[Biojava-l] Setting anchors in AnchoredPairwiseSequenceAligner

[Daniel Cameron]

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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