* Added root detection algorithm to save
* OBO-Edit chooses much better default selection paths when a search
  result is selected
* Non-transitive links are now hidden by default
* Added isa complete filter
<h3>Release Name: 1.100-beta1</h3>
<b>Notes:</b>
<b>Changes:</b>
* Moved to XML format for configuration files
* Added buttons to add and remove data adapter profiles
* Added &quot;Are you sure you want to exit?&quot; feature
* Added graph plugin save capability for PNG, DOT and XDOT format
* Lowered memory use
* Added text edit autocommit mode
* Added warnings for lost text edits when not in autocommit mode
* Added XML sub-layouts
* Added lots of new XML layout tags
* Added -parsecomments and -writecomments tags to obo2obo
* Added text field checks for incomplete sentences, missing title
  case, extra whitespace characters
<h3>Release Name: 1.002-beta3</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug in saving consider tags in OBO format
* Fixed bug where destroy confirmation message might appear
  behind the main window
* Fixed bug where OBO serializer was writing newlines in comments
  incorrectly
* Added obo2obo script
* Parent-child merges (or merges between any terms) are now allowed.
  See the user's manual for potential dangers of this new behavior.
* Merged terms are now assigned a definition and comment consisting of
  the definition/comment of the source and target terms concatenated
  together.
* Any number of replacement or consider terms are allowed for obsolete
  terms.
<h3>Release Name: OBO-Edit 1.002-beta2</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where OBO serializer was writing newlines in comments incorrectly
* Added obo2obo script
* Parent-child merges (or merges between any terms) are now allowed. (See the user's manual for potential dangers of this new behavior)
* Merged terms are now assigned a definition and comment consisting of the definition/comment of the source and target terms concatenated together.
* Any number of replacement or consider terms are allowed for obsolete terms.
<h3>Release Name: OBO-Edit 1.002-beta1</h3>
<b>Notes:</b>
<b>Changes:</b>
* Fixed bug where OBO serializer was writing newlines in comments incorrectly
* Added obo2obo script
<h3>Release Name: 1.000-beta27</h3>
<b>Notes:</b>
<b>Changes:</b>
* Self-loops no longer allowed from Cross Product editor

Latest revision as of 15:35, 30 June 2014

Release Name: 2.000-beta25

Notes: Bye, y'all!

Changes:

  • Graph DAG Viewer succinct mode is fixed! (SF 1829694)
  • Fixed some layout problems in Configuration Manager
  • Added a "has multiple roots" search criterion (SF 1833117)
  • Modification stamps are now optional (SF 1820650)
  • Made a stab at stabilizing progress window size (SF 1816415)
  • Fixed bug where Configuration Manager would not save if window close button (as opposed to titlebar close button) was clicked
  • Fixed bug where invisible zombie components could be trapped in a layout if an undocked component was closed using the window close button (rather than the titlebar button)
  • Fixed minor bug in search configuration
  • Rebuilt image plugin

Release Name: 2.000-beta24

Changes:

  • (See beta23 release notes for many other changes)
  • Fixed bug where menus would not appear (SF 1845378)
  • Removed option to create a desktop link from installer (SF 1845378)

Release Name: 2.000-beta23

Changes:

Added framework to attach help topics to components. If a component has a help
         topic attached, a little question mark button appears in the title bar. When
         the button is clicked, help for that component is displayed.
Text edits no longer lost when a new search item is selected (SF 1844991)
Fixed numerous bugs in custom verification checks
Fixed bug where Graph Editor would not properly display explanations for some
         links (thanks to Chris for fixing this)
Fixed bug where the save dialog would appear when there were fatal errors in the
         ontology (all the more ironic because it appeared after a message explaining that you
         will not be allowed to save until these errors are fixed)
Redundant and implied links once again have a distinctive appearance - you will need
         to delete ~/.oboeditbeta/filter_prefs.xml to get the new default settings (SF 1844745)
Many changes to text editor quickfix system (SF 1844885):
         * Added quickfix for "no punctuation at end of sentence" error
         * Added quickfix for "non-url characters in dbxref" error
         * In text editor panes, errors are highlighted in red. Errors that can be quickfixed
           are also underlined.
         * In list editors (like the dbxref editor or the synonym editor), items that contain
           errors are listed in red. Items that can be quickfixed display a quickfix icon
           next to them. Quickfixes can be applied by right-clicking an item and selecting
           a fix from the menu.
         * Quickfixes are now available in the synonym text text editor.

