Unknown:
--------
? optimize storage of GenBank file within sequence object (to use entire format specification)
? make biolegato support drag and drop
    http://java.sun.com/docs/books/tutorial/uiswing/dnd/dropmodedemo.html


- applet support
- add .biolegato directory support
    - various configuration files
    - colour mask files?
    - interprocess communications files?
- emboss/acd plugin
- Biolegato's own menu and sequence file specifications
    - submenus
    - external group set features
- extract using binary objects (serialization)

Version 0.7.1 (future):
-----------------------
- build test suite
    - core
    - ezmenus
    - gde canvas
    - file formats
- OS X app path support ?
    - add $APP_PATH/Contents/Resources to BioLegato search dirs on OS X
    - add $JAVAROOT support for app packaging
- look into java multithreading?
- consider moving parts of biolegato to separate executables so as to further save on memory
- make a multi-lined menu object
- heavily test undoable support

Version 0.7.0 (current release):
--------------------------------
* <default> for colour mask if nothing is selected
* <multiple selected...> for dropdowns in getsequence that have multiple selections
* copy/paste ensure that it creates new objects
* remove subseq method to improve speed and memory usage
* character based colour mask support (CSV based)
    * header: AA<tab>Colour
    * each line after: characters<tab>#RGB
	example: RHKSY<tab>#A077EF
* add seqcolourdir to properties (will represent the directory with all of the default character colour masks)
* add GDE file format "group" feature
    * add saving of group number
    * add support to read group numbers from files
* add BIOLEGATO_HOME support to BioLegato
* add parsing of other environment variables work for properties
* make seqcolour dirs only load .csv files
* add current directory to .blproperties search path
* updated manpage
* make build.xml generate non-core documentation (currently documentation exists, but is not generated by build.xml)

Version 0.6.2:
--------------
* undo/redo
    * make undo/redo objects that are x,y compatible
    * add undo/redo objects to BLTextArea & GDETextArea
    * update undoable commenting
    * add undo/redo support to GDEList
    * undo/redo on/off property
* make multiple sequence getinfo
* make all group sequences highlighted when one sequence is highlighted
* fix group deletion bug
* seperate list/canvas delete functions (list can remove sequences, canvas can only remove characters from a sequence)
* fix menu windows
    * order of options
    * saving of defaults
    * fix combobox/choicelist saving of defaults
* fix right click menus
* make clipboard able to paste strings from texteditors into biolegato
* implement limit undo stack size parameter
* fix @returns javadoc
* improve how undo/redo on/off property works (make memory conservative versions of functions - booleans)
* improve how textarea scrolls
* fix issue with windows not disposing
* fix undo support
* highlight groups within a list on double click
* select group right menu and Edit menu feature
* fixed choiceorder issue
* make standard contrasting colours properties controlled
* static BLMain
* fix filechooser new file display bugs
* fix filechooser name bug

+----------------+
|****************|
|* OLD VERSIONS *|
|****************|
+----------------+

Version 0.6.1:
--------------
* standardize variable name for BLMain to program
* remove selection objects
* join/split canvas (GDE) into two parts
* restructure menu reading to make more abstract (ezmenu)
* minimize memory imprint of menu widgets
    * RunWindow
    * GDEComboBox
    * GDEChoiceList
    * GDEFileChooser
    * GDETextField
    * GDEChooser
    * GDESlider
* remove selections objects
* attach biolegato to the system clipboard
    http://www.exampledepot.com/egs/java.awt.datatransfer/ToClip.html
* fix features program
* improve SeqDoc finalize method

Version 0.6.0:
--------------
* put quotation marks around all filenames from file_chooser
* optimize refresh size (obtaining length of longest line)
* make commands launch automatically if there are no arguments
* split canvas into seperate plugin jar from menu
* move seqdoc character insertions into Sequence
* implement GDE group editing (all modifications are done on the group of sequences simultaneously)
    * make all text operations x,y based (should increase biolegato speed)
	* make seqdoc x,y based
	    * add x,y seqdoc functions
	    * change all calls to use x,y functions
	    * remove all linear insert/delete functions
	    * remove offset support for seqdoc elements
		* remove offset related functions
		* remove sequence wrapper
	    * fix co-ordinate retrieval
	* make bltextarea insert/delete x,y based
	* make gdetestarea insert/delete x,y based
	* make all x and y's final ints
	* make seqdoc x,y deletion non-rectangular (same as textlines function
	* fix textlines and textrectangle deletion functions
    * add grouping functionality
	* group and an ungroup button
	* add simple group support
	* add group insert/delete code
	* add group number indicator in canvas pane (in front of list - can be inside the list)
	* group permissions (change permissions so if you change one sequence, you change the entire group)
* make rectangular section the default
* remove linear selection option
* make sure that textarea foreground colours do not get greyed out when working with the jlist
* fix selection painting
* add change case menu item
* fix vertical scroll bar

