can anyone help me with the following:
I mapped a set of peptides (short AA sequences) to a set of proteins using exact string matching. Now, I would like to compare the locations of the mapped peptide to each other, in order to find peptides that locate next to one another. To me this problem sounds like something one could tackle with ranges on AAStrings objects. So I created a AAString to preresent the protein of interest:
> poi 384-letter "AAString" instance seq: MSSMQMDPELAKQLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFR...AVEATLRKKAEKFQAHLTKKFRWDFTSEPEDCAPVVVELPEGIETA
and a set of Views to present the mapped peptides:
Views on a 384-letter AAString subject
start end width
 1 10 10 [MSSMQMDPEL]
 10 17 8 [LAKQLFFE]
 25 29 5 [NMPKG]
Are there any BioC functions that can be used to analyse these Views? Like Finding views that follow each other at zero distance, or the next neighbour...I saw that such functions exist for ranged integers (IRanges):
But somehow these functions do not like Views on AAStrings:
> pcompare(v1, v1[-1]) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'pcompare' for signature '"AAString", "AAString"' > class(v1)  "XStringViews" attr(,"package")  "Biostrings"
Is there a way to make this work?