thanks a lot for the support. I had changed the code, if I'd have got access to the CVS. When you changed the code, I will be very grateful if you can inform me . I need it for a work on a project for the university.
Daniel > -----Ursprüngliche Nachricht----- > Von: "Mark Schreiber" <[EMAIL PROTECTED]> > Gesendet: 29.08.07 16:36:38 > An: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> > CC: [email protected] > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > Just looked at the CVS on line. You are very likely correct. > > There used to be a listener for changes in the Alphabet but this was > mistakenly removed as it was thought to be redundant. A diff view is > here > (http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/src/org/biojava/bio/symbol/LinearAlphabetIndex.java.diff?r1=1.12&r2=1.13&cvsroot=biojava) > > I will check it back in tomorrow unless some one beats me to it. A > JUnit test is also required to make sure this works. > > - Mark > > On 8/29/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Hi all, hi Mark > > > > thanks for the fast Answer. > > > > I looked at the code and perhaps solved the problem. > > > > During initialisation of the ProfileHMM ( bevore method connectModel() is > > called ) the transWeights are set with SimpleDistributions sd. These sd > > again are initialized with an empty Alphabet (no symbol). (*) > > > > These Distributions keeps an indexer Object which is used during the > > training process where the exception occurs. > > > > because of (*) the number of indexed symbols is 0 (indexer.symbols.length > > == 0) and the (FiniteAlphabet)indexer.alphaRef.get() has length 0 too. > > (Indexer is of type LinearAlphabetIndex) > > > > When connectModel() is called the Alphabets ( which are the same as > > indexer.alphaRef ) are filled with some symbols (EmissionState, DotState > > ...) (**) BUT the indexer.symbols.length will not be changed (***). > > > > This causes the following exception: > > In SimpleDistribution.Trainer.trainImpl is a method called getWeights(). > > This will return a double list of length indexer.getAlphabet() which is the > > same of indexer.alphaRef. Because of (**) this will have a length n>0. So > > that the for loop in this piece of code runs from 0 to n. Here the > > exception occurs. indexer.symbolForIndex(i) (0<=i<n) cause the error > > because of (***) indexer.symbols are empty. > > > > I think it must be changed the symbols of the indexer Object in the > > connectModel() method too. But I'm not really sure because I didn't worked > > with biojava so long. > > > > I'm sorry for my bad English but I hope that I could help a little. > > Many greetings > > Daniel > > > > > -----Ursprüngliche Nachricht----- > > > Von: "Mark Schreiber" <[EMAIL PROTECTED]> > > > Gesendet: 28.08.07 16:28:23 > > > An: "Daniel Rohrbach" <[EMAIL PROTECTED]> > > > CC: [email protected] > > > Betreff: Re: [Biojava-l] problems with the profilehmm demo > > > > > > > > > > Hi - > > > > > > This is a bug that has been submitted to bugzilla. Strangely it was > > > not an issue in the pre-releases of biojava. I was kind of hoping > > > someone else would fix it but I guess I will have to find time to take > > > a look. > > > > > > - Mark > > > > > > On 8/28/07, Daniel Rohrbach <[EMAIL PROTECTED]> wrote: > > > > Hi all, > > > > > > > > i'm trying to run the "How do I make a ProfileHMM" example but it > > > > doesn't want to work. I copied the code to my program and when I start > > > > it I get the following exceptions: > > > > > > > > Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't > > > > find symbol for index 0 > > > > at > > > > org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106) > > > > at > > > > org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332) > > > > at > > > > org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306) > > > > at > > > > org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126) > > > > at biojavatests.HMMTest.main(HMMTest.java:71) > > > > > > > > The error occurs at mt.train(). It seems that there was no, wrong or > > > > empty alphabet set for the trainer that shall be used. > > > > > > > > here the link to the examplepage: > > > > http://biojava.org/wiki/BioJava:CookBook:DP:HMM > > > > any help on this topic? > > > > > > > > Thanks in advance > > > > __________________________________________________________________________ > > > > Erweitern Sie FreeMail zu einem noch leistungsstärkeren E-Mail-Postfach! > > > > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > > > > > > > > > > > _______________________________________________ > > > > Biojava-l mailing list - [email protected] > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > > _______________________________________________________________________ > > Jetzt neu! 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