[Biojava-l] Setting anchors in AnchoredPairwiseSequenceAligner

[Andreas Prlic]

Hi Daniel,

Clearly we need some documentation for this.

Looking at the source: if you get to AbstractMatrixAligner.align() you can
see how the anchors are being used.

I just took a brief look, so I might be wrong, but I think the int[] array
should have the length of the query sequence and each position indicates
the counterpart in the target sequence. Positions that are <=0 should be
considered not to be anchored. If this is right, then this should be very
close to what you were expecting.

Can you take a closer look and confirm if this works for you?

Thanks,

Andreas











On Sun, Nov 24, 2013 at 11:22 PM, Daniel Cameron <cameron.d at wehi.edu.au>wrote:

> Hello all
>
> I'm looking the BioJava API for anchored alignment and I'm unsure of how
> to set alignment anchors. The API exposes int[] get/setAnchor() which is
> confusing me somewhat and I'm unsure of what a BioJava anchor actually is.
> My use case is the comparison of two sequences which I have a priori
> knowledge of particular positions so I was expecting an API where I could
> specify base positions in the query to correspond different positions in
> the target. Eg: I was query base 4 to align to target base 10 and query
> base 100 to align to target base 80. Is this possible?
>
> With anchor being only an int[] and the source looking like this is not an
> array of paired values, how would one go about performing the above
> alignment?
>
>
> Thanks
> Daniel Cameron
>
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