Changes for version 0.62 - 2004-07-28
- No major new functionality - small bug fix release
- AnnotationParser.pm
- fixed capitalization bugs when calling goidsByDatabaseId() in nameIsAnnotated() instead of goIdsByDatabaseId() on lines 1592 and 1617 - thanks to lfriedl@cs.umass.edu for spotting this.
- GoView.conf
- Fixed typo in GoView.conf : totalNumGene should be totalNumGenes - thanks to John Matese for spotting this one.
- GO::TermFinder
- Made __databaseIds() method of GO::TermFinder public, and named it genesDatabaseIds, as I realized it is the only way that a client can determine how many genes were actually used when calculating p-values. Before, I was using the number of genes that were passed in, but they will get collapsed if more than one maps to the same databaseId.
- batchGOView.pl
- Modified batchGOView.pl to use the genesDatabaseIds method. Removed its use of the CategorizeGenes function in GO::Utils::General, as I don't think was was any reasonable logic for using it (that I can remember).
- GO::TermFinder
- Fixed lots of spurious warnings that were due to checking the state of a variable before it had been set, when using a user defined background population - thanks to Jeremy Gollub for spotting this one.
- GO::TermFinder
- If a gene is padded in multiple times in either the list of genes of interest, or the background population, you should only be warned about that gene once for each list, rather than every time the gene is encountered.
Modules
abstract base class defining interface for how Annotation information should be provided
parses a gene annotation file
provides information about a node in the Gene Ontology
abstract base class providing API for the provision on Gene Ontology information
Provides API for retrieving data from Gene Ontology files
identify GO nodes that annotate a group of genes with a significant p-value
prints an html table of the results of GO::TermFinder
prints results of GO::TermFinder as a text report
simply utility module for dealing with file parsing
provides some general utilities for clients of other GO classes
Creates a gif or png image for visualizing the GO DAG
a helper class for GO::View to deal with the image
