Dear Robert,
I think, there is a problem with your sequence. It contains SEC and for
biojava it is an unknown AA.
Try this:
...
FiniteAlphabet alpha = ProteinTools.getAlphabet();
alphabet.addSymbol(new
SimpleDotState('U',"SEL",Annotation.EMPTY_ANNOTATION));
...
Marco
> -----Ursprüngliche Nachricht-----
> Von: Robert Stones [SMTP:[EMAIL PROTECTED]
> Gesendet am: Mittwoch, 25. Juni 2003 16:41
> An: [EMAIL PROTECTED]
> Betreff: [Biojava-l] error using the proteomic package
>
> I keep getting this error using the proteomic package when performing
> simulated digests on proteins and some peptides with masses are not
> being generated:
>
> Has anybody got an example code for setting proteases and working out
> masses?
>
> org.biojava.bio.symbol.IllegalSymbolException: No mass Set for Symbol
> [GLU SER GLY PHE LEU PRO ALA VAL ASN SEC HIS MET THR TYR ARG ILE LYS GLN
> TRP CYS ASP]
> at org.biojava.bio.proteomics.MassCalc.getVMasses(MassCalc.java:365)
>
> my code
>
> try
> {
> seq = si.nextSequence();
> Annotation anno = seq.getAnnotation();
>
> it = seq.features();
> }//try
> catch (BioException bex)
> {
> System.out.println(bex);
> }
>
> while ( it.hasNext() )
> {
> Feature f = (Feature) it.next();
>
> if (f.getType().equals("Peptide"))
> {
> try
> {
> MassCalc massCalc = new
> MassCalc(SymbolPropertyTable.MONO_MASS,
> true);
> double[] masses =
> massCalc.getVariableMasses(f.getSymbols());
> double mass = masses[0];
> }//try
>
>
> catch(Exception is)
> {
> is.printStackTrace();
> }
> }
> }
>
>
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
