Hi
I save profile HMM and read it back through java serialization. But the problem is
sometimes it works but sometimes not.
My code is as below:
FileOutputStream fos_md = new FileOutputStream(md_file);
ObjectOutputStream oos_md = new ObjectOutputStream(fos_md);
oos_md.writeObject(dp[i].getModel());
oos_md.close();
FileInputStream fis_md = new FileInputStream(md_file);
ObjectInputStream ois_md = new ObjectInputStream(fis_md);
ProfileHMM model = (ProfileHMM) ois_md.readObject();
ois_md.close();
tdp[i] = DPFactory.DEFAULT.createDP(model);
I got the error message like this:
org.biojava.bio.BioError: State d-74 is known in states but is not listed
in the transFrom table
at
org.biojava.bio.dp.SimpleMarkovModel.transitionsFrom(SimpleMarkovModel.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 Test.main(Test.java:96)
Is There anytings to do with the length of the model? Because It's seem no problem
with the short model.
Thanks
Tisanai
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