I have started to use JAVA for my daily work.
Now I would like to get started with biojava.
On my WINDOWS 2000 laptop I have dowloaded the biojava.jar, bytecode.jar,
xerces.jar into the c:\biojava directory. Then added the classpath.
To test the set-up I went into the demos directory and did
jav
Hi.
I've been tinkering with IntegerAlphabet and DoubleAlphabet with Mark
Schreiber. We were having some strange bugs and tracked them down to the
multiple symbols representing the same integer or double. Apparently
Thomas and I thought it was a good idea for symbols in infinite
alphabets not
> You can find all classes implementing Alignment by greping the source
> tree for "implements Alignment" - I can only find
> org.biojava.bio.symbol.SimpleAlignment, but I may have missed
> something.
>
> Matthew
There are some classes in org.biojava.bio.alignment that do as well.
- Mark
===
>Would this method return an iterator over each sequence in the
>alignment? Sounds usefull to me. I have always taken an iterator over
>the labels and fetched each sequence from the alignment by each of these
>labels.
Yeah, it's meant to simplify that process. It would return an instance of a b
You're a star Keith. This is one of our few recurrent classes of bug. Do
we have regression tests for this (in embl, genbank and fasta) yet?
Matthew
Keith James wrote:
>>" " == saerts <[EMAIL PROTECTED]> writes:
>
>
> > Hello, There appears to be a problem when writing a sequence
Hello,
What do you think about adding a toSequenceIterator() method to the Alignment
interface? I think it would involve creating a new SequenceIterator implementation
and updating everything that implements Alignment. I would take care of that, if you
guys could tell me every new class tha
> " " == saerts <[EMAIL PROTECTED]> writes:
> Hello, There appears to be a problem when writing a sequence to
> file in EMBL format, but only if it contains a multiple of 60
> nucleotides (there are 60 nt's on each line) -> the last line
> of nucleotides is not written an
