org.biojava3.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

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile
Profile.StringFormat
 
Method Summary
 C getCompoundInQueryAt(int alignmentIndex)
          Returns the Compound in query sequence at given column index in alignment.
 C getCompoundInTargetAt(int alignmentIndex)
          Returns the Compound in target sequence at given column index in alignment.
 int getIndexInQueryAt(int alignmentIndex)
          Returns the query index corresponding to a given alignment column.
 int getIndexInQueryForTargetAt(int targetIndex)
          Returns the query index corresponding to a given target index.
 int getIndexInTargetAt(int alignmentIndex)
          Returns the target index corresponding to a given alignment column.
 int getIndexInTargetForQueryAt(int queryIndex)
          Returns the target index corresponding to a given query index.
 int getNumIdenticals()
          Returns the number of indices for which both the query and target sequences have an identical Compound.
 int getNumSimilars()
          Returns the number of indices for which both the query and target sequences have a similar Compound.
 AlignedSequence<S,C> getQuery()
          Returns the first AlignedSequence of the pair.
 AlignedSequence<S,C> getTarget()
          Returns the second AlignedSequence of the pair.
 
Methods inherited from interface org.biojava3.alignment.template.Profile
getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, toString, toString, toString
 
Methods inherited from interface java.lang.Iterable
iterator
 

Method Detail

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