[Biojava-l] Re: Biojava-l Digest, Vol 6, Issue 11
Robert Stones
r.stones at csl.gov.uk
Thu Jun 12 10:05:28 EDT 2003
Hi
I have a problem with the removing features from sequence exception:
Feature Peptide org.biojava.bio.proteomics.Digest [1,6]
java.util.ConcurrentModificationException
at
java.util.AbstractList$Itr.checkForComodification(AbstractList.java:444)
at java.util.AbstractList$Itr.next(AbstractList.java:417)
Does anybody have any example code to fix it?
My code from Organism Objects I create:
for (int g=0;g < Organisms.size() ; g++ )
{
Organism org = (Organism) Organisms.get(g);
SequenceIterator si = org.getDB().sequenceIterator();
try
{
while(si.hasNext())
{
Sequence Seq = si.nextSequence();
Iterator i = Seq.features();
while ( i.hasNext() )
{
Feature f = (Feature) i.next();
if (f.getType().equals("Peptide"))
{
FeatureVector.addElement(f);
System.out.println(f.toString());
Seq.removeFeature(f);
}
}
}//while
}//try
catch (BioException be)
{
System.out.println(be);
}
catch (ChangeVetoException cv)
{
System.out.println(cv);
}
}//for
biojava-l-request at biojava.org wrote:
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> 1. It's time to know Russia and Russian outsourcing for FREE!
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> 2. SW and NW (Stephen Montgomery)
> 3. Re: SW and NW (Thomas Down)
> 4. Refactoring
> TranslationTable/ReversibleTranslationTable/RNATools (David Huen)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Jun 2003 11:48:41 -0700
> From: "Outsourcing Conference" <gegrass14974edge_8 at yahoo.com>
> Subject: [Biojava-l] It's time to know Russia and Russian outsourcing
> for FREE!
> To: <biojava-l at biojava.org>
> Message-ID: <20030613094.30151.qmail at mail.yahoo.com>
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> Just fill in the application and win the free trip to St.-Petersburg, Russia!
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> Russian Software Outsourcing Conference. In Saint-Petersburg there will be
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> ------------------------------
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> Message: 2
> Date: Tue, 10 Jun 2003 12:04:47 -0700
> From: Stephen Montgomery <smontgom at bcgsc.bc.ca>
> Subject: [Biojava-l] SW and NW
> To: biojava-l at biojava.org
> Message-ID: <3EE62BCF.4060504 at bcgsc.bc.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Searching the archives, there was some talk/submissions regarding
> putting in Smith-Waterman in biojava.
> It doesn't look like this ever made it in though.
> I wasn't able to track down where the code may have ended up. (a google
> search shows a SW submission to biojava in august)
> Thanks.
>
> Cheers,
> Stephen
>
> ------------------------------
>
> Message: 3
> Date: Tue, 10 Jun 2003 20:56:49 +0100
> From: Thomas Down <thomas at derkholm.net>
> Subject: Re: [Biojava-l] SW and NW
> To: Stephen Montgomery <smontgom at bcgsc.bc.ca>
> Cc: biojava-l at biojava.org
> Message-ID: <20030610195649.GA6547 at firechild>
> Content-Type: text/plain; charset=us-ascii
>
> Once upon a time, Stephen Montgomery wrote:
> > Searching the archives, there was some talk/submissions regarding
> > putting in Smith-Waterman in biojava.
> > It doesn't look like this ever made it in though.
> > I wasn't able to track down where the code may have ended up. (a google
> > search shows a SW submission to biojava in august)
>
> I don't recall a submission as such. But Smith-Waterman (and
> most other `exhaustive' sequence-alignment algorithms) can be
> implemented using pairwise dynamic programming techniques. BioJava has
> included a fairly flexible DP toolkit for several years now.
> For an example, see the file demos/dp/PairwiseAlignment.java
> in the biojava source tree.
>
> Does this sort of thing do what you want?
>
> Thomas.
>
> PS. If you actually want fast, non-exhaustive, sequence
> alignment, the experimental org.biojava.bio.program.ssaha
> package may be helpful.
>
> ------------------------------
>
> Message: 4
> Date: Tue, 10 Jun 2003 23:19:46 +0100
> From: David Huen <david.huen at ntlworld.com>
> Subject: [Biojava-l] Refactoring
> TranslationTable/ReversibleTranslationTable/RNATools
> To: biojava-l at biojava.org
> Message-ID: <200306102319.46159.david.huen at ntlworld.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I have derived AbstractTranslationTable and
> AbstractReversibleTranslationTable classes from existing code and
> reimplemented the above classes over these classes. The code seems to pass
> all existing tests but if you should observe peculiar behaviour, please do
> report it here.
>
> These changes are in preparation for support of codons/codon frequency
> tables/etc which may best belong in a CodonTools class perhaps? Logically
> then, the getGeneticCode() call should move to CodonTools but that will
> break things. A ManyToOneTranslationTable class may be required to support
> returning a List of codons that encode a particular residue.
>
> Regards,
> David Huen
>
> ------------------------------
>
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> End of Biojava-l Digest, Vol 6, Issue 11
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