Hi all,
I was wondering if there is an easily-retrievable alphabet that includes
all symbols from RNA and DNA sequences; a sort of 'global nucleotide
sequence' alphabet that would include g, a, c, t, and u. This would be
helpful for my application that does not know what kind of sequence it is
go
On Thu, Oct 24, 2002 at 01:27:01PM -0400, Dave Barkan wrote:
> Hi all,
>
> I was wondering if there is an easily-retrievable alphabet that includes
> all symbols from RNA and DNA sequences; a sort of 'global nucleotide
> sequence' alphabet that would include g, a, c, t, and u. This would be
> hel
> Is there a MacOS X JDK1.4 yet? I know there's one coming,
> but I thought it was still a little way coming.
>
My mistake, I thought apple had released this but apparently only a
developers preview version is available. Also J2SE1.4.X will only be
available for OSX 10.2 http://developer.apple.
Given that the returned location refers to the local sequence,I prefer the
id of the local sequence.
Thanks
-Original Message-
From: Matthew Pocock [mailto:matthew_pocock@;yahoo.co.uk]
Sent: Thursday, October 24, 2002 4:40 PM
To: Stephane Marcel; biojava
Subject: Re: [Biojava-l] [Biojav
> Is it normal or the result should be:
> AL123465true[123,567]
> nullfalse [363963,367351]
> nullfalse [368780,369208]
>
Also, would you prefer to get the id of the local
sequence rather than null for local regions?
Matthew
__
Hi Stephane,
Looks like a bug to me. It turns out it's my fault
from when first writing the code. Line 200 of
RemoteFeature.java has a == that should be a !=. Fixed
in cvs. Apologies.
Matthew
--- Stephane Marcel
<[EMAIL PROTECTED]> wrote: > Hi,
>
> when I read the doc of the Class
> RemoteFeat
Hi,
when I read the doc of the Class RemoteFeature.Region I can see that :
isRemote() should return true if the sequence is a remote sequence (a clone
for example) and getSeqID() will return the ID of the remote sequence.
But if I try this:
for(Iterator i = regions.iterator(); i.hasNext(); )
Yes. There are two classes - PackedDNASymbolList was
the original try, and PackedSymbolList was mark 2.
PackedSymbolList lets you choose how to map symbols to
bit patterns, and to use the compact representation
(no ambiguities) or the complete one (with
ambiguities). If you don't care about the det
On Linux at least there are some showstopper Java2D bugs which
manifest themselves in 1.4, but not 1.3:
Symptom 1:
With antialiasing off
PairwiseDiagonalRenderer shows *many* fewer lines than expected but
also shows artefactual lines in the wrong places. All the hundreds of
missing lines appear
On Thu, Oct 24, 2002 at 11:37:16AM +1300, Schreiber, Mark wrote:
> Hi -
>
> The 1.4 JDK has been around for quite a while know and is available for
> all the usual OS and IDE suspects. Might it be time to officially merge
> all of the 1.4 stuff into Biojava? Possibly making another release,
> bioj
On Thu, Oct 24, 2002 at 11:34:40AM +1300, Schreiber, Mark wrote:
> Hi -
>
> There is a PackedSymbolList and a PackedDNASymbolList in
> org.biojava.bio.symbol. Can't say I've used them but I think they
> operate pretty much the same as normal SymbolLists.
I've used PackedSymbolList on a few occasi
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