Schreiber, Mark wrote:
I don't know is BioJava has a PDB reader, I know there is a PDB to XML
type of converter but it seems a shame to not have some way to read PDB
(it keeps us very sequence centric). Does anyone have one they want to
donate?
- Mark
Can we write a PDB-xml -> sequenceIO adaptor? I
FYI, the JavaDoc utility cuts off most of that script which is why I couldn't find it in the online documentation (which looks strangely incomplete as a result). Everything down to the " " part shows up normally. After that, nothing else gets JavaDoc'd. Is there a bug in Javadoc that anyone is a
Mmm. That's the topological sort of the states. It makes sure that when
the DP recursion does a foreach(state), it loops over them in an order
whereby all info is calculated that a state needs before it is reached.
I am fairly sure that the body of the stateList() method can't infinite
loop - a
On Fri, 11 Jul 2003, Matthew Pocock wrote:
> > Also, I'm not really sure how to go about using the StAX stuff.
>
> Are the biojava and source-forge StAX APIs synchronized now? Anybody
> know? Perhaps we should write a simple StAX tutorial. I'll see if I get
> any time in the next week.
The bioja
A rather complex example using the sf StAX is at
> http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/vocabulary/vocabulary-sandbox/src/java/vocabulary/simple/SimpleVocabularyMLReader.java
michael
On Fri, 11 Jul 2003, Michael Heuer wrote:
>
> On Fri, 11 Jul 2003, Matthew Pocock wrote:
>
> > > A
Once upon a time, Yu Wang wrote:
> Dear Sr/Madam,
>
> I am trying to build NetBSD package for biojava1.3, and I want to build
> everything from source so when this package is ported to some other OS, it
> still work.
Okay, there's now a bytecode-0.92.tar.gz file in:
http://www.biojava.org/do
If you go to transitionsTo(), aprox line 666, you will see the text:
workingSet.add(i);
This should read
workingSet.add(i.next());
This removes your infinite loop.
There is an efficiency problem somewhere - stateList is being called
once per itteration, which is slow for complex models. I wil
>> However, when I take over the world with genetically
>> engineered T-rex's with the help of biojava, then I won't be
>> joking any longer. Oops, did I reveal my evil plan out loud again?
>T-Rex's are so last Jurassic Period.
>- Mark
mini T-Rexen would be nice but miniature elephants as pets
Anyone ever get the following error while building biojava-live? I tried updating
with the new bytecode jar file to see if that would help, but nope, no such luck.
-
On Fri, 11 Jul 2003, DeAngelo Lampkin wrote:
> Anyone ever get the following error while building biojava-live? I tried updating
> with the new bytecode jar file to see if that would help, but nope, no such luck.
> -
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