You do realize that many of the other classes in biojava are 1 based rather
than 0 based. Lets keep one standard, I don't care which. Having some
functions 1 based and some 0 based will drive many insane, in fact I've
already lost a developer to the current standard being 1 based :).
-Robin
-
On Tue, 4 Sep 2001, Emig, Robin wrote:
> You do realize that many of the other classes in biojava are 1 based rather
> than 0 based. Lets keep one standard, I don't care which. Having some
> functions 1 based and some 0 based will drive many insane, in fact I've
> already lost a developer to the
Dear Sir:
I would like to recompile biojava-live by myself in my
local computer. Unfortunately, it seems missing
several files in your source code, such as element,
xmlpeerbuilder, saxexceiption. Maybe more. Would
please help me to check all the classes. All these
classes are not in your jar file
Hi folks,
I've been hacking away at the problem of Renderers drawing at high
sequence/graphics coordinates. I've written another implementation of
SequenceRenderContext which borrows code from SequencePanel (and a
concept from Artemis); it always draws from zero placed at the edge of
the visible
On Tue, Sep 04, 2001 at 09:49:32AM -0700, xuxian zhang wrote:
> Dear Sir:
>
> I would like to recompile biojava-live by myself in my
> local computer. Unfortunately, it seems missing
> several files in your source code, such as element,
> xmlpeerbuilder, saxexceiption. Maybe more. Would
> please
On Tue, Sep 04, 2001 at 05:53:18PM +0100, Keith James wrote:
>
> I've been hacking away at the problem of Renderers drawing at high
> sequence/graphics coordinates. I've written another implementation of
> SequenceRenderContext which borrows code from SequencePanel (and a
> concept from Artemis);
So what your saying is that if you have the sequence ATGGAC, that
the first A is position 1 in the sequence/symbol list, but position 0 in the
frame/phase. I realize that 0,1,2 may be the most common convention, but
does anyone else see how that can get confusing?
-Robin
-Original Mes
On Tue, 4 Sep 2001, Emig, Robin wrote:
> So what your saying is that if you have the sequence ATGGAC, that
> the first A is position 1 in the sequence/symbol list, but position 0 in the
> frame/phase. I realize that 0,1,2 may be the most common convention, but
> does anyone else see how tha
Hello all,
I'm getting start a study about biojava package I saw some points that
I would know about.
-> About the modeling of the class Feature, instead of use a
recursive structure where Feature implements a FeatureHolder, the FeatureHolder
could be like a Propretie
On Tue, 4 Sep 2001 [EMAIL PROTECTED] wrote:
>
> -> About the modeling of the class Feature, instead of use a
> recursive structure where Feature implements a FeatureHolder, the FeatureHolder
> could be like a Propreties that already exists in java.util? It's hold the tree
> fe
"Emig, Robin" wrote:
> So what your saying is that if you have the sequence ATGGAC, that
> the first A is position 1 in the sequence/symbol list, but position 0 in the
> frame/phase. I realize that 0,1,2 may be the most common convention, but
> does anyone else see how that can get confus
I'm not sure if I'm calling it wrong, or if there's a problem. I'm trying
to create a DNA sequence, and translate that into a protein sequence with:
SymbolList prtList = RNATools.translate(RNATools.transcribe(dnaList));
What happens is that I get:
Exception in thread "main" org.biojava.bio.sy
On Tue, Sep 04, 2001 at 08:14:02PM +0100, Simon Brocklehurst wrote:
>
> In general, I think there are no right or wrongs with this kind of thing. For
> example, in regard of *sequences* starting at zero or one, it can obviously be
> sensibly argued that index positions should start at zero, to m
On Tue, 4 Sep 2001, Emig, Robin wrote:
> So what your saying is that if you have the sequence ATGGAC, that
> the first A is position 1 in the sequence/symbol list, but position 0 in the
> frame/phase. I realize that 0,1,2 may be the most common convention, but
> does anyone else see how tha
On Tue, 4 Sep 2001, Ewan Birney wrote:
> On Tue, 4 Sep 2001, Emig, Robin wrote:
>
> > So what your saying is that if you have the sequence ATGGAC, that
> > the first A is position 1 in the sequence/symbol list, but position 0 in the
> > frame/phase. I realize that 0,1,2 may be the most commo
It might help to keep separate the notion of internal models and external
formats. Parsers and exporters can be the liason between internal models
and external formats. This includes GUI visualization. One possibility
might be to use 0 based numbering internally and the appropriate numbering
for e
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