Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Commits on Mar 27, 2015
  1. @cbrueffer
Commits on Mar 26, 2015
  1. @peterjc
Commits on Mar 15, 2015
  1. @peterjc

    Example does not have a stop codon.

    peterjc authored
    Pointed out on mailing list, this probably changed in 2008
    b135d28
Commits on Feb 25, 2015
  1. @peterjc
  2. @erasche @peterjc

    Reflow long lines to make flake happy

    erasche authored peterjc committed
  3. @erasche @peterjc

    Refactor into separate instantiations to fix jython failure

    erasche authored peterjc committed
Commits on Feb 24, 2015
  1. @peterjc
Commits on Feb 17, 2015
  1. @peterjc
  2. @erasche @peterjc

    Correct repeated initialisation of keys

    erasche authored peterjc committed
    Thanks to @bow for the suggestion, the _INSTRUMENT_SPECIFIC_TAGS dict
    was being initialised repeatedly.
  3. @erasche @peterjc
  4. @erasche @peterjc

    Remove duplicate key

    erasche authored peterjc committed
  5. @erasche @peterjc

    Implement rest of ABIF spec

    erasche authored peterjc committed
  6. Fix for issue #461 to handle the change in output format in meme

    Michiel de Hoon authored
Commits on Feb 12, 2015
  1. @peterjc

    Thank Gleb Kuznetsov for GenBank work

    peterjc authored
    See pull request #472
Commits on Feb 10, 2015
  1. @glebkuznetsov
Commits on Feb 4, 2015
  1. @peterjc
  2. @peterjc
Commits on Jan 30, 2015
  1. @peterjc
Commits on Jan 26, 2015
  1. @etal
Commits on Jan 25, 2015
  1. @peterjc

    Don't install T-COFFEE under TravisCI

    peterjc authored
    Recently the TravisCI builds have been stalling during
    test_TCoffee_tool.py which suggests a recent update to
    T-COFFEE is cause a problem somehow. This change will
    allow us to confirm if T-COFFEE is invovled.
Commits on Jan 22, 2015
  1. @peterjc
Commits on Jan 20, 2015
  1. @peterjc

    Fix typo in dependency check

    peterjc authored
  2. @peterjc

    HexColor with alpha transparency broken on ReportLab 2.6

    peterjc authored
    We could cope with the argument name change from alpha to hasAlpha
    between ReportLab 2.6 and 2.7, but Under ReportLab 2.6, both
    HexColor('#8080F780') and HexColor('#8080F780', alpha=True)
    fail with:
    
        Traceback (most recent call last):
          File ".../site-packages/reportlab/lib/colors.py", line 365, in HexColor
            return Color((val>>24)&0xFF/255.0,((val>>16)&0xFF)/255.0,((val>>8)&0xFF)/255.0,(val&0xFF)/255.0)
        TypeError: unsupported operand type(s) for &: 'int' and 'float'
    
    Essentially we seem to need at least ReportLab 2.7 for transparency.
    
    See discussion on GitHub #458 and #463.
Commits on Jan 18, 2015
  1. @peterjc

    Clearer error message; update failing test.

    peterjc authored
    One of the orchid examples now returns different enough
    results that the test was failing. The new error message
    makes it much easier to pick another positive example to
    add to the the white-list.
Commits on Jan 17, 2015
  1. @peterjc
Commits on Jan 16, 2015
  1. @widdowquinn

    KGML_vis.py: Catch argument error for HexColor hasAlpha/alpha

    widdowquinn authored
    Implemented bugfix suggested by Peter Cock.
Commits on Jan 14, 2015
  1. @tiagoantao

    Bug on parsing loci name

    tiagoantao authored
Commits on Jan 11, 2015
  1. @tiagoantao

    type

    tiagoantao authored
Commits on Jan 9, 2015
  1. @peterjc
  2. @brandoninvergo @peterjc

    fix more assertions for Python 2.6

    brandoninvergo authored peterjc committed
  3. @brandoninvergo @peterjc

    fix assertions for Python 2.6

    brandoninvergo authored peterjc committed
  4. @brandoninvergo @peterjc

    add test cases for bad codeml tree parsing

    brandoninvergo authored peterjc committed
  5. @brandoninvergo @peterjc

    fix #453: codeml (Bio.Phylo.PAML) tree regexp

    brandoninvergo authored peterjc committed
Commits on Jan 8, 2015
  1. @widdowquinn

    KGML_vis.py: Added handling of alpha-channel transparency.

    widdowquinn authored
    bgcolor and fgcolor attributes of KGML elements now render with transparency
    if an alpha channel is specified either as a 4-element tuple, 4-value hex
    string, or Reportlab Color object.
    
    The test_KGML_graphics.py tests are modified to test transparency of
    stroke (fgcolor) and fill (bgcolor).
  2. @widdowquinn
Something went wrong with that request. Please try again.