Validates input sequences and gap penalties. Checks that input sequences use the same alphabet. Checks that each symbol in the input sequences exists in the similarity matrix. Checks that gap penalties are less than or equal to 0. Throws exception if sequences fail these checks. Writes warning to ApplicationLog if gap penalty or penalties are positive.

protected void ValidateAlignInput(
	ISequence inputA,
	ISequence inputB
)

Protected Sub ValidateAlignInput ( 
	inputA As ISequence,
	inputB As ISequence
)

protected:
void ValidateAlignInput(
	ISequence^ inputA, 
	ISequence^ inputB
)

member ValidateAlignInput : 
        inputA : ISequence * 
        inputB : ISequence -> unit