Release Name: 2.000-beta22

Changes:

Global renderers are now used to display search results
Fixed problem where live verification data would not be updated properly when
         definition dbxref problems have been fixed (SF 1844213)
The big, distracting text editor error message panel has been removed. Now
         error messages appear in the text editor's title bar. Mousing over the title
         bar will display a tooltip listing the errors.
Remove redundant links problem (SF 1844193) and associated reasoned link
         deletion bugs are fixed.
Platform independent launcher bug fixed (SF 1843989)
Log files are being generated correctly again (SF 1844183)
Garbage tabs no longer appear if OBO-Edit is shut down with search results
         still visible (SF 1844184)
Fixed disappearing global/local selection mode buttons (SF 1838678)
Added new log messages to aid in diagnosis of rogue popup menu problem
         (SF 1839411)
Fixed problem where list editors (like the synonym editor) could cause
         unexpected changes if the selection changed while the editor panel was
         still open (SF 1837056)


Release Name: 2.000-beta21

Changes:

Fixed bug where synonym dbxrefs would be lost on synonym edit (SF 1843460)
Added editor for synonym dbxrefs
Dbxref listing is now always the same size in synonym editor (SF 1843405)
Live error highlighting in the text editor now works properly
All TableList editors (like the dbxref editors and the synonym editor) now commit their changes
   the minute they are unfocused, which should make them easier to use

Release Name: 2.000-beta20

Changes:

Added customizable heat maps
Right-clicking a component's title bar allows you to change the title
Search control now remembers last settings
Search results text is now customizable in search control settings
Added new Icons & Colors tab in configuration manager (SF 1838664)
Added icons for OBO-Edit application and installer
The Mac OS "Quit" and "About" menus are now properly handled
         by OBO-Edit
Text edits now autocommit if another edit occurs (for example,
         if you have pending text edits and you create a new term, your text
         edits are no longer lost)
Changed Parent Editor appearance to make things fit on the screen
         better
Fixed unhandled exceptions when clicking "classes", "properties",
         etc (SF 1840390)
Fixed undo/redo failures (SF 1839564, SF 1839564)
Fixed shortcut key bugs (SF 1838830, SF 1836524)
Fixed bug where "<new term>" did not appear correctly after new
         terms were created (SF 1838829)
Made "working" popup look a little better (SF 1838787)
Fixed bug where search results disappeared between layout switches
         (SF 1838784)
Fixed bug where panels would not update correctly after new ontology load
         (SF 1838764), and for good measure fixed some other screen update bugs in
         the graph editor, including bugs that left stray arrows floating around
Fixed graphical artifacts and switched-around button behaviors in
         term change tracker (SF 1838679)
Fixed problem where a change in the autocommit setting did not cause
         "commit" and "revert" buttons to immediately appear (SF 1838673)
Fixed parent editor drag and drop button (SF 1838669)
Fixed bug where namespace changes would not be saved (SF 1838656)
Fixed icon browsing problem (SF 1838651)
Fixed bug where OBO-Edit would not display installer-generated
         memory settings on Mac OS (SF 1838648)
Installer now WILL create a desktop icon if you ask it to (SF 1838648)
If there are unsaved changes to an ontology, a special message appears
         in the quit confirmation dialog (SF 1838644) (note that this message
         will appear whether or not you have "confirm on exit" checked, on the
         theory that anyone would want to know about this potential disaster)
Fixed spurious "unsaved changes" message (SF 1837005)
It is now possible to re-select already selected search results
         (SF 1836549)

Release Name: 2.000-beta19

Changes:

Added Import... to the file menu
Added Fix ids... to the file menu
Added a verification system check for bad ids. The id fix options are all
         available as quickfixes
Added a new system for installing custom graph decorators

Release Name: 2.000-beta18

Changes:

