[Biojava-l] Phred Sequence

[Schreiber, Mark]

Yes, just me violating all the principles of OO programming :(

I'll change it to return a Symbol (which would have been the sensible
thing for me to do in the first place). I'll check to CVS in about an
hour.

- Mark


> -----Original Message-----
> From: David Waring [mailto:dwaring at u.washington.edu] 
> Sent: Saturday, 8 March 2003 8:47 a.m.
> To: Schreiber, Mark; biojava
> Subject: RE: [Biojava-l] Phred Sequence
> 
> 
> I was using biojava 1.2. There seems to be a partial fix in 
> biojava-live. I just updated and rebuilt my biojava-live and 
> when I use it I get a different error. When I try to call 
> getDNAAt(1) or getDNA() I get the following error when there are ns
> 
> Exception in thread "main" java.lang.ClassCastException: 
> org.biojava.bio.symbol. AlphabetManager$WellKnownBasisSymbol
>         at 
> org.biojava.bio.program.phred.PhredTools.dnaSymbolFromPhred(PhredTool
> s.java:89)
>         at 
> org.biojava.bio.program.phred.PhredSequence.getDNAAt(PhredSequence.ja
> va:107)
>         at readPhred.main(readPhred.java:51)
> {dwaring}sydney:%>
> 
> Looking at the PhredTools code the problem seems obvious. It 
> is trying to return an Atomic Symbol.
> 
>   public static final AtomicSymbol dnaSymbolFromPhred(Symbol phredSym)
> 
> 
> 
> > -----Original Message-----
> > From: Schreiber, Mark [mailto:mark.schreiber at agresearch.co.nz]
> > Sent: Wednesday, March 05, 2003 7:45 PM
> > To: David Waring; biojava
> > Subject: RE: [Biojava-l] Phred Sequence
> >
> >
> > Hi -
> >
> > I was trying to replicate this error to fix it but I can't (has 
> > someone kindly fixed it for me??). The following code seems to work 
> > fine
> >
> >     System.out.println("Testing n symbol");
> >     Symbol ambig = PhredTools.getPhredSymbol(DNATools.n(),
> > IntegerAlphabet.getInstance().getSymbol(12));
> >     System.out.println("Successfuly constructed "+ambig.getName());
> >
> > Producing
> >
> > Testing n symbol
> > Successfuly constructed ([cytosine adenine thymine guanine] 12)
> >
> > Are you still having problems with this? Are you using BioJava live?
> >
> > - Mark
> >
> >
> > > -----Original Message-----
> > > From: David Waring [mailto:dwaring at u.washington.edu]
> > > Sent: Thursday, 20 February 2003 4:20 p.m.
> > > To: biojava
> > > Subject: [Biojava-l] Phred Sequence
> > >
> > >
> > > I am writing code to parse a .phd file and create a 
> PhredSequence. 
> > > It is failing with an IllegalSymbolException when I have 
> an 'n' in 
> > > the sequence. Do CrossProductAlphabets only take AtomicSymbols?
> > >
> > > David
> > >
> > >
> > > Exception in thread "main"
> > > org.biojava.bio.symbol.IllegalSymbolException:
> > > Token
> > > `([cytosine adenine guanine thymine] 2)' does not appear 
> as a named 
> > > symbol in al phabet `PHRED'
> > >         at 
> > > 
> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.
> > > j
> > > ava:105)
> > >         at
> > > 
> org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
> > > va:162)
> > > rethrown as org.biojava.utils.NestedError
> > >         at
> > > 
> org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
> > > va:164)
> > >         at
> > > 
> org.biojava.bio.program.phred.PhredTools.createPhred(PhredTools.java:
> > > 142)
> > >         at
> > > 
> edu.washington.genome.seqio.phd.PhredBuilder.makeSequence(PhredBuilde
> > > r.java:238)
> > >         at
> > > 
> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:10
> > > 1)
> > >         at readPhd.main(readPhd.java:45)
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at biojava.org 
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > 
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