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 <[email protected]>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 > > ______________________________________________________________________ > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
