Merge pull request #14 from pm67nz/master

Drawing code tidy and fixes for when there are no tracks to draw.
enable custom feature creation for genbank parsing

[NEW] RichGenbankParser gets a add_annotation argument. This is a user specified
    callback function fort constructing annotations. This is useful for handling
    incomplete feature specifications for less well characterised genomes.
    Usage is documented in the cookbook.
RichGenbankParser correctly adds rc features

[FIXED] spans for reverse complemented features were being incorrectly reversed.
    This has been fixed and a test file and associetaed test added.
cannot inherit from annotation _Feature

[CHANGED] adding a test to expose problems with inheriting from
    cogent.core.annotation._Feature. Many methods are hard-wired to return
    a _Feature class instance. This patch just introduces a test demonstrating
    this issue. A fix is in the next patch.
support subclassing of _Feature

[FIXED] patch that improves support for inheriting from _Feature. This patch
    allows the test introduced in the previous patch to pass.
Bug fixes for t_two_sample and mc_t_two_sample.

Fixed bug in cogent.maths.stats.test.t_two_sample that returned a t-statistic with the wrong sign if the first distribution contained multiple values and the second distribution contained only a single value (this was validated against R's t.test). Unit test has been updated accordingly.

cogent.maths.stats.test.mc_t_two_sample now handles distributions (as well as permuted distributions) without variance (in the past it would crash with an uninformative error message in these cases). For example, if comparing [1,1,2] to [2,2,1], a possible permutation is [1,1,1] vs [2,2,2], which would return a t-statistic of None. This caused mc_t_two_sample to crash. This was validated against R's Deducer::perm.t.test.

To fix these bugs, added new optional argument none_on_zero_variance to cogent.maths.stats.test.t_two_sample and cogent.maths.stats.test.t_one_observation that is True by default to not modify the previous behavior or change the interface of the two functions.

Updated and added unit tests for these special cases.
Added check for t == 0 when negating t.

Added corresponding unit test.
consistency between input spans and getCoordinates

[NEW] Map class get's a getCoordinates() method. It chekcs the self.Reverse
    property for establishing how to order start/end values in the returned
    series. _Annotatble.getCoordinates() method now uses this method on Map.
[FIXED] On reverse strand _Feature, getCoordinates() did not return a value
    that was usable. Instead of [(end, start), ..] you got [(start, end), ..].
    The latter could not be used to recreate the _Feature. This is now fixed.
Merge pull request #17 from jrrideout/mc_t_two_sample_fix

Bug fixes for t_two_sample and mc_t_two_sample.
Docs now point to GitHub issue tracker.
Merge pull request #19 from jrrideout/docs_github_port_fix

Docs now point to GitHub issue tracker.
Implemented getTranscriptByStableId method in genome.py
Added test for getTranscriptByStableId
Added a Gene property and _get_gene method to the Transcript class in region.py
Minor fix to _get_gene method of Transcript class in region.py. Should test before commiting!
Minor fix to getTranscriptByStableId in genome.py and more comprehensive tests in test_genome.py.
Merge pull request #22 from gawbul/master

Implemented a getTranscriptByStableId method in response to issue #21
Update README.md
fixed mixed indentation types and other whitespace clean up
tests of getting transcript by stable_id were broken

[FIXED] did not correctly reference the human genome instance