On Friday 16 December 2005 09:25, David Huen wrote:
>
> If that is the kind of case you want to deal with, I would believe the
> SSAHA code in BJ may be adapted to your purposes but this comment does not
> arise from direct personal experience.
The biojava SSAHA code is likely to be quite efficien
On Dec 16 2005, Mark Fortner wrote:
Richard,
Thanks for the example. Your approach is very similar to a non-BioJava
approach that I had worked out earlier. I was wondering if the
BioJava(x) API provides any performance benefit over simply running a
window along a character stream?
The wor
Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
Mark,
Thanks for the info. This is sort of a test project for us. We have a
few classes and data structures in C++ that handle operations like
sequence io and packing, and are fairly fast. However, we've also come
to the
rtner
To: biojava-list
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
Richard,
Thanks for the example. Your approach is very similar to a non-BioJava
approach that I had worked out earlier. I was wondering i
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>>-Original Message-
>>From: [EMAIL PROTECTED]
>>[mailto:[EMAIL PROTECTED] On Behalf Of David Huen
>>Sent: Friday, December 16, 2005 7:34 AM
>>To: [EMAIL PROTECTED]
>>Cc: biojava-list
>>Subject: Re: [Biojava-l] Sequen
L PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Mark Fortner
> Sent: Friday, December 16, 2005 10:36 AM
> To: biojava-list
> Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
>
>
> Richard,
> Thanks for the example. Your approach is very similar to a
ts content to any
other person. Thank you.
-
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David Huen
Sent: Friday, December 16, 2005 7:34 AM
To: [EMAIL PROTECTED]
Cc: biojava-list
Subject: Re: [Biojav
Schreiber/GP/Novartis)
Subject: RE: [Biojava-l] Sequence Iteration in BioJava(x)
orderNSymbolList splits the sequence into non-overlapping chunks. What
is required here is chunks that are only one base different (further on)
than the previous chunk.
The simplest way would be th
6, 2005 7:34 AM
> To: [EMAIL PROTECTED]
> Cc: biojava-list
> Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
>
>
> On Dec 15 2005, Mark Fortner wrote:
> I think what you want is the SymbolListViews.orderNSymbolList method.
>
> It will take a SymbolList and tur
On Dec 15 2005, Mark Fortner wrote:
I think what you want is the SymbolListViews.orderNSymbolList method.
It will take a SymbolList and turn it into another where it is viewed in
another compound alphabet of the required order.
I'm looking for the best way to iterate through all
nmers within
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