[Biojava-l] unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Michael L. Heuer
All, Perhaps I'm making an incorrect assumption, but shouldn't a String element handler return the string value of just the current element? I'm seeing a concatenation of all the values: [java] There was 1 failure: [java] 1) testStringElementHandlerBase(ConfusedStAXHandlerTest) "expected: bu

Re: [Biojava-l] unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Thomas Down
On Tue, Sep 18, 2001 at 10:50:13AM -0400, Michael L. Heuer wrote: > > All, > > Perhaps I'm making an incorrect assumption, but shouldn't a String > element handler return the string value of just the current element? I'm > seeing a concatenation of all the values: > > [java] There was 1 failu

[Biojava-l] Re: unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Christopher Pickslay
All of the StAXContentHandlerBase implementations appear to share this problem. They each contain a StringBuffer field that is initialized along with the class, rather than in startElement(). So not only will they cause this behavior with sequential elements, but it means a StAXContentHandlerB

[Biojava-l] Re: unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Michael L. Heuer
On Tue, 18 Sep 2001, Christopher Pickslay wrote: > All of the StAXContentHandlerBase implementations appear to share this > problem. They each contain a StringBuffer field that is initialized along > with the class, rather than in startElement(). So not only will they cause > this behavior with

[Biojava-l] Re: unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Thomas Down
On Tue, Sep 18, 2001 at 10:39:14AM -0700, Christopher Pickslay wrote: > > As to how to treat child elements, I'd recommend having > StringElementHandlerBase throw an exception (as it currently does). But it > would be a good idea to add a MixedElementHandlerBase class which allows > for the re

Re: [Biojava-l] Re: unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Thomas Down
On Tue, Sep 18, 2001 at 03:12:20PM -0400, Michael L. Heuer wrote: > > On Tue, 18 Sep 2001, Christopher Pickslay wrote: > > > All of the StAXContentHandlerBase implementations appear to share this > > problem. They each contain a StringBuffer field that is initialized along > > with the class, ra

[Biojava-l] annotation tools

2001-09-18 Thread David Waring
I know this is a little off topic but I hope someone in these groups can help. I will be starting to annotate human genomic sequences that we are finishing here at the UWGC. I have been looking for tools to run genscan and then blast predicted genes, and eventually (after some human intervention)

[Biojava-l] Re: unexpected behavior in StAX, StringElementHandlerBase

2001-09-18 Thread Christopher Pickslay
> > > > All of the StAXContentHandlerBase implementations appear to share this > > > problem. They each contain a StringBuffer field that is initialized along > > > with the class, rather than in startElement(). So not only will they > cause > > > this behavior with sequential elements, but it m