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:[EMAIL PROTECTED] > Sent: Thu 6/12/2003 8:05 PM > To: [EMAIL PROTECTED] > 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 > > [EMAIL PROTECTED] wrote: > > > > Send Biojava-l mailing list submissions to > > [EMAIL PROTECTED] > > > > 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 > > [EMAIL PROTECTED] > > > > You can reach the person managing the list at > > [EMAIL PROTECTED] > > > > 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" <[EMAIL PROTECTED]> > > Subject: [Biojava-l] It's time to know Russia and Russian outsourcing > > for FREE! > > To: <[EMAIL PROTECTED]> > > Message-ID: <[EMAIL PROTECTED]> > > 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 <[EMAIL PROTECTED]> > > Subject: [Biojava-l] SW and NW > > To: [EMAIL PROTECTED] > > Message-ID: <[EMAIL PROTECTED]> > > 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 <[EMAIL PROTECTED]> > > Subject: Re: [Biojava-l] SW and NW > > To: Stephen Montgomery <[EMAIL PROTECTED]> > > Cc: [EMAIL PROTECTED] > > Message-ID: <[EMAIL PROTECTED]> > > 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 <[EMAIL PROTECTED]> > > Subject: [Biojava-l] Refactoring > > TranslationTable/ReversibleTranslationTable/RNATools > > To: [EMAIL PROTECTED] > > Message-ID: <[EMAIL PROTECTED]> > > 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 - [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-l > > > > End of Biojava-l Digest, Vol 6, Issue 11 > > **************************************** > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > 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. > ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
