Unecessary fix for proxy support in NCBIWWW
added a gc_content method method to the GenericPositionMatrix in Bio.motifs (contributed by Anthony Mathelier of UBC)
removed some whitespace
Avoid NaN results if p is zero
Two blank lines between classes (PEP8)
Fix lots of overly long lines, try to follow PEP8 for property docstrings
Omit argument with default value
Adding static argument to Bio.Application, use for BWA
Fix for missing isnan on Python 2.5
Clarify docstring import for newcomers.

This wasn't needed for the doctest to work (by default a
doctest has the module's namespace preloaded). See:
http://lists.open-bio.org/pipermail/biopython/2013-May/008578.html
optionalcascade now requires container and item attr names as args

Hit has also been updated to initialize with some default values
Remove explicit '._items' slicing in optionalcascade

For QueryResult to use optionalcascade instead of partialcascade, this is
needed; as explicit '._items' indexing will return the Hit key instead of the
Hit object.
Merge partialcascade into optionalcascade
More explicit conditional handling in FastaIO

Also, since query_description should be validated by QueryResult, we reset the
Hit's query description attribute prior to appending to a QueryResult.
Initialize QueryResult with/without IDs and/or Hits and change default values to None
Change Hit's default attribute values and allow for flexible setting from empty Hit
Remove attribute checking in optionalcascade getter

For performance reasons. Now we're relying on the object's validation methods.
Refactor validation out of fullcascade into the container objects
Update QueryResult.__init__ pattern to match Hit's
Update HSPFragment default args