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Commits on Feb 22, 2012
  1. Merge pull request #2 from neomorphic/master

    authored
    Minor updates to the code. Mostly cleanup.
Commits on Jan 25, 2012
  1. @neomorphic

    Added more output options

    neomorphic authored
    There are now -data and -fh options in addition to the -file parameter
    passed to draw_logo. This allows for the rendered image data to be
    placed in an already opened file handle or into a reference to a scalar.
  2. @neomorphic

    Moved scripts to scripts directory

    neomorphic authored
    This stops them from being installed in the lib directory. An EXE_FILES
    line was added to the Makefile.PL to tell make which scripts need the
    path modified on installation and where to put them.
Commits on Jan 23, 2012
  1. @neomorphic

    Restored strict and warnings pragmas to modules

    neomorphic authored
    There were a number of modules where the strict and warnings pragmas
    had been removed. I restored these and fixed the warning message in
    HMM/Profile (caused by PDL returning the string 'BAD' instead
    of a number) by checking the string to make sure it is numeric, before
    testing it.
  2. @neomorphic

    Restored strict and warnings pragma to Utilities

    neomorphic authored
    The strict and warning pragmas were removed to get the code to compile.
    Fixing the way that variables are created for use with Exporter has
    allowed the restoration of the failing pragmas.
  3. @neomorphic

    Removed META.yml from the manifest.

    neomorphic authored
    The META.yml file gets added to the module directory when running 'make
    dist', so we don't need to have it in the MANIFEST file that is stored in
    source control.
  4. @neomorphic

    Fixed 'redefined sub' warning

    neomorphic authored
    The flat subroutine was being imported from PDL::LiteF and then
    redefined in the HMM::Profile module. Since I don't think the intention
    was to override the PDL function, I renamed the HMM version of the
    subroutine to flatten.
  5. @neomorphic
  6. @neomorphic

    Fixed printf warnings.

    neomorphic authored
    printf in perl does not need the () as it does in C? So removing them
    will make the printf behave as expected in the perl community.
  7. @neomorphic

    Removed whitespace

    neomorphic authored
  8. @neomorphic

    Restored warnings pragma

    neomorphic authored
    We want warnings. Also removed trailing whitespaces.
  9. Merge pull request #1 from traviswheeler/master

    authored
    new log-odds-based letter heights, and more - Looks good, need to test but seems clean
Commits on Jan 20, 2012
  1. @traviswheeler

    Added comment.

    traviswheeler authored
  2. Updates to HMM/Profile.pm and HMM/Utilities.pm that allow an optional

    Travis Wheeler authored
    alternate method of splitting column heights. The default is still
    the old way of using emission probabilities; the new way is to use
    log odds scores, and only let positive-scoring residues play a part
    in the column. This is acheived by adding the '--height_logodds 1'
    flag to a call to draw_logo.
    
    Implemented a fix to let HMM-Logo read newer formats from HMMER's
    hmmbuild, as the new format 3/e caused crashes in the old '_parseFile3'
    function.
    
    Implements a new function 'print_logo_dimensions' that works like
    'draw_logo', but instead of creating a png, it prints out the dimensions
    of each HMM position (insert widths, and residue height/widths). This
    is a cleaner format than the 'flat' output, and will enable post-
    processing of those dimensions.
    
    pulls the "foreach my $key (@drawOrder){" block of code in 'draw_logo'
    into the 'else' case, to avoid the occasional bug of printing residue
    stacks inside the insert columns.
    
    make_profile.pl is added in order to provide an example for using the
    above changes.  (I chose not to modify hmm2logo.pl, but wouldn't mind
    if changes from make_profile.pl were placed into hmm2logo.pl, then
    make_profile was removed).
Commits on Jan 12, 2012
  1. Imported to Github

    authored
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