OBO-Edit 2.0 beta release notes

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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.