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

Schreiber, Mark mark.schreiber@agresearch.co.nz
Tue, 8 Oct 2002 08:53:41 +1300


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
> 
=======================================================================
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.
=======================================================================