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 ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
