AW: [Biojava-l] error using the proteomic package

[Schaerfke, Marco, Dr., Xzillion/DE]

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:r.stones at csl.gov.uk]
> Gesendet am:	Mittwoch, 25. Juni 2003 16:41
> An:	biojava-l at biojava.org
> 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();
> 			}
> 		}
> 	}	
> 
>