Revision history for GO-TermFinder group of modules.

0.60 Wed May  5 15:04:06 2004

	- GO::TermFinder

	The multiple hypothesis correction is no longer done using the
        custom method, but instead uses a Bonferroni correction.

	Correcting p-values by running simulations is now available,
	to allow you to control the Family Wise Error rate.

	Added the ability to calculate the False Discovery Rate, as a
    	potential means of avoiding the whole p-value problem.

	see the pod for GO::TermFinder, as well as docs/GO-TermFinder.doc
	for more information on these.

	- tools

	updated the batchGOView.pl tool, and the analyze.pl tool, in
	the examples directory, to support printing out of the False
	Discovery Rate if calculated.  They also both use the newly
	created GO::TermFinderReport::Text object, to consolidate code, and
	to keep their reports consistent with one another.

	- README

	Tried to make it a little clearer as to how to install the libraries.

0.50 Tue Dec 16 17:34:50 2003

	Big news is that a version of Shuai Weng's (from SGD) GO::View
	module has been added in, which can create a graphic
	representation of the results of GO::TermFinder.  This gives a
	much better way to intuitively look at the results.  A bunch
	of other stuff was added in to support this, including a batch
	processor that will generate an html pages with a graphic for
	any number of input lists of genes.  See batchGOView.pl and
	examples.html in the examples directory.

	- GO::TermFinder

	Fixed a nasty bug that was actually due to a bug in Perl (I
	swear!) that meant that clients of the GO::TermFinder would
	have a runtime error if they did not recognize one or more of
	the genes that it was provided with.  This should no longer
	happen, and I have written additional tests to make sure it
	never happens again!

0.40 Tue Dec  2 18:41:10 2003

	- GO::TermFinder

	Added in the ability to define a subpopulation of genes as the
	background from which the interesting genes were drawn.  See
	pod for constuctor of GO::TermFinder for more details.

0.30 Wed Nov 26 11:48:57 2003

	- GO::AnnotationProvider::AnnotationParser

	Extensive reworking of the code, such that it is now case
	insensitive, with certain caveats.  See the pod for that
	module for more details.

	- GO::TermFinder

	No longer considers the root node, or its child (the aspect)
	as hypotheses, as they are known a priori to have a p-value of
	1.

	- GO::Node

	Added lengthOfShortestPathToRoot and meanLengthOfPathsToRoot
	methods.

	- added in new tests for the AnnotationParser that make sure
	  that the behaviour with respect to case insensitivity is
	  correct.

0.23 Sat Nov  1 11:56:43 2003

	- GO::OntologyProvider::OntologyParser;

	Added in check that a given non-comment line can actually have
	a GOID extracted, which makes the error a more informative
	when such a line is encountered, due to an error in an
	ontology file.

0.22 Sun Oct 19 16:54:38 2003

	- GO::TermFinder

	Fix for test that could occasionally fail that relied on
        the sort order of the pValue array when two items had the
        same pvalue.  It now sorts such cases explicitly by goid,
        so the result should always be the same.

0.21 Thu Oct 16 19:00:14 2003

	- GO::TermFinder

	Fix for situation when a gene identifier wasn't recognized,
	but wasn't handled properly - thanks to Shuai Weng for bring
	it to my attention.

	Cleaned up the code that calculates the p-values to make it
	easier to write a test-suite, which will allow me to make
	other desired changes with more confidence.

	- tests

	Created tests for the GO::TermFinder module itself, that pass
	under both OSX and Solaris in my testing - this should make it
	much easier to modify in future with less concern for failing
	to notice new bugs.

	- examples

	Added a new example, that makes it easier to analyze multiple
	files of gene names.

	- suppressed some warnings that occured due to some undefs
	  being used.
	
	- fixed some documentation typos

0.2  Mon Apr 14 17:55:28 2003

	- added in code such that the findTerms() method will return
	  enough data for you to be able to work out which genes in
	  the list you provided were annotated to which GO nodes.

	- started some work on Annotation, AnnotatedGene, and
	  Reference objects.  Nothing is using them yet though.
	
	- added in over 100 tests(!).  Still lots more to do, but this
	  should help keep the code honest...

0.1  Fri Mar  7 13:51:32 2003

	- original version; created by h2xs 1.21 with options
		-n GO-TermFinder -X
