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

    • 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