[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
> 
> biojava-l-request at biojava.org wrote:
> >
> > Send Biojava-l mailing list submissions to
> >         biojava-l at biojava.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         http://biojava.org/mailman/listinfo/biojava-l
> > or, via email, send a message with subject or body 'help' to
> >         biojava-l-request at biojava.org
> >
> > You can reach the person managing the list at
> >         biojava-l-owner at biojava.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Biojava-l digest..."
> >
> > Today's Topics:
> >
> >    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>
> > Message-ID: <20030613094.30151.qmail at mail.yahoo.com>
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > Just fill in the application and win the free trip to St.-Petersburg, Russia!
> > http://software-development.us
> >
> > >From July 24th till July 27th 2003 in Saint-Petersburg there will be held a
> > Russian Software Outsourcing Conference. In Saint-Petersburg there will be
> > celebrations of the 300th anniversary of the city. You will be able to work
> > at the conference and have a vacation in one of the most beautiful cities
> > of Europe at the same time.
> >
> > To participate in the Conference or to subscribe to our newsletter, please,
> > follow this link http://software-development.us   and fill in the application.
> >
> > All qualified applications will automatically participate in the lottery for
> > a free trip.
> >
> > 10 free trips altogether.
> > Free trip includes:
> > - Accommodation:  Corinthia Nevskij Palace
> > - Lufthansa first class ticket
> > - Romantic dinner for two with caviar and with wonderful view on the Neva.
> > - Participation in the Conference.
> >
> > You can fill in the application on http://software-development.us
> >
> > Please know that we do not want to send you information regarding our special
> > offers if you do not wish to receive it. If you would no longer like us to
> > contact you or you feel that you have received this email in error, you may
> > click here to unsubscribe :
> > http://software-development.us/contact_us.html
> >
> > ------------------------------
> >
> > 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
> > http://biojava.org/mailman/listinfo/biojava-l
> >
> > End of Biojava-l Digest, Vol 6, Issue 11
> > ****************************************
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================


More information about the Biojava-l mailing list