Deleted unused function 'sharedFunction(…)'
Deleted unused function 'sharedFunction(…)'
Added function getEvidenceCode(…) to extract GO annotations' evidence codes from uniprot dbReference tags.
Corrected tests of function extractExperimentallyVerifiedGoAnnos(…)
Updated function retrieveExperimentallyVerifiedGOAnnotations(…)

function now returns a three column data.frame formatted as the GO
annotations returned by GOstats and function
extractExperimentallyVerifiedGoAnnos(…). Tests pass fine, too.
Merge remote-tracking branch 'origin/master' into incl_db_go_annos
Function retrieveExperimentallyVerifiedGOAnnos now always returns a three column data.frame
Function retrieveExperimentallyVerifiedGOAnnos now truly always returns a three column data.frame
New function to add parent GO term annotations to existing GO annos
Removed deprecated function to measure sequence and domain architecture distances
New function combines GO annotations from live GO-DB and Uniprot in a single data.frame (formatted as in GOstats)
Removed TESTS of deprecated function to measure sequence and domain architecture distances
Adjusting runPhyloFun.R to deal with refactored GO annotation df

Added comments to new methods.

Refactored method goTypeAnnotationMatrices(…) to deal with the new GO
annotation data frames.
Added list of all UniprotKB accessions of proteins with trusted GO annotations. Also made script downloadUniprotSeqs.R download exactly these sequences by default, if no file with other accessions is provided.
Refactored goAnnotationSpaceList(…) to work with new GO anno data frames
Refactored GO annotation and GO annotation space lists to work with new simple data frames
Refactored annotationMatrixForBayesNetwork(…) to handle new simple GO annotation data frames
Fixed function extendGOAnnosWithParents(…) to handle multiple evidence codes in otherwise unique GO annotations. Also added a cleanup function uniqueGOAnnotationsWithMostSignificantEvidenceCodes(…) with the same effect to filter GO annotation data frames.
Refactored general functions of PhyloFun. Test-Run works. - Missing HTML-Plot
PhyloFun will now only be started on Queries with hits in the sequence similarity search