> "Kalle" == =?UTF-8?B?S2FsbGUgTsOkc2x1bmQ=?= writes:
[...]
Kalle> The second part is the thing i dont like. To me, the core
Kalle> properties that defines what an Alignment is, doesnt
Kalle> contain the functionality of being able to make
Kalle> SimpleSequences out of Symb
Singh, Nimesh wrote:
>Given any implementation of an alignment, there is no guarantee that the alignment
>will have links to the original underlying sequences.
>
I know this might be a bit finicky, and that you are most likely already
aware of this. But, An alignment
doesnt necesarily hold Seq
-
From: Kalle Näslund [mailto:[EMAIL PROTECTED]]
Sent: Fri 7/26/2002 11:52 AM
To: Singh, Nimesh
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] adding toSequenceIterator method for Alignment
Singh, Nimesh wrote:
Singh, Nimesh wrote:
> I've created a class called AlignmentSequenceIterator that I intend to put in
>the org.biojava.bio.seq package. It will do the real work. I've also added
>public SequenceIterator sequenceIterator() {
>return new AlignmentSequenceIterator(this);
>
Cool. Looks good. Commit away. Could you add some javadocs (class &
constructor)?
Matthew
Singh, Nimesh wrote:
> I've created a class called AlignmentSequenceIterator that I intend to put in
>the org.biojava.bio.seq package. It will do the real work. I've also added
> public Seq
I've created a class called AlignmentSequenceIterator that I intend to put in the
org.biojava.bio.seq package. It will do the real work. I've also added
public SequenceIterator sequenceIterator() {
return new AlignmentSequenceIterator(this);
}
to each alignment
> You can find all classes implementing Alignment by greping the source
> tree for "implements Alignment" - I can only find
> org.biojava.bio.symbol.SimpleAlignment, but I may have missed
> something.
>
> Matthew
There are some classes in org.biojava.bio.alignment that do as well.
- Mark
===
>Would this method return an iterator over each sequence in the
>alignment? Sounds usefull to me. I have always taken an iterator over
>the labels and fetched each sequence from the alignment by each of these
>labels.
Yeah, it's meant to simplify that process. It would return an instance of a b
Hello,
What do you think about adding a toSequenceIterator() method to the Alignment
interface? I think it would involve creating a new SequenceIterator implementation
and updating everything that implements Alignment. I would take care of that, if you
guys could tell me every new class tha