Version 0.5.8:
--------------
* add pseudo-comment parsing (#@)
* file chooser plugin for GDE menu format argtype:file_chooser
* make type detection intrinsic to the sequence class
* fix BLProperties reset function
* factor out colour mask into own package
    * ImportFileAction
    * GDEColourMaskMap
    * GDEColourMaskFile
* make Sequence class intrinsic character testing (Unambiguous/Ambiguous/Alignment Gap)
    * update GDEPositionColour map to use intrinsic testing (for skipdash setting)
* make colour mask support more generic
    * make different map types
    * all maps have a name
    * make masks into file filters which create maps
* make version/command prompt displayable independent of whether a windowing system is installed
* add autodetect type support for GenBank files written by readseq (i.e., no type field)

Version 0.5.7:
--------------
* look over and update entire BioLegato javadoc and commenting
    * look over and update entire javadoc and commenting for biolegato core
        * org.biolegato.core.data.seqdoc
        * org.biolegato.core.data.seqdoc.undo
        * org.biolegato.core.data.sequence
        * org.biolegato.core.main
        * org.biolegato.core.plugins
        * org.biolegato.core.plugintypes
        * org.biolegato.core.properties
    * look over and update entire javadoc and commenting for biolegato GDE support
        * org.biolegato.ezmenu
        * org.biolegato.ezmenu.variables
        * org.biolegato.gdesupport.canvas
        * org.biolegato.gdesupport.canvas.colour
        * org.biolegato.gdesupport.canvas.listeners
        * org.biolegato.gdesupport.canvas.selections
        * org.biolegato.gdesupport.files
        * org.biolegato.gdesupport.menu
    * look over and update entire javadoc and commenting for biolegato standalone plugins
        * GenBank2008
        * FastA
* update manpage content
* optimize colour map draw function to use character array directly
* remove CommandWindow
* add deselect button to SelectByNameWindow
* add J and O to protein unambiguos
* FastA
    * autodetect sequence type
	* default to DNA
	* U only found in RNA
	* F,E,J,L,O,Q,X,Z,* only found in protein
    * only read gi number for name in fasta format
    * see why fasta does not default its colours
    * everything after first space on > line on fasta file is a description
* fix .equals when using a constant to put the constant first
* translateTo bug
* Ribosome produces out1 file with 1 byte in it
    * check priority of parsing (make sure that arg choices of out1, etc. get parsed)

Version 0.5.6:
--------------
* add "I" (synonymous to "D") to ambiguous DNA characters
* fix orignalgb storage
* fix genbank parsing
* make genbank parsing more robust
* make protections sequence dependent
* make protections also protect against insertions
* change colour for letters R,K,H (make teal more obvious)
* add minimum size to help textbox
* updated column numbers to start at 1,1
* updated selectAll function to select name pane
* fixed greying out of text canvas

Version 0.5.5:
--------------
* change originalgb not to store redundant information
* get default DNA/RNA colours to agree with GDE
* get default protein colours to agree with GDE
* fix defaults for character protections
* fix error handling to be more robust
* fix which characters are considered unambiguous

Version 0.5.4:
--------------
* optimize selection canvas repaints
* optimize GenBank file parsing (look at I/O methods)
    * optimize I/O speed
    * optimize string concatenation - use string buffer
* optimize all string concats to use string buffers
* make standard colouring more distinct (colourmap)
* make font spacing smaller in text area
* fix GenBank file parsing bug

Version 0.5.3:
--------------
* fix select all + cut list bug
* fix textarea delete bug
* further optimize textarea painting so each repaint call is co-ordinate specific
* fix textarea font width to look better (center each letter in the column).
* optimize seqdoc insert/delete to use arrays
* change how textarea and list are greyed out

Version 0.5.2:
--------------
* fix bugs regarding "text sequences" (#3 low priority from email) --- can't reproduce bug
* optimize textarea painting to use repaint
* fix deletion problem
* Get rid of New sequence from the GDE canvas, when bioLegato first starts up. (#1 low priority from email)
* empty canvas support (so biolegato can start off without any sequences)
* add "select by name" from GDE
* look into _ (underscore) bug for fonts larger than 20pt (textarea)
* fix file bug

