[Biojava-l] remove features
Robert Stones
r.stones at csl.gov.uk
Thu Jun 12 14:08:38 EDT 2003
Could anyone give me an example where you can remove features from a
Sequence Object.
"Schreiber, Mark" wrote:
>
> Hi -
>
> The problem is that you are trying to remove a feature while iterating over the features. The basic Iterator contract means that an iterator locks any collection it is iterating over. If you attempt to add or remove any part of the collection you will get an exception as the iterator wont be able to work out where it is up to.
>
> You might be best to use a for loop over an array instead.
>
> - Mark
>
> -----Original Message-----
> From: Robert Stones [mailto:r.stones at csl.gov.uk]
> Sent: Thu 6/12/2003 8:05 PM
> To: biojava-l at biojava.org
> Cc:
> Subject: [Biojava-l] Re: Biojava-l Digest, Vol 6, Issue 11
>
> 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
>
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> > Today's Topics:
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> > 1. It's time to know Russia and Russian outsourcing for FREE!
> > (Outsourcing Conference)
> > 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>
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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
> >
> > ------------------------------
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l at biojava.org
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> >
> > End of Biojava-l Digest, Vol 6, Issue 11
> > ****************************************
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