Package org.biojava.nbio.core.alignment

Class SimpleSequencePair<S extends Sequence<C>,C extends Compound>

java.lang.Object
org.biojava.nbio.core.alignment.SimpleProfile<S,C>
org.biojava.nbio.core.alignment.SimpleSequencePair<S,C>
Type Parameters:
S - each element of the alignment Profile is of type S
C - each element of an AlignedSequence is a Compound of type C
All Implemented Interfaces:
Serializable, Iterable<AlignedSequence<S,C>>, Profile<S,C>, SequencePair<S,C>
public class SimpleSequencePair<S extends Sequence<C>,C extends Compound> extends SimpleProfile<S,C> implements SequencePair<S,C>
Implements a data structure for the results of pairwise sequence alignment.
Author:
Mark Chapman, Paolo Pavan
See Also:

  • Constructor Details

    • SimpleSequencePair

      public SimpleSequencePair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)
      Creates a pair profile for the given already aligned sequences.
      Parameters:
      query - the first sequence of the pair
      target - the second sequence of the pair
      Throws:
      IllegalArgumentException - if sequences differ in size

    • SimpleSequencePair

      public SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
      Creates a pair profile for the given sequences with a global alignment.
      Parameters:
      query - the first sequence of the pair
      target - the second sequence of the pair
      sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment
      sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment
      Throws:
      IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments

    • SimpleSequencePair

      public SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)
      Creates a pair profile for the given sequences with a local alignment.
      Parameters:
      query - the first sequence of the pair
      target - the second sequence of the pair
      sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment
      xb - number of Compounds skipped in the query sequence before the aligned region
      xa - number of Compounds skipped in the query sequence after the aligned region
      sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment
      yb - number of Compounds skipped in the target sequence before the aligned region
      ya - number of Compounds skipped in the target sequence after the aligned region
      Throws:
      IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments

  • Method Details