/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.seq.homol; import org.biojava.bio.seq.FeatureHolder; import org.biojava.bio.symbol.Alignment; import org.biojava.utils.ChangeType; /** *
* Signifies that two or more features are homologous. *
* *Blast hits or local multiple-sequence alignments can be * represented as a set of features on sequences that have an * alignment. The features will probably implement * HomologyFeature. *
* * @author Matthew Pocock * @author Keith James * @since 1.2 */ public interface Homology { /** * Signals that the alignment describing the homologous sequences * has changed. For implementations which implement *Changeable
.
*/
public static final ChangeType ALIGNMENT =
new ChangeType("The alignment has been changed",
"org.biojava.bio.seq.homol.Homology",
"ALIGNMENT");
/**
* Retrieve the set of features that mark homologous regions.
*
* @return the FeatureHolder containing each homologous region
*/
FeatureHolder getFeatures();
/**
* Retrieve the Alignment that specifies how the homologous regions are
* aligned. The labels of the alignment are the HomologyFeature objects.
*
* @return the Alignment between the HomologyFeatures
*/
Alignment getAlignment();
}