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 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
