added S3 as.data.frame methods
refactored ProteinGroup creation

cleared structure and changed to use environment for protein group table
added lower bounds for fitting of  scale parameter of Tlsd
simplified .as.vect to use the setNames function
improved formatting of properties.R file
fixed import of MzIdentML - should work now for Mascot and ProteomeDiscoverer
upped to version 1.7.1
Merge branch 'ptm' into devel
fixed bugs in filterSpectraPhosphoRS
Merge branch 'ptm' of /slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib into ptm
Merge branch 'ptm' of /slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib into ptm
fixed mascot-parser - delta-score caluclations within parser are not working for now

old version is renamed mascotParserDelta_defunct.pl
added entrez Protein info import
parser entrez GIs and uniprot ACs better
updated to version 1.7.2
added new terms for protein columns
added Deamidated definition
added preliminary mzIdentML 1.1.0 support [not fully tested]
fix naming bug [identifications]
resolved spectrum.quant ids