[Biojava-l] Sensible Circularity

[Schreiber, Mark]

Hi -

Following discussions at BOSC I have changed the circular coordinates
system such that a 0 coordinate is sensibly handled.

Previously the base 1 was the first base of the sequence and base -1 was
the equivalent of the last base of the sequence. Trying to get at 0
would throw an exception. Eg:

Linear		 1  2  3  4  5  6  7  8
Circular		 1  2  3 ....       -2 -1

Now the base zero can be thought of as the base immediately before the
first base (in the case of a circular sequence the last base of the
seqeunce) base -1 is the penultimate base and 1 is still the first base.
Eg

Linear		 1  2  3  4  5  6  7  8
Circular		 1  2  3 ....       -1  0

Now that 0 has a home, for loops work properly and all the math gets a
whole lot simpler. I hope it doesn't interfere with genbank, I'm pretty
sure genbank doesn't use negative coordinates. Anyhow this also nicely
sidesteps the whole number from one vs number from zero argument. Zero
now refers to the base before the first base which in a circular
sequence is the last base. Sort of a number to zero?

Anyhow I hope this doesn't break too much code (other than my own).

Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

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