BCToolComplement *complementTool = [BCToolComplement 
           complementToolWithSequence: mySequence];

    BCSequence *complementSequence = [complementTool  
           sequenceComplement];

    BCToolComplement *complementTool = [BCToolComplement 
           complementToolWithSequence: mySequence];

    BCSequence *reverseComplementSequence = [complementTool 
           sequenceComplement];

    BCToolMassCalculator *mwCalculator = [BCToolMassCalculator
             massCalculatorWithSequence: mySequence];

@]

- (BCSequence *) reverseComplement
{
    BCToolComplement *complementTool = [BCToolComplement complementToolWithSequence: mySequence];

    [complementTool setReverse: YES];

    BCSequence *reverseComplementSequence = [complementTool sequenceComplement];
}

If the sequence that is passed to BCToolComplement is not a DNA or RNA sequence, the tool returns a copy of the input sequence. This prevents a complement operation being carried out on for instance a protein sequence.

To obtain some information about a sequence, BioCocoa provides a special class: BCSequenceTool. This class does nothing by itself, but has many subclasses, each for a particular task. For instance, to calculate the average molecular weight of a sequence, use the following code:

	BCToolMassCalculator *mwCalculator = [BCToolMassCalculator massCalculatorWithSequence: mySequence];

Because a sequence can have ambiguous symbols, this tool actually calculates an lower and upper MW limit, both of which are stored in the array the this class returns. Note that in this case 'average' means the MW is calculated using the average of the weight of each isotope in a atom. You can also calculate the MW using the monoisotopic wight of each atom.

Manipulating a sequence

    BCToolComplement *complementTool = [BCToolComplement complementToolWithSequence: mySequence];

    BCSequence *complementSequence = [complementTool sequenceComplement];

Obtaining information about a sequence

	BCToolMassCalculator *mwCalculator = [BCToolMassCalculator massCalculatorWithSequence: [self theDNA]];
	[mwCalculator setMassType: BCAverage];
	NSArray * mw = [mwCalculator calculateMass];

Because a sequence can have ambiguous symbols, this tool actually calculates an lower and upper MW limit, both of which are stored in the array the this class returns.

This page will contain a collection of short how-to's for BioCocoa.

SVN Tutorial - Accessing and using the BioCocoa SVN server

This page will contain a collection of short how-to's for BioCocoa.