Hi Alastair, BioJava 1.X can do distributions, however there is no counterpart for this yet in BioJava 3.
Andreas On Wed, Apr 6, 2011 at 9:40 AM, Alastair Kilpatrick <[email protected]> wrote: > Thanks - I had just downloaded the BioJava jars manually so that's > fixed the CookBook code. However, I've made some changes in order to > align DNA sequences instead and am running into more errors - this > code: > > public static void main(String[] args) { > String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"}; > List<DNASequence> lst = new ArrayList<DNASequence>(); > for(String seq : seqs) { > lst.add(new DNASequence(seq)); > } > Profile<DNASequence, NucleotideCompound> profile = > Alignments.getMultipleSequenceAlignment(lst); //** > System.out.println(profile); > ConcurrencyTools.shutdown(); > } > > gives: > java.util.concurrent.ExecutionException: java.lang.NullPointerException > at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source) > at java.util.concurrent.FutureTask.get(Unknown Source) > at > org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) > at > org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) > at > org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173) > at CookbookMSA.main(CookbookMSA.java:49) > > at the 'alignment' line (**) - not sure what the problem is here, I > see that getMultipleSequenceAlignment() has an extra argument(s) in > the Javadoc but these weren't required in the example? > Final question (hopefully!) - once I have the alignments I require I'd > like to create a sequence logo - is there a way of doing this in > BioJava3? From a google search I've seen references to > DistributionTools.distOverAlignment() and similar, but can't find > anything like that in the new api. > > Thanks again, sorry everyone for all the questions! > > Alastair > > > On 6 April 2011 12:09, Scooter Willis <[email protected]> wrote: >> >> You need to use the forester.jar file from the biojava3 code check out. If >> you are using maven this should be automatic. >> >> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" >> <[email protected]> wrote: >> >> Dear all, >> I'm pretty new to BioJava so I may be missing something - I've checked >> through the list archives without much luck. >> I've been trying to do some multiple sequence alignments but I've been >> running into strange errors. To try and find where the problem is, >> I've just copied the code straight from >> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but >> I'm still getting an error: >> >> Caused by: java.lang.ClassNotFoundException: >> org.forester.phylogenyinference.DistanceMatrix >> >> It would seem that this is something to do with forester.jar, which I >> had to download separately (from http://code.google.com/p/forester/) >> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment - >> when I look through the jar in Eclipse, there isn't anything named >> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data', >> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something >> I'm doing wrong, or is it the case that either one of BioJava or >> forester has been updated and things have broken somewhere (I see the >> CookBook page was updated in July 2010 but forester was updated just >> last month)? Either way, any ideas would be much appreciated! >> >> Many thanks, >> Alastair Kilpatrick >> >> PhD candidate, >> School of Informatics, University of Edinburgh >> _______________________________________________ >> 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
