[Biojava-dev] Using DNASequence reverseComplement

[PATERSON Trevor]

Sorry for raising that behemoth earlier..

I have a separate problem with the DNASequence API -

Probably I just don't understand how to use the View objects


If I make a DNASequence

DNASequence seq = new DNASequence("AAAAACCCCGGGTT");

i.e. length = 14,

I might reasonably want to get the ReverseComplement of bases 11-14, which should 'be' "AACC"

But I cannot manage to get this in one easy step....

seq.toString(): AAAAACCCCGGGTT --> FINE

seq.getReverseComplement().getSequenceAsString(): AACCCGGGGTTTTT --> FINE

But when I try to use bounds on this complement - methods refer back to the original seq's iterator, not the complement

seq.getReverseComplement().getSequenceAsString(11,14,Strand.POSITIVE): GGTT 
	i.e the same as seq.getSequenceAsString(11,14,Strand.POSITIVE)
seq.getReverseComplement().getSequenceAsString(11,14,Strand.NEGATIVE): TTGG
	i.e the same as seq.getSequenceAsString(11,14,Strand.NEGATIVE)

Is this the desired behaviour? How would I get the desired reverseComplement fragment?

The only obvious way that I can see is  

                DNASequence subseq = new DNASequence(seq.getSequenceAsString(11, 14, Strand.POSITIVE));
                System.out.println(""+ subseq.getReverseComplement().getSequenceAsString());

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On a related point I was mightily confused by the Strand.POSITIVE/Strand.NEGATIVE enumeration

I was naively interpreting them to refer to the strand of the DNA: 
Whereas they infact refer to the directionality of the Iterator *on the same Strand*

A better name might be Direction:FORWARDS/Direction.BACKWARDS?
Positive and negative strand has loaded biological meaning for newbies like me ( sense versus antisense )
So I made the assumption that a Strand.NEGATIVE call would itself reverseComplement
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