Version 0.4.1  (7 Mar 2008)

- Updated Jmol to 11.4.RC8
- Code cleanup, making things simpler, adding Javadocs
- Trac 50 (Jmol Command Bar) : http://kody.dnsalias.com:8181/trac/ticket/50
- Trac 51 (Config panel cleanup) : http://kody.dnsalias.com:8181/trac/ticket/51
- Trac 53 (Credits) : http://kody.dnsalias.com:8181/trac/ticket/53

Version 0.4.0 (4 Mar 2008)

- Trac 44 (Config Jmol Color) : http://kody.dnsalias.com:8181/trac/ticket/44
- Trac 45 (Select anchor & column only) : http://kody.dnsalias.com:8181/trac/ticket/45
- Trac 46 (Overview) : http://kody.dnsalias.com:8181/trac/ticket/46
- Trac 47 (Jmol - setTitle) : http://kody.dnsalias.com:8181/trac/ticket/47
- Trac 48 (Anchor - first row) : http://kody.dnsalias.com:8181/trac/ticket/48

Version 0.3.1 (28 Feb 2008)

- Trac 42 (Amino & Shapely colors) : http://kody.dnsalias.com:8181/trac/ticket/42
- Trac 43 (MSA remove last) : http://kody.dnsalias.com:8181/trac/ticket/43
- Trac 36 (Jmol toggle select) : http://kody.dnsalias.com:8181/trac/ticket/36

Version 0.3.0 (28 Feb 2008)

- Began cleanup work on Jmol (ToolBar, CommandBar, etc.)
- Cleaned up MSA MouseListeners - no longer get out of bounds message
- Updated Jmol to 11.4.RC7
- Trac 35 (Controller) : http://kody.dnsalias.com:8181/trac/ticket/35
- Trac 38 (Jmol Integration) : http://kody.dnsalias.com:8181/trac/ticket/38

Version 0.2.2 (26 Feb 2008)

- Updated Jmol to 11.4.RC6
- Trac 30 (Status bar cleanup) : http://kody.dnsalias.com:8181/trac/ticket/30
- Trac 31 (Display GAP) : http://kody.dnsalias.com:8181/trac/ticket/31
- Trac 34 (System Monitor) : http://kody.dnsalias.com:8181/trac/ticket/34
- Trac 35 (Controller) : http://kody.dnsalias.com:8181/trac/ticket/35
- Trac 38 (Jmol Integration) : http://kody.dnsalias.com:8181/trac/ticket/38
- Trac 40 (DnD Mac OS X) : http://kody.dnsalias.com:8181/trac/ticket/40

Version 0.2.1

- Updated Jmol to 11.4.RC5
- Trac 6 (Render shape) : http://kody.dnsalias.com:8181/trac/ticket/6
- Trac 8 (Enable Performance Test) : http://kody.dnsalias.com:8181/trac/ticket/8
- Trac 14 (MSA Background colour) : http://kody.dnsalias.com:8181/trac/ticket/14
- Trac 18 (Right-click on Jmol) : http://kody.dnsalias.com:8181/trac/ticket/18
- Trac 26 (Delete Sequence) : http://kody.dnsalias.com:8181/trac/ticket/26
- Trac 29 (Add PDB Anchor visual) : http://kody.dnsalias.com:8181/trac/ticket/29

Version 0.2.0

- removed all ‘future work’ E.g. Google Docs, Freebase
- fixed the Jmol popup menu
- moved code to Upton Lab source repository
- Updated Jmol to 11.4.RC4

Version 0.1.8

- simple text file upload to Google Docs
- simplified AminoAcid class
- simplified MSAEditorViewer class
- it’s now much easier to add new rendering methods and cell colors
- updated Configuration and ConfigurationPanel
- simplified the ToolBar; there is now only one drop down for ‘Rendering’
- updated Jmol to 11.2.9 (still have menu issue)

Version 0.1.7

- updated File->Open dialog for .fa, .fasta, .aln, and .pdb files
- checksums are computed for a sequence with all inserts/gaps removed
- continue experiments with Google Docs
- continue experiments with freebase alpha
- changed Main to be a singleton (not sure if this will simplify things or not)

Version 0.1.6

- updated Jmol to 11.2.8 (still have menu issue)
- new version history window
- continued to work on ’settings’ window
- developing application configuration file
- experimenting with the GData API from Google

Version 0.1.5

- updated Jmol to 11.2.7 (still have menu issue)
- added XRef class (it currently holds CRC64 and SHA1 checksums)
- added a search UniProt link to CustomRowHeader
- fixed a bug when saving fixed width FASTA files
- started work on settings panel

Version 0.1.4

- fixed a delete bug in CustomRowHeader
- simplifying the CustomRowHeader display
- added TEXT ALIAS ON
- simplified the paint method in MSPanel by using
Graphics.create(x, y, width, height)
- updated Jmol to 11.2.6 (fixed some of the popup menu problem)
- working on cell/col/row selection
- Loading VersionHistory from file

Version 0.1.3

- Added ResourceFactory
- Removed ImageFactory
- Removed SampleDataFactory
- Trying to restrict resize from getting too small
- Replace menu bar with toolbar - KISS
- Cleaning up the CustomRowHeader
- Annoying bug in 2nd line of CustomRowHeader

Version 0.1.2

- Updated Jmol to 11.2.3
- Some problem with the menu
- Added ‘File Open…’ menu item