Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-16 Thread Matthew Pocock
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-16 Thread David Huen
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread mark . schreiber
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread Mark Fortner
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread mark . schreiber
--- > > > > >>-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

RE: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread Richard HOLLAND
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread Mark Fortner
a-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 turn it into another where it is viewed in another compound alphabet of the required order. I'm looking f

RE: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread mark . schreiber
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

RE: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread Richard HOLLAND
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

Re: [Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread David Huen
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

[Biojava-l] Sequence Iteration in BioJava(x)

2005-12-15 Thread Mark Fortner
I'm looking for the best way to iterate through all nmers within a given sequence. For example, given a sequence that looks like this: ACTGACTGACTG If I extract all trimers from this I should get: ACT CTG TGA GAC ACT CTG TGA GAC ACT CTG Is there an existing class that will allow me to iterate