Matthew Pocock; David Waring
> Cc: biojava
> Subject: RE: [Biojava-l] Alignments
>
>
> Hi -
>
> Right off the bat I would like to say that the Phred package was poorly
> designed. I can say that cause I made it ;-)
>
> The major problem with it was that initially I co
Hi -
Right off the bat I would like to say that the Phred package was poorly
designed. I can say that cause I made it ;-)
The major problem with it was that initially I couldn't think of a way
to store the infinite integer alphabet with the DNA alphabet as a
cross-product. This problem is actual
David Waring wrote:
> I presume that this is api-short-hand for inserting gaps before or after
> a particular sequence in the alignment? This would be functionally
> equivalent to using a gapped sequence to view the alignment component
> and adding gaps at 0 or at length.
>
> This is not exactly
> -Original Message-
> From: Matthew Pocock [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, May 14, 2002 2:02 PM
> To: David Waring
> Cc: biojava
> Subject: Re: [Biojava-l] Alignments
>
>
> Hi David,
>
> David Waring wrote:
> > I will soon be adding a
Hi David,
David Waring wrote:
> I will soon be adding a bunch of classes related to Alignments. I should
> have these ready today or tomorrow. I hate naming things so if anyone can
> come up with better names especially for ARAlignment I am open to
> suggestions.
>
> Interface UnequalLengthAlign
I will soon be adding a bunch of classes related to Alignments. I should
have these ready today or tomorrow. I hate naming things so if anyone can
come up with better names especially for ARAlignment I am open to
suggestions.
Interface UnequalLengthAlignment (allows having sequences of different
