[Biococoa-dev] using alignment code

[Koen van der Drift]

Hi,

Being curious how the alignment works, I added the following code to 
one of the demos:

	// do some testing for the alignment code
	
	BCSequence	*first = [BCSequence 
sequenceWithString:@"CTATGTTGATTTGGAA"];
	BCSequence	*second = [BCSequence sequenceWithString:@"ATGGTGATTTTGAA"];
	
	BCSequenceAlignment	*alignArray = [BCSequenceAlignment 
needlemanWunschAlignmentWithSequences:
							[NSArray arrayWithObjects: first, second, nil] properties: nil];

	NSLog ( @"the first alignment sequence is %@", [alignArray 
sequenceAtIndex:2] );
	NSLog ( @"the second alignment sequence is %@", [alignArray 
sequenceAtIndex:1] );


The output is as follwos:

2005-03-30 17:01:20.529 Translation[24738] the first alignment sequence 
is
2005-03-30 17:01:20.530 Translation[24738] the second alignment 
sequence is ?ATGGTGATTTTGAA


First question, is this the correct approach?
Second question is, what do I use for the 'properties'?



cheers,

- Koen.