Changelog
From Bioinformatics.Org Wiki
Contents |
Version 0.7
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
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
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
- 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
- make seqdoc x,y based
- 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 all text operations x,y based (should increase biolegato speed)
- 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
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
- look over and update entire javadoc and commenting for biolegato GDE support
- look over and update entire javadoc and commenting for biolegato standalone plugins
- 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
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
- TextArea
- 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
- DNA/RNA
- 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)
pre 0.4
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