[Biojava-l] error using the proteomic package

[Robert Stones]

Hi get a deprecation warning

javac  -deprecation  com/biojava/digest/TestDigest.java

com/biojava/digest/TestDigest.java:24:
warning:Protease(java.lang.String,boolean) in
org.biojava.bio.proteomics.Protease has been deprecated

      Protease pp = new Protease("RK", true, "P");


Keith James wrote:
> 
> >>>>> "Robert" == Robert Stones <r.stones at csl.gov.uk> writes:
> 
>     Robert> I keep getting this error using the proteomic package when
>     Robert> performing simulated digests on proteins and some peptides
>     Robert> with masses are not being generated:
> 
>     Robert> Has anybody got an example code for setting proteases and
>     Robert> working out masses?
> 
>     Robert> org.biojava.bio.symbol.IllegalSymbolException: No mass Set
>     Robert> for Symbol [GLU SER GLY PHE LEU PRO ALA VAL ASN SEC HIS
>     Robert> MET THR TYR ARG ILE LYS GLN TRP CYS ASP] at
>     Robert> org.biojava.bio.proteomics.MassCalc.getVMasses(MassCalc.java:365)
> 
> That stringified Symbol looks like an ambiguity symbol for all amino
> acids. Do your proteins have X's in them?
> 
> Looking at the code is seems that masses are set for unambiguous
> residues, but there is no fancy estimation of mass ranges based on
> ambiguities.
> 
> Keith
> 
> --
> 
> - Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -