Hi, HMM serialization (or persistance) seems to be an ongoing problem for people. We (OK - I) wrote this code a long time ago, back in the dark ages when I didn't know much about programming. Does anyone want to fix this mess once and for all, and write a HMM persistance API? It sounds like that would be a realy helpfull thing to have.
Matthew --- Lachlan Coin <[EMAIL PROTECTED]> wrote: > 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" > <[EMAIL PROTECTED]> > > To: "Tisanai" <[EMAIL PROTECTED]>, > <[EMAIL PROTECTED]> > > > > 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:[EMAIL PROTECTED]] > > > Sent: Tuesday, 8 October 2002 2:40 a.m. > > > To: [EMAIL PROTECTED] > > > 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 - [EMAIL PROTECTED] > > > 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. > > > ======================================================================= > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
