org.nmdp.ngs.align.PairwiseAlignment Maven / Gradle / Ivy
/*
ngs-align Sequence alignment.
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.align;
import java.util.List;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.alignment.AlignmentPair;
/**
* Pairwise DNA sequence alignment.
*/
public interface PairwiseAlignment {
/** Default local alignment gap penalties, match -1 replace 3 insert 2 delete 2 extend 1. */
final GapPenalties DEFAULT_LOCAL_GAP_PENALTIES = GapPenalties.create(-1, 3, 2, 2, 1);
/** Default global alignment gap penalties, match 0 replace 2 insert 4 delete 4 extend 6. */
final GapPenalties DEFAULT_GLOBAL_GAP_PENALTIES = GapPenalties.create(0, 2, 4, 4, 6);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties.
*
* @see #DEFAULT_LOCAL_GAP_PENALTIES
* @param query query DNA sequence, must not be null
* @param subject subject DNA sequence, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(Sequence query, Sequence subject);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param query query DNA sequence, must not be null
* @param subject subject DNA sequence, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(Sequence query, Sequence subject, GapPenalties gapPenalties);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties.
*
* @see #DEFAULT_LOCAL_GAP_PENALTIES
* @param query query DNA sequence, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(Sequence query, List subjects);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param query query DNA sequence, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(Sequence query, List subjects, GapPenalties gapPenalties);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties.
*
* @see #DEFAULT_LOCAL_GAP_PENALTIES
* @param queries list of query DNA sequences, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(List queries, List subjects);
/**
* Return the alignment pairs from local alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param queries list of query DNA sequences, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from local alignment of the query and subject DNA sequences
* with the default local alignment gap penalties
*/
Iterable local(List queries, List subjects, GapPenalties gapPenalties);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties.
*
* @see #DEFAULT_LOCAL_GAP_PENALTIES
* @param query query DNA sequence, must not be null
* @param subject subject DNA sequence, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(Sequence query, Sequence subject);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param query query DNA sequence, must not be null
* @param subject subject DNA sequence, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(Sequence query, Sequence subject, GapPenalties gapPenalties);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties.
*
* @see #DEFAULT_GLOBAL_GAP_PENALTIES
* @param query query DNA sequence, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(Sequence query, List subjects);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param query query DNA sequence, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(Sequence query, List subjects, GapPenalties gapPenalties);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties.
*
* @see #DEFAULT_GLOBAL_GAP_PENALTIES
* @param queries list of query DNA sequences, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(List queries, List subjects);
/**
* Return the alignment pairs from global alignment of the query and subject DNA sequences
* with the specified gap penalties.
*
* @param queries list of query DNA sequences, must not be null
* @param subjects list of subject DNA sequences, must not be null
* @param gapPenalties gap penalties, must not be null
* @return zero or more alignment pairs from global alignment of the query and subject DNA sequences
* with the default global alignment gap penalties
*/
Iterable global(List queries, List subjects, GapPenalties gapPenalties);
}
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