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! Schützen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
