Package org.biojava.nbio.core.alignment.template

Interface SequencePair<S extends Sequence<C>,C extends Compound>

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 Superinterfaces:
Iterable<AlignedSequence<S,C>>, Profile<S,C>
All Known Subinterfaces:
MutableSequencePair<S,C>
All Known Implementing Classes:
SimpleSequencePair
public interface SequencePair<S extends Sequence<C>,C extends Compound> extends Profile<S,C>
Defines a data structure for the results of pairwise sequence alignment.
Author:
Mark Chapman, Paolo Pavan

  • Method Details

    • getCompoundInQueryAt

      C getCompoundInQueryAt(int alignmentIndex)
      Returns the Compound in query sequence at given column index in alignment.
      Parameters:
      alignmentIndex - column index in alignment
      Returns:
      the query sequence element
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

    • getCompoundInTargetAt

      C getCompoundInTargetAt(int alignmentIndex)
      Returns the Compound in target sequence at given column index in alignment.
      Parameters:
      alignmentIndex - column index in alignment
      Returns:
      the target sequence element
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

    • getIndexInQueryAt

      int getIndexInQueryAt(int alignmentIndex)
      Returns the query index corresponding to a given alignment column.
      Parameters:
      alignmentIndex - column index in alignment
      Returns:
      index in query Sequence
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

    • getIndexInQueryForTargetAt

      int getIndexInQueryForTargetAt(int targetIndex)
      Returns the query index corresponding to a given target index.
      Parameters:
      targetIndex - index in target Sequence
      Returns:
      index in query Sequence
      Throws:
      IndexOutOfBoundsException - if targetIndex < 1 or targetIndex > getTarget().getLength()

    • getIndexInTargetAt

      int getIndexInTargetAt(int alignmentIndex)
      Returns the target index corresponding to a given alignment column.
      Parameters:
      alignmentIndex - column index in alignment
      Returns:
      index in target Sequence
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Profile.getLength()

    • getIndexInTargetForQueryAt

      int getIndexInTargetForQueryAt(int queryIndex)
      Returns the target index corresponding to a given query index.
      Parameters:
      queryIndex - index in query Sequence
      Returns:
      index in target Sequence
      Throws:
      IndexOutOfBoundsException - if queryIndex < 1 or queryIndex > getQuery().getLength()

    • getNumIdenticals

      int getNumIdenticals()
      Returns the number of indices for which both the query and target sequences have an identical Compound.
      Returns:
      the number of identical indices

    • getPercentageOfIdentity

      double getPercentageOfIdentity(boolean countGaps)
      Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
      Parameters:
      countGaps - If true, gap positions are counted as mismatches, i.e., the percentage is normalized by the alignment length. If false, gap positions are not counted, i.e. the percentage is normalized by the number of aligned residue pairs. See May (2004). "Percent sequence identity: the need to be explicit."
      Returns:
      the percentage of sequence identity as a fraction in [0,1]

    • getNumSimilars

      int getNumSimilars()
      Returns the number of indices for which both the query and target sequences have a similar Compound.
      Returns:
      the number of similar indices

    • getQuery

      AlignedSequence<S,C> getQuery()
      Returns the first AlignedSequence of the pair.
      Returns:
      the first AlignedSequence of the pair

    • getTarget

      AlignedSequence<S,C> getTarget()
      Returns the second AlignedSequence of the pair.
      Returns:
      the second AlignedSequence of the pair