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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> bioinformatics programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
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