ApE- A Plasmid Editor
	by M. Wayne Davis

Version History

• 1.10.4 (3/10/06)
  • Find displays a message when find fails.
  • Speech (Mac native only, for now)
  • Live updating of enzyme selector with changes in selection
  • Fixed bug: backwards asymmetric 5 and 6 cutters
  • Fixed bug: recomb tool: comment is from the wrong source
  • Align: affine gap penalty
  • SCF trace files can be opened
  • "Genes" added back to text map.
  • "print color" checkbox in menus
  • Gateway cloning tool
  • Aqua wormbase blast use javascript, fixes potential incompatibility to wormbase
• 1.10.2 (1/18/06)
  • Several appearace upgrades in OS X.
  • Fixed bug with hidden/transparent features in graphic maps.
  • Changed Primer hyperlinks to red text instead of red background.
  • ABI traces can be printed as full pages.
  • ABI files now appear in the recent files list.
  • Fixed bug in popup menus on graphic maps
• 1.10.1 (12/26/05)
  • Text can now be printed with color highlighting (this can be slow in MSWindows).
• 1.10 (12/26/05)
  • Upgraded the Tcl/Tk runtime for windows and Mac
  • All fonts are available in preferences
  • Graphic maps- features are now hyperlinked
  • Graphic maps- features are now stacked in circular maps
  • Rebase can be accessed by right/apple clicking on an enzyme in the enzyme selection dialog
• 1.09.1 (8/17/05)
  • bug: OS X numbers on left side were wrong
  • Added NCBI EMBL nucleotide database querry tool
• 1.09 (8/13/05)
  • New Features can be added directly to the sequence without adding them to the feature definition library
  • bug: Saving features that span the origin is now fixed
  • Totaly redesigned the text map dialog
  • Added features as text graphics and translation of cds features on the text map
  • Tab key now switches between the sequence and the file comment boxes
  • Changed the look of the toolbar on XP and OS X
  • Added right click menu on sequence windows
  • Fixed minor bug in scanning for 4-cutter enzymes at the last six bases of a linear sequence
  • Added the option for transparent features
  • Updated Windows metafile and printing routines. Arcs are now drawn more smoothly
• 1.08 (6/22/05)
  • Save in Genbank format
  • Copy prefs and ladders to user prefs dir (big improvement in multi-user systems)
  • Edit button in configure features dialog
  • Prefs: enzyme directory, save format, format warning, selection translate
  • Add/edit features: set saved flag 0
  • column # in the list enzymes dialog.
  • File, date label in digest windows
  • List features: wider tabs
  • File duplicate: file comment: return after from x to y
  • bug: duplicate sequence:feature order not preserved
  • bug: feature display properties: delete: selection unset
• 1.07.2 (3/5/05)
  • Fixed a bug in editing comment fields
  • Fixed a bug when strider enzyme files have spaces in the enzyme names
• 1.07 (3/5/05)
  • Can load diferent translation files in the preferences window
  • abi files can be aligned to each other and to sequence files
  • Fixed some bugs in printing text windows
  • X-scaling abi window
  • New window menu item arangement
  • Fixed bug in compatible enzymes listing
  • Fixed bug in New feature window
  • Mass % in digest window
  • Tooltips show up in the toolbar in OSX
  • Drag and drop works for shortcut files (Windows only)
• 1.06b (2/1/05)
  • Fixed bug in windows causing paste to fail, among other catastrophic failures.
  • Fixed Quit bug in Aqua and Linux (introduced in v1.05 or 1.06)
  • Possibly fixed bug causing no buttons shown in Aqua dialogs
  • Fixed Apple-n -o and -q when no windows open (Aqua)
  • Fixed bug when closing a new window very quickly
• 1.06 (1/22/05)
  • Changed buttons for Edit feature library dialog
  • New fix for window resize bug
  • Fixed bug causing loss of first char of file comments
  • Fixed bug in new enzyme dialog: all lowercase restriction site
  • Now asks to save any unsaved feature library or enzyme sets
  • Made the feature library edit dialog resizable in Aqua (OS X)
  • Fixed bug in new enzyme dialog: invisible OK button in Aqua
  • Drag and drop in windows can resolve shortcut files
  • Added Mass % calculation to the digest window table
  • Added several hotkeys
  • Added several new preference items
  • Preferences are saved when the program quits
• 1.05a (12/22/2004)
  • Added "Difference" calculation to enzyme selector
  • Added reverse complement to ABI trace window
  • Added print window to ABI trace window
  • Added save as svg or wmf to ABI trace window
  • Fixed copy/save/print when scaled over window size in ABI trace window
  • Fixed window lockup in rare text window resize conditions
  • Added Read Enzyme Groups
  • Added a new enzyme file to supplied files
• 1.05 (12/18/2004)
  • Added printing of text analysis windows (Windows and OS X)
  • Added opening of editseq DNA files
  • Fixed a bug in save text as text file
• 1.04c- OS X only(12/12/2004)
  • Added OS X native print dialogs.
  • Fixed a bug in the OS X "Edit Features Library" dialog menu
• 1.04b- OS X only (12/11/2004)
  • Fixed scrolling bug
• 1.04a (12/11/2004)
  • Ctrl-N, Ctrl-O, Ctll-S, etc. work when typing into the comment field
  • Font scaling in eps, metafile and svg files more accurate
  • Y-zoom scale bar in ABI trace files
  • Can change name and color of displayed features
  • Lock/Unlock files for editing
  • Moved Features and Enzyme files to separate directories
• 1.03c (12/04/2004)
  • Mac bug fix for loading Feature files (Can't find Feature file)
• 1.03
  • Minor bug fixes from version 1.00 (11/29/2004)