Keilwagen: Created page with "'''Create a discrete alphabet:''' String[] symbols = {"A", "C", "G", "T", "-"}; DiscreteAlphabet abc = new DiscreteAlphabet( true, symbols ); '''..."

2011-06-06T07:50:39Z

Created page with "'''Create a discrete alphabet:''' <source lang="java5"> String[] symbols = {"A", "C", "G", "T", "-"}; DiscreteAlphabet abc = new DiscreteAlphabet( true, symbols ); </source> '''..."

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'''Create a discrete alphabet:'''
<source lang="java5">
String[] symbols = {"A", "C", "G", "T", "-"};
DiscreteAlphabet abc = new DiscreteAlphabet( true, symbols );
</source>

'''Create a discrete alphabet that allows to build the reverse complement of a sequence:'''
<source lang="java5">
int[] revComp = new int[symbols.length];
revComp[0] = 3; //symbols[0]^rc = symbols[3]
revComp[1] = 2; //symbols[1]^rc = symbols[2]
revComp[2] = 1; //symbols[2]^rc = symbols[1]
revComp[3] = 0; //symbols[3]^rc = symbols[0]
revComp[4] = 4; //symbols[4]^rc = symbols[4]

GenericComplementableDiscreteAlphabet abc2 = new GenericComplementableDiscreteAlphabet( true, symbols, revComp );
</source>

'''Test alphabet:'''
<source lang="java5">
Sequence seq = Sequence.create( new AlphabetContainer( abc2 ), "ACGT-" );
Sequence rc = seq.reverseComplement();
System.out.println( seq );
System.out.println( rc );
</source>

Create a discrete alphabet - Revision history

Keilwagen: Created page with "'''Create a discrete alphabet:''' String[] symbols = {"A", "C", "G", "T", "-"}; DiscreteAlphabet abc = new DiscreteAlphabet( true, symbols ); '''..."