[Biojava-l] Phred Sequences

[Schreiber, Mark]

Hi -

I have updated all of the Phred package to make use of a DNA X Sub
Integer cross product alphabet. The SubInteger Alphabet is essentially a
finite subset of the infinite IntegerAlphabet and can be constructed
using the static methods of the IntegerAlphabet class. Probably an
equivalent could be made for the Double alphabet although this would
still be infinite (technically not true but I am choosing to ignore the
finer points of floating point precision).

The PhredSequence is now created using a single crossproduct SymbolList
avoiding the previous awkwardness of using two symbollists. Some
convenience methods have been added to get the DNA or integer Symbol
from any position (the traditional symbolAt() will return the
CrossProduct Symbol). There are also static methods in the PhredTools
class to make a number of operations simple.

The GappedPhredSymbolList is now completely unessecary and has been
removed.

I will do some more testing of these classes just to make sure
everything has survived the crossproduct changeover.

- Mark

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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