Version 0.4.1

Changes in version 0.4.1 (Mar 12, 2010)

New Functionality

  • Kamino now supports applying a different color to each individual segment in a multi-segment feature.
  • Added Invitrogen’s “1 Kb Plus DNA Ladder” as well as Bionexus’s “Hi-Lo DNA Marker” to the Simulate Gel dialog.
  • Map view now alerts you to features that could not be displayed.

Enhancements

  • Added “Copy Translation” action to the right click feature context menu
  • Kamino will now warn you before opening files produced by newer versions if the file format has changed.
  • Enhanced sorting by feature color, features that are shades of gray are now placed after all other colors.
  • Improved painting of pliancy and selection for features in map and enzymes view.
  • Various textual, color, and alignment enhancements
  • Kamino can now decode segment names from GenBank files exported from Kamino.
  • The features dialog now limits you to making 500 segments. Similarly, if you try to make a 501th segment using the Create Feature Segment, Kamino will warn you of this limit instead.
  • Turned off auto completing in the Go To and Select Range dialog since it got in the way. You can still use the pull down menus to use the predefined values for the start and end of the sequence.
  • You can now add/remove 5′ phosphorylation to existing primers in the PCR dialog without making a new primer. Similarly, the dialog will no longer complain you need a unique name.
  • Enhanced the GenBank importer to decode directionality of oriT and REP_ORIGIN type features.
  • Enhanced the GenBank exporter to better describe the directionality of oriT and REP_ORIGIN type features.

Bug Fixes

  • Fixed a bug with copying feature translations that begin with an alternative start codon.
  • Improved mouse wheel and trackpad scrolling of sequence view. This will be improved further in the next release.
  • When importing from GenBank, we now preserve formatting in feature descriptions and overall sequence comments (new lines, indenting, etc.).
  • Fixed a regression that prevented scrolling sequence view to show a selection that was made in a different view.
  • Copying and pasting from the Keyboard Shortcuts dialog into Word and other programs now behaves much better on OS X.
  • Modified the Gene Construction Kit importer to use the filename as the construct name, not data that was misunderstood within such files.
  • Features and Primers view now adjust column widths properly when changing the font size.
  • Fixed a bug that resulted in feature translations in sequence view sometimes displaying straddling codons on two lines instead of on the line that contains the two out of three codon bases.
  • Fixed a bug that sometimes resulted in an insertion point cursor being painted at both the beginning and end of the sequence in Sequence view.
  • Fixed a regression in 0.4.0 that resulted in all primers being loaded as phosphorylated.
  • If during the process of cloning, arbitrary edits, or making a new file from a election, if a feature that uses an alternative start codon loses it’s first codon in the translation the resulting feature will now no longer indicate it starts with an alternative start codon.
  • Fixed a bug that could cause the Make, Edit, and Duplicate Primer dialogs get stuck and indicate no binding sites were detected even though binding sites do exist. Now, when searching for binding sites the preview widget indicates just that.
  • Fixed a bug where after saving case changes, these were not used when making a primer from a selection.
  • Fixed a bug in the GenBank importer that failed to import all feature segments if they were broken up across multiple lines in the source file or the segment descriptions had spaces within them.
  • Fixed a bug in the GenBank importer where escaped quotes were not unescaped when decoding feature comments, etc.

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