Version 0.5.1:
--------------
* optimized file write algorithm
* add source parameter to seqdoc listener methods
* put co-ordinates closer together
* fix select all bug (in textarea)
* fix select all list bug - copy out
* check "extract by features"
* remove files after closed (if supposed to be deleted)

Version 0.5.0:
--------------
* move "Get info..." from the "Canvas" heading to the "Edit" heading
* fix canvas scrolling (high priority)
    * fix oversized canvas bug
    * look at scroll speed of big sequences
    * look at scroll vertical for new sequences loaded from files/command line
* reorganize seqdoc listener structure
* reorganize seqdoc to use addSequence and removeSequence for data manipulation
* global clipboard support
* fix refresh on font changes
* fix selection position issues (end of line)
* fix choice_list make only able to select one
* make choice list scrollable
* scroll support for big combo boxes (#1 high priority from email)
* fix genbank reading circular sequences (#2 high priority from email)
* change where paste inserts sequences (#3 high priority from email)
* disable "ENTER" key new sequence creation
* File --> New sequence - If a sequence name is already selected, the new sequence gets the same name (fix this bug).  (#2 low priority from email)
* In sequence properties, grey out non applicable fields based on type (#4 low priority from email)
    (below is a list of what fields are used for each type)
    * DNA/RNA: Direction, Topoplogy, Strandedness, Colour Mask
    * Protein: Colour Mask
    * Text: Colour Mask
* restructure properties

Version 0.4.4:
--------------
* deprecate choice_list in favour of choice_menu --- list as warning
* add select all
* add copy/cut/paste to GDEList
* add copy/cut/paste/selectAll to GDEList right click menu
* look into further improvement in GDE argument replacement
* fix multiple file creation problem
* fix output file reading
* refactor GDE subclasses
* change default help path

Version 0.4.3:
--------------
* Add items to edit menu
    * cut
    * copy
    * paste
* fixed edit menu position
* fixed makefile "clean"
* fix gde JList
* check out temporary file creation bug
* check :CDS issue

Version 0.4.2:
--------------
* Statistics line in GDE Canvas
    * row and column of the cursor
    * Insert status
* implement insert key
* make colours contrast
* Right click menus
    * TextArea
        * Cut
        * Copy
        * Paste
        * Canvas properties
    * Sequence list
        * Get info
        * Canvas properties
* position colour mask support
    * interface support
    * file support
    * internal support
* fixed colour map bug (selected text does not appear blue for DNA/RNA and PROTEIN sequences
* change sequence direction default to "5' to 3'"

Version 0.4.1:
--------------
* move canvas properties to menu
* Colour themes
    * internal rendering support
    * default GDE canvas character based colour scheme
        * DNA/RNA
            * A = red
            * B,D,H,N,M,R,S,V,W,Y = yellow
            * C = blue
            * G = black
            * U,T = lime green
            * X = yellow 'N'
            * all others = grey '-'
        * PROTEIN
            * A,G,P,S,T = fuchsia
            * B,D,E,N,Q,Z = black
            * C = red
            * F,W,Y = blue
            * H,K,R = turquoise
            * I,L,M,V = lime green
            * X,* = yellow
            * all others = grey
* fix caret scroll issues in GDE canvas
* add jar plugin support
* add menu shortcut to "Get info"
* package GDE support into a jar plugin
* fix font change cursor error
* fix deletion bug
* fix temporary file creation bug
* fix GDE argument replacement order bug
* ensure BIOLEGATO_ON works properly

Version 0.4.0:
--------------
* Add filename handler to command line (limit to biolegato native formats) --
high priority
* Update canvas on changes
* GDE get info (add to root canvas)
    * name
    * type
    * strandedness
    * direction
    * topology
* Properties for BioLegato GDE canvas
    * Set protections (default: only alignment gaps)
        * Alignment gaps (-)
        * Unambiguous characters
            * DNA/RNA (A,C,G,T,U)
            * Protein (all non-ambiguous)
        * Ambiguous characters
            * DNA/RNA (all other characters)
            * Protein (B,Z,*,X)

Version 0.3.3:
--------------
* Fix off by one error in Text selection
* Implement choice_list as a dropdown
* Double check defaults
* Fix ordering

Test things side-by-side in GDE and BioLegato


