[Biojava-l] Re: Biojava-l Digest, Vol 6, Issue 11
Matthew Pocock
matthew_pocock at yahoo.co.uk
Thu Jun 12 10:55:55 EDT 2003
Hi Robert,
Could you include the complete stack-trace? These exceptions come from
the collections framework when a collection you are iterating over is
modified with add/remove directly, rather than through the iterator.
However, without the full stack-trace, it's going to be hard to know
exactly what code is reponsible for triggering this.
Matthew
Robert Stones wrote:
> 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
>
--
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk
More information about the Biojava-l
mailing list