MTPairwiseSequenceAlignment

This class computes pairwise sequence alignments either globally (Needleman-Wunsch) or locally (Smith-Waterman).

* read-only access
-(NSString*)description	returns textual representation
-(MTChain*)chain1	returns the first chain (3.4); this is the static chain
-(MTChain*)chain2	returns the second chain (3.4); this chain is matched onto the first chain
-(NSString*)getSequence1	returns sequence1
-(NSString*)getSequence2	returns sequence2
-(NSArray*)alignmentPositions	returns array (9.3) of alignment positions (3.12)
-(MTSelection*)getSelection1	returns the aligned residues in sequence1 as a selection (3.13)
-(MTSelection*)getSelection2	returns the aligned residues in sequence2 as a selection (3.13)
-(int)gop	returns the current gap opening penalty
-(int)gep	returns the current gap extension penalty
* operations
-(void)setSubstitutionMatrix: (Class)msubst	sets the substitution matrix, which affects all further computations
-(void)setGop: (int)p_gop	sets the gap opening penalty
-(void)setGep: (int)p_gep	sets the gap extension penalty
-(void)computeGlobalAlignment	computes global alignment (Needleman-Wunsch)
-(void)computeLocalAlignment	computes local alignment (Smith-Waterman)
* analyze
-(int)countPairs	counts alignment positions in alignment
-(int)countUngappedPairs	counts aligned pairs only
-(int)countIdenticalPairs	counts aligned pairs only
* input/output
-(void)writeFastaToStream: (MTStream*)stream	writes pairwise alignment in Fasta format to the given stream (5.1)
* creation
+(MTPairwiseSequenceAlignment*)alignmentBetweenChain: (MTChain*)chain1 andChain:(MTChain*)chain2	creates a new instance working on chain1 and chain2 (3.4)