textbender.d.transfer
Interface MutantAbstractor

All Known Implementing Classes:

RecombinantXHTML

public interface MutantAbstractor

.

Method Summary

Object

abstract_transferMutant(Element embeddableAbstractSequence, StringBuilder b) Returns an abstract form of a gene's sequence, suitable for detecting mutations to record in ancestry.

Method Detail

abstract_transferMutant

Object abstract_transferMutant(Element embeddableAbstractSequence,
                               StringBuilder b)

Returns an abstract form of a gene's sequence, suitable for detecting mutations to record in ancestry. Use this method to compare sequences of the same gene between two generations; a difference signals a mutation significant enough to record in the gene's formal transfer ancestry.

     Object a1 = abstract_transferMutant( decodedFromArchiveF1 );
     Object a2 = abstract_transferMutant( abstract_embeddable( geneF2 ));
     boolean isMutationF2 = !a2.equals( a1 );
     

Here the input F1 sequence was decoded from an ancestry archive in embeddable form; and the input F2 sequence is in a compatible abstract form (embeddable).

Parameters:

embeddableAbstractSequence - embeddable-abstract form of the gene's sequence

b - string builder to use, overwriting its existing content

Returns:

abstract form of the sequence