Fixed OBO 1.2 save bug (SF 1827542)
Fixed bugs when saving filtered files with range & domain defined
Changed method of starting load/save operations

Release Name: 2.000-beta17

Changes:

Added new rendering system
Added Image Display Component
Added Configurable Message Component
You can now autotype individual words in an autocomplete box using Ctrl+Space (on any platform)
    or Command+Shift+Space (on macs only)
    or Ctrl+Shift+Space (on non-mac-platforms only)
Fixed problem where arrowheads would drift around while scrolling the ontology editor panel
Changed wording of "load" menu item to Load Ontologies (SF 1826388)
Changed default ordering of data adapters to something sensible (SF 1826388)
Added clearer error messages when a file of the wrong type is loaded by
         the serial adapter (SF 1826388)
Fixed broken autocomplete in Cross Products panel (SF 1825311)
Fixed bugs in list editors (SF 1824736 + others)
Fixed "change relationship type" bug (SF 1824731)
Disabled autopanning in the graph editor (SF 1820642)
Fixed "multiple globe icons" problem (SF 1820621 & 1820134)
Fixed graph dag viewer problems (SF 1820621)

Release Name: 2.000-beta16

Notes: To use the new image saving plugin, create the following folder:

~/.oboeditbeta/extensions

and put the jar file in there. When you start OBO-Edit, every component will have a tiny camera icon in the title bar that lets you save an image of the component in a number of different formats. Also, when you right-click in the graph editor, you have the option to save an image of the current graph (unlike the title bar button, the image will contain the entire graph, even if the whole graph doesn't fit on the screen).

Changes:

Added lots o' hotkeys, see release notes on sourceforge
Reworded obsolete warning message (SF 1810837)
Fixed bugs in ancestor & descendant searching (SF 1811624)
Fixed commit keyboard shortcut (SF 1811771)
Fixed save bug (SF 1811658)
Added ability to expand the full path to a term in the Graph Editor
         (this can be disabled in the configuration screen) (SF 1811581)
When multiple child terms are added, they are assigned to the parent namespace
         (SF 1814547)
Default id rule is no longer broken (SF 1811685)
Text edit hotkey now works (SF 1811771)
Fixed problem where table lists in the text editor did not autocommit
         pending edits when their values are requested. This manifested as bugs
         in the dbxref and synonym editing lists (SF 1814568).
Added add/remove buttons to renderer lists in Global Filter Manager
Load/save error details are once again displayed
Created image saving plugin
No more flickers of movement in graph no-animations mode
Added option to hide "Search results" prefix for search results (SF 1816398)

Release Name: a>

Changes:

Added ability to remove consider/replaced-by terms with the right-click "delete" option
Added in-panel "popup-window" that appears when a parent/child expansion control
         is clicked in the graph editor
Disabled default spell checking when saving
Fixed icon configuration bugs
Fixed text editor bugs
Fixed drag and drop bugs
Fixed autocommit bugs
Fixed right-click editing menu bugs
Fixed expanding children when right-clicking in graph editor

Release Name: 2.000-beta14

Changes:

Fixed Save As lockups
Fixed autocomplete bugs
Changed autocomplete box in search control to initiate a search if enter is
         pressed when the autocomplete popup is hidden
Added lightbulb tooltips in new search controls
Graph editor tooltips are no longer animated in no-animations mode
Fixed bugs in reasoning over intersections with sub-properties
Graph editor now only pans to a newly selected node if it is not currently on the screen
Fixed bug where OBO-Edit would not exit properly if closed from the window controls
Added possible fixes for Windows XP problems - if problems persist, try the
         command-line switch -J-DuseModalProgressMonitors=false to disable a potentially
         problematic feature on Windows
Improved animation disabling code
Animations can now be disabled in the graph dag viewer
Added unicode character searching
Progress windows now automatically choose the correct size
Added better progress bar updating for long-running tasks
Added support for plugins

Release Name: 2.000-beta13

Changes:

Faster graph relayout
Changed expand/collapse graph editor controls
Graph editor node boxes are now sized to just fit the node label
Link lines in graph editor will no longer appear above term boxes
Changed default font size to 12 point
Fixed bugs in reloading saved renderers
User-added links are no longer trimmed by the reasoner

