Class MTPairwiseSequenceAlignment

Inherits from:

NSObject

Declared in:

../libmoltalk/MTPairwiseSequenceAlignment.oh

Class Hierarchy

    NSObject
      |
      +---MTPairwiseSequenceAlignment

Last modified:

06-Jun-2006 (../libmoltalk/MTPairwiseSequenceAlignment.m)

Instance Variables

private MTChain *chain1

private MTChain *chain2

private NSMutableArray *positions

private BOOL computed

private int f_gop, f_gep

private Class substitutionMatrix

Method Index

• commonly used methods
  

  -(NSString*)description

• readonly access
  

  -(NSArray*)alignmentPositions

  -(MTChain*)chain1

  -(MTChain*)chain2

  -(int)gep

  -(MTSelection*)getSelection1

  -(MTSelection*)getSelection2

  -(NSString*)getSequence1

  -(NSString*)getSequence2

  -(int)gop

• operations
  

  -(void)computeGlobalAlignment

  -(void)computeLocalAlignment

  -(int)countIdenticalPairs

  -(int)countPairs

  -(int)countUngappedPairs

  -(void)setGep:(int)p_gep

  -(void)setGop:(int)p_gop

  -(void)setSubstitutionMatrix: (Class)p_substm

• input/output -(void)fromStreamAsFASTA:(Stream*)stream;
  

  -(id)writeFastaToStream: (MTStream*)str

• creation
  

  +(MTPairwiseSequenceAlignment*)alignmentBetweenChain:(MTChain*)chain1 andChain:(MTChain*)chain2

Methods

+(MTPairwiseSequenceAlignment*)alignmentBetweenChain:(MTChain*)p_chain1 andChain:(MTChain*)p_chain2

creation

-(NSArray*)alignmentPositions

-(MTChain*)chain1

readonly access

-(MTChain*)chain2

-(void)computeGlobalAlignment

compute the global (Needleman-Wunsch) alignment between the two class MTChain, derive the structural alignment based on the pairwise assignment

-(void)computeLocalAlignment

compute the local (Smith-Waterman) alignment between the two class MTChain, derive the structural alignment based on the pairwise assignment

-(int)countIdenticalPairs

-(int)countPairs

-(int)countUngappedPairs

-(NSString*)description

-(int)gep

-(MTSelection*)getSelection1

-(MTSelection*)getSelection2

-(NSString*)getSequence1

-(NSString*)getSequence2

-(int)gop

-(void)setGep:(int)p_gep

-(void)setGop:(int)p_gop

-(void)setSubstitutionMatrix: (Class)p_substm

operations

-(id)writeFastaToStream: (MTStream*)str

input/output -(void)fromStreamAsFASTA:(Stream*)stream;