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Commits on Nov 29, 2016
Commits on Nov 26, 2016
Commits on Nov 25, 2016
  1. Updated webpage content

    alexholehouse committed Nov 25, 2016
  2. Update to 0.1.10

    Major update that includes a number of big changes
    1) Improvement to plotting functions. Linear composition analysis now dynamically alters text size and line thickness to refelct sequence length, allowing high resolution fugures to be generated without the need for extensive post-processing
    
    2) General linear plotting functions now dynamically set the edge withd on bars such that when sequences are long the edge width tends to zero. This fixes the issue where for longer sequences the bar edges would overwhelm the total bar width. meaning bar color was lost
    
    3) New PPII propensity scales added (Kallenbach and Creamer)
    
    4) New sequence shuffling function (get_shuffle()) that allows for a sequence to be efficienctly shuffled. In addition to efficienct shuffling, an arbitrary number of residues can be 'frozen', so shuffling occurs over a subset of residues. Useful when we wish to hold key motifs fixed but shuffle the remainder of the sequence.
    
    5) The get_Omega parameter was updated with the appropriate reference to the newly published work
    
    6) Additional tests added
    alexholehouse committed Nov 25, 2016
Commits on Oct 11, 2016
  1. Updated setup and README for PyPI to reflect newest version. ALSO upd…

    …ated setup.py so that scipy is now a dependency
    alexholehouse committed Oct 11, 2016
Commits on Oct 6, 2016
Commits on Oct 1, 2016
  1. Updated version to 0.1.9

    alexholehouse committed Oct 1, 2016
Commits on Sep 30, 2016
  1. This update introduces general patterning parameters as well as vario…

    …us other minor updates. The proline patterning parameter (Omega) is updated here to reflect the new name (formerly known as kappa-p-charge)
    alexholehouse committed Sep 30, 2016
Commits on Jul 7, 2016
  1. New linear composition analysis tool added. Uses univariate spline fi…

    …tting to filter noise from a sliding window analysis. Currently only specific groupings provided BUT the code was written to facilitate arbitrary analysis in the future
    alexholehouse committed Jul 7, 2016
Commits on Jul 6, 2016
  1. Comment update

    alexholehouse committed Jul 6, 2016
Commits on Apr 15, 2016
Commits on Mar 29, 2016
  1. Update for 0.1.8.post1

    alexholehouse committed Mar 29, 2016
Commits on Mar 28, 2016
Commits on Mar 17, 2016
  1. Major updated - lots of tests and additional features and PPII propen…

    …sity stuff which is as of yet untested...
    alexholehouse committed Mar 17, 2016
Commits on Oct 12, 2015
  1. Merge pull request #2 from cxhernandez/py3

    Py3 functionality and pep8 compliance
    alexholehouse committed Oct 12, 2015
Commits on Oct 1, 2015
  1. py3

    cxhernandez committed Oct 1, 2015
  2. pep8

    cxhernandez committed Oct 1, 2015
Commits on Sep 9, 2015
Commits on Jul 1, 2015
Commits on Jun 30, 2015
Commits on Jun 29, 2015
  1. Added in functionality for Lempel-Ziv-Welch complexity, but need to d…

    …ouble check implementation
    alexholehouse committed Jun 29, 2015
Commits on Jun 28, 2015
  1. Implemented linguistic complexity but may not be working quite right.…

    … Need to benchmark against original code...
    alexholehouse committed Jun 28, 2015
Commits on Jun 27, 2015
  1. Updated interface, added a whole host of sanity checking for input, a…

    …nd improved documentation, naming conventions on some of the complexity variables, and generally improved the WF code
    alexholehouse committed Jun 27, 2015
Commits on Jun 26, 2015
  1. Created working model of the alphabet reduction code, as well as impl…

    …emented Wootton complexity measure
    alexholehouse committed Jun 26, 2015
Commits on Jun 25, 2015
  1. Preparing for the building of sequence complexity measure. Moved the …

    …existing complexity function out of sequence.py and into the newly created sequenceComplexity.py file
    alexholehouse committed Jun 25, 2015
Commits on Jun 24, 2015
  1. Improved documentation of functions - specifically added references, …

    …cleaned up spacing, and added better documentation for the get_full_phosphoatstatus_kappa_distribution() function
    alexholehouse committed Jun 24, 2015
Commits on Jun 22, 2015