Version 0.2

Changes in version 0.2 (Apr 3, 2008)

  • Added automatic documentation and display in a new history view. Ancestral sequences can be resurrected with a single click.
  • Improved import filters. Kamino will now try to import any file, regardless of the file’s extension. In order words Kamino can can import files that use non-standard extensions or omit the extension all together.
  • Overhauled strand and selection painting in map view. Selections now properly match up with their true endpoints. Sticky enzyme selections are now shown as sticky in map view. The sequence is now shown at double stranded. When one or more enzymes are chosen the location at which both the top and bottom strands are actually cut is now emphasizes by showing a break in the strand.
  • Added tick marks and labels to circular map view. Overhauled tick marks and labels in linear map view.
  • The recent files list has been moved into it’s own cascading menu (File → Open Recent File…), and this list can now be cleared using a new “Clear List” action.
  • Fixed some run-on translation painting bugs in sequence view when in frame fusions should result in no run-on being displayed since the features both abut each other.
  • Fixed a bug that caused ORF’s to be incorrectly displayed after performing arbitrary modifications (removals, replacements, insertions).
  • Fixed a bug that caused sequence view to revert to showing all ORF frames from top/bottom strands after performing arbitrary modifications.
  • Fixed a bug that caused all ORF frames being printed in sequence view instead of just the top or bottom strands when that was what the user actually wanted.
  • When printing sequence view ORF letter codes are no longer rasterized, thus if you save the print to a PDF you can now select ORF letter codes, copy, and paste them into other documents from the printed PDF. Since these glyphs are no longer rasterized the output quality is also slightly better.
  • Fixed a slew of origin-spanning ORF bugs.
  • Letter codes that require codons that straddle the origin are now displayed in sequence view.
  • Spelling mistakes are now only flagged in the various spell checking enhanced text edits on OSX when the text edit has focus.
  • Fixed various cloning bugs that involved cutting and blunting using restriction sites that wrap around the numerically defined origin.
  • When linearizing a sequence or making a new file from a selection the new document is opened to the same tab as the just viewed document.
  • Fixed a FASTA importer stability bug that could cause Kamino to crash when trying to import empty FASTA sequences (or files consistent of a single comment line).
  • Fixed a core search engine (MICA) stability bug which could result in a crash when dealing with degenerate sequences.
  • Fixed an infinite loop bug when computing run-on translations for a short sequence with two features that act as each other’s friends (aka each is in frame with each other and no stop codons exist).
  • Fixed a bug where if you placed the cursor, then did a select all the cursor was still painted, this time at the origin, in both sequence and map views.
  • Enhanced the rounded ovals shown around enzymes in sequence, map, and restriction sites views.
  • Pliancy and selected stems with MCS’s are now far more visible in map view, as these highlighted stems are painted after other (black) stems are painted first.
  • Various textual improvements.

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