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
[EMAIL PROTECTED] wrote:
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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)
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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
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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
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