## @knitr startup, results='hide', echo=FALSE, message=FALSE
library(mzID)
ps.options(pointsize=12)



## @knitr parsing, tidy=TRUE
mzResults <- mzID("http://psi-pi.googlecode.com/svn/trunk/examples/1_1examples/Mascot_NA_example.mzid")
mzResults



## @knitr class_overview, tidy=TRUE
showClass('mzID')



## @knitr flattening, tidy=TRUE
flatResults <- flatten(mzResults)
names(flatResults)
nrow(flatResults)

#The length of an mzID object is the number of PSM's
length(mzResults)



## @knitr inspection, tidy=TRUE
flatResults$length
nchar(flatResults$sequence)
substr(flatResults$sequence, 1, 10)