[Biojava-l] IllegalSymbolException

Dear all, I encounter the following Exception when I opened a dna sequence with whitespace: IllegalSymbolException how to solve this problem ? Thanks Yves ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/bioj

Re: [Biojava-l] Finding Annotation keys for parsed reportsand inconsistent Blast parsing errors...

DeAngelo Lampkin wrote: Is there some place that lists all the keys that are stored in Annotations for various types of reports that are parsed (specifically BLAST in my case)? Or are we stuck with manually going in,? listing them all and "seeing before trying". Say it ain't so! :) At the momen

Re: [Biojava-l] Finding Annotation keys for parsed reports andinconsistent Blast parsing errors...

> "DL" == DeAngelo Lampkin <[EMAIL PROTECTED]> writes: DL> Is there some place that lists all the keys that are stored in DL> Annotations for various types of reports that are parsed DL> (specifically BLAST in my case)? Or are we stuck with manually DL> going in,? listing them

[Biojava-l] You major CVD commit

Hi, I did my daily cvs update stuff and collected the mods that you described in the mailing list. I end up with these errors: [javac] Compiling 49 source files to /Users/foisys/biojava-live/ant-build/classes/main [javac] /Users/foisys/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl

Re: [Biojava-l] You major CVD commit

Once upon a time, Sylvain Foisy wrote: > Hi, > > I did my daily cvs update stuff and collected the mods that you described in > the mailing list. I end up with these errors: Some files got moved around during this change. Because the BioJava build scripts make a copy of the source tree before co

[Biojava-l] Re: You major CVD commit

Hy Symvain, As Thomas said, try: ant clean ant If this doesn't work, then I have probably forgotten to do a cvs remove on ProjectedFeatureHolder Matthew Sylvain Foisy wrote: Hi, I did my daily cvs update stuff and collected the mods that you described in the mailing list. I end up with these

[Biojava-l] Massaging multi-query BLAST XML output...

Hi guys, First of all, thanks to Keith and Matthew on the assist with the last question. And to the rest, shame on you all for not helping sooner! :) So now for my newest question concerning parsing Blast XML files; specifically the mangled XML file that come out as a result of a multiple quer

RE: [Biojava-l] Massaging multi-query BLAST XML output...

There where a couple of posts on this about two weeks ago, some solutions where posted to the list, however I think David Huen was going to post something "official" to BioJava-live on CVS. See the JavaDoc comments on org.biojava.bio.program.sax.blastxml.BlastOutputHandler for various options and

Re: [Biojava-l] Massaging multi-query BLAST XML output...

On Wed, 9 Jul 2003, DeAngelo Lampkin wrote: > Hi guys, > > First of all, thanks to Keith and Matthew on the assist with the last question. And > to the rest, shame on you all for not helping sooner! :) Fast paid-for service and development can hopefully be obtained from Biojava Consulting. But

[Biojava-l] Bug in SeqIOTools.writeSwissProt() method?

Hi guys, SeqIOTools.writeSwissprot(OutputStream, SequenceIterator) goes like this: SequenceFormat former = new EmblLikeFormat(); PrintStream ps = new PrintStream(os); while (in.hasNext()) { former.writeSequence(in.nextSequence(), ps); } and EmblLikeFormat.writeSequence(S