[Biojava-l] Re: Biojava-l digest, Vol 1 #776 - 5 msgs

[Lachlan Coin]

Hi

Having made a mistake in serialising HMMs before - are you writing your
serialised object at several points in the code?  Unless you write all of
the models at the same point, they will not work when you read them back
in.

Cheers,

Lachlan

>
> Message: 1
> Subject: RE: [Biojava-l] Create DP object from profileHMM class file
> Date: Tue, 8 Oct 2002 08:53:41 +1300
> From: "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>
> To: "Tisanai" <T.Krisanathamakul@dcs.shef.ac.uk>, <biojava-l@biojava.org>
>
> Hi -
>
> The error is coming from the 64th line of your program (at
> T_Zscore.main(T_Zscore.java:64))
>
> I can see two places that the error might be coming from but I need to
> know which line is the 64th line of the program.
>
> Is it: ProfileHMM model = (ProfileHMM) ois_md.readObject();
>
> Or is it: dp[i] = DPFactory.DEFAULT.createDP(model);
>
>
>
> > -----Original Message-----
> > From: Tisanai [mailto:T.Krisanathamakul@dcs.shef.ac.uk]
> > Sent: Tuesday, 8 October 2002 2:40 a.m.
> > To: biojava-l@biojava.org
> > Subject: [Biojava-l] Create DP object from profileHMM class file
> >
> >
> > Hi
> >
> >    By this code I would like to create DP object from several
> > phmm file.
> >
> >        for(int i=0;i<md_out_lst.align.length;i++){
> >         String model_out_name = md_out_lst.align[i];
> >         File md_file = new File(model_out_name);
> >
> >         FileInputStream fis_md = new FileInputStream(md_file);
> >         ObjectInputStream ois_md = new ObjectInputStream(fis_md);
> >         ProfileHMM model = (ProfileHMM) ois_md.readObject();
> >         ois_md.close();
> >         dp[i] = DPFactory.DEFAULT.createDP(model);
> >        }
> >
> >    I found that  it always stuck at the second file (i=2). If
> > there is only one file in my list this code will work fine.
> > But if there is more than one file in the list when it try to
> > create the second dp object (dp[1]). This kind of error will
> > shown out:
> >
> >             org.biojava.bio.BioError: State d-15 is known in
> > states  but is not listed in the transFrom table
> > 	at
> > org.biojava.bio.dp.SimpleMarkovModel.transitionsFrom(SimpleMar
> > kovModel.java:227)
> > 	at
> > org.biojava.bio.dp.DP$HMMOrderByTransition.transitionsTo(DP.java:599)
> >             at
> > org.biojava.bio.dp.DP$HMMOrderByTransition.compare(DP.java:586)
> > 	at org.biojava.bio.dp.DP.stateList(DP.java:123)
> > 	at org.biojava.bio.dp.DP.update(DP.java:353)
> > 	at org.biojava.bio.dp.onehead.SingleDP.update(SingleDP.java:49)
> > 	at org.biojava.bio.dp.DP.<init>(DP.java:377)
> > 	at org.biojava.bio.dp.onehead.SingleDP.<init>(SingleDP.java:41)
> > 	at
> > org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory
> .java:53)
> > 	at T_Zscore.main(T_Zscore.java:64)
> >
> >     How can I fix my code?
> >
> > Thank
> > Tisanai
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
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