[Biojava-l] Create DP object from profileHMM class file

[Schreiber, Mark]

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
> 
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> http://biojava.org/mailman/listinfo/biojava-l
> 
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