[Biojava-l] MassCalc question.

[Schreiber, Mark]

Hi -

This is a bug that has been fixed in biojava-live and the 1.3 branch on CVS. It will also be available in the biojava 1.3.1 release which will be out very soon. (as soon as I solve my ftp problems and put it up on the site!)

- Mark


> -----Original Message-----
> From: Suman Kanuganti [mailto:bioinformatics4suman at yahoo.com] 
> Sent: Thursday, 20 November 2003 7:12 p.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] MassCalc question.
> 
> 
> Ok; I am having problem with using MassCalc class. It
> always an IllegalSymbolException though the symbol
> list is correct. 
> I have written this,
> 
>    SequenceIterator iter =
> MySeqTools.myReadFastaAA(args[0]);
> 
>     while(iter.hasNext()){
>       Sequence seq = iter.nextSequence();
>       SymbolList syml = (SymbolList)seq;
>       System.out.println(syml.seqString());
>       MassCalc mCalc = new 
> MassCalc(SymbolPropertyTable.MONO_MASS, true);
>       double mass = mCalc.getMass(syml);
>       System.out.println("Mass:
> "+seq.getName()+"\t"+mass);
>     }
> 
> 
> while result in error
> 
> Exception in thread "main"
> org.biojava.bio.symbol.IllegalSymbolException: The
> SymbolList was not using the protein alphabet
> 
> Any one can help me with this,
> 
> Thanks,
> Suman K
> 
> =====
> Suman K
> BioInformatics Associate,
> Genomics Research,
> Newton Lab,
> University of Missouri - Columbia.
> 
> __________________________________
> Do you Yahoo!?
> Free Pop-Up Blocker - Get it now
> http://companion.yahoo.com/ 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================