package textbender.d.transfer; // Copyright 2007, Michael Allan.  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Textbender Software"), to deal in the Textbender Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicence, and/or sell copies of the Textbender Software, and to permit persons to whom the Textbender Software is furnished to do so, subject to the following conditions: The preceding copyright notice and this permission notice shall be included in all copies or substantial portions of the Textbender Software. THE TEXTBENDER SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE TEXTBENDER SOFTWARE OR THE USE OR OTHER DEALINGS IN THE TEXTBENDER SOFTWARE.

import java.util.*;
import org.w3c.dom.*;


/** .
  */
public interface MutantAbstractor
{


   // - M u t a n t - A b s t r a c t o r ------------------------------------------------


    /** 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.
      * <pre>
      *     Object a1 = abstract_transferMutant( decodedFromArchiveF1 );
      *     Object a2 = abstract_transferMutant( {@linkplain textbender.d.gene.Gene#abstract_embeddable(Element,List) abstract_embeddable}( geneF2 ));
      *     boolean isMutationF2 = !a2.equals( a1 );
      *     </pre>
      * <p>
      *     Here the input F1 sequence was decoded from an ancestry archive in
      *     <a href='http://reluk.ca/project/textbender/d/gene/note.xht#Embeddable-Sequence-Form'
      *                                                                 >embeddable form</a>;
      *     and the input F2 sequence is in a compatible abstract form (embeddable).
      *     </p>
      *
      *     @param embeddableAbstractSequence
      *         {@linkplain textbender.d.gene.Gene#abstract_embeddable(Element,List) embeddable-abstract form}
      *         of the gene's sequence
      *     @param b string builder to use, overwriting its existing content
      *
      *     @return abstract form of the sequence
      */
    public Object abstract_transferMutant(
        final Element embeddableAbstractSequence, final StringBuilder b );



}