Release Name: 2.000-beta12

Changes:

Fixed bugs where sometimes screen would go blank when showing a new component
Big reasoner speedups
BIG editing speedups
New search interface
Updated filtering interface in most places (old filtering system is still in use for filtered saves)
Graph Editor now supports filtering (but not rendering)

Release Name: 2.000-beta11

Changes:

Fixed bugs in obo2obo
Fixed bug in dbxref checking that greatly increases speed of verification checks
Fixed bug where links don't work properly in verification results page
Dbxref verification no longer reports % as a non-dbxref character
Added resizable graph overview panel to the graph editor
Added "Remove redundant links..." menu item
Fixed bug where panning the graph editor would cause view to jump wildly
Dbxref library buttons now work
Fixed bug where dag graph view would be disconnected if there were many is_a
         links between the selected term and the first non-is_a link in a transitive path
Graph editor now does text wrapping
OBO-Edit no longer applies font changes to menus - instead it uses the system
         default. This should allow better integration with a given platform's look and feel

Release Name: 2.000-beta10

Changes:

Improved Graph DAG Viewer display
Fixed bugs in search panel selection that would make it impossible to select search
         results if many intersection definitions were loaded
Dangling relationship types are now supported
Fixed bugs in displaying dangling references in the intersection editor
Changed implementation of links in OBO-Edit so that most link objects should use
         about half the space they used to use (this is significant, particularly when the
         reasoner is running, because there are *far* more links than terms)
Fixed reasoner bugs that would manifest with certain kinds of redundant links
Improved support for reading in links implied by an external reasoner
Platform independent OBO-Edit launcher now reads memory settings correctly
Font changes update immediately. No need to restart!
Fixed inconsistencies in typeface, background colors and button colors

Release Name: 2.000-beta9

Changes:

Added scale bar to graph editor
Changed the way toolbar is added to the graph editor to save space

Release Name: 2.00-beta8

Changes:

Fixed bugs in implied link expansion menu
Fixed search bugs
Fixed bug where Configuration Manager settings were lost
Greatly sped up save of Configuration Manager settings
Individual component settings now save properly
Added OWL URL reader adapter

Release Name: 2.000-beta7

Changes:

Beta versions now write settings to the .oboeditbeta directory

Release Name: 2.000-beta6

Changes:

obomerge now properly merges consider and replaced_by tags
New memory settings screen in installers

Release Name: a>

Changes:

Added global selection controls to component title bars
Added filter control button to component title bars
Reinstated autosave; autosave files are now in OBO format
Disabling graph editor animations now disables tooltip popup animations as well
Added ability to right-click highlighted errors in text editor and choose a
         quick fix from the popup menu
 obo2obo now supports dangling links in loaded-in files

Release Name: 2.000-beta4

Notes: Known issues:

  • Some text edit errors are reported too many times
  • Modal progress boxes (like the reasoner progress box) sometimes do not disappear properly on Mac OS
  • Autocommit mode is always on

Changes:

Fixed search
Changed to IDW docking framework
Changed the way automatic error reporting works
Changed synonym editor to list-based editor
Enabled basic perspective switching in the text editor
Added quick configuration buttons to docking headers

Release Name: 2.000-beta3

Changes:

  • Fixed swing-based memory leaks
  • Added an option to turn off graph editor animations

Release Name: 2.000-beta2

Notes: Known issues:

  * The text edit tool graph editing tool may have problems
  * Text-edit error checking is disabled
  * Some quick-fixes are not available
  * The automatic error loader will occassionally report a non-existent error, usually one about definitions with no dbxrefs,
        even though they're there
  * The user's guide is totally out of date

Changes:

Fixed some problems in graph-based editing
Added the javadocking system
Added some spellcheck features
Added dynamic error checking displays
The settings directory can now be specified with the "-Dprefsdir=" option

Release Name: 2.000-beta1

Notes: This is the first beta release of OBO-Edit 2.0. It's going to be buggier than you're used to in an OBO-Edit release, but we need user feedback on the new graph editor.