org.biojava3.alignment
Class SimpleProfilePair<S extends Sequence<C>,C extends Compound>

java.lang.Object
  extended by org.biojava3.alignment.SimpleProfile<S,C>
      extended by org.biojava3.alignment.SimpleProfilePair<S,C>
Type Parameters:
S - each element of an alignment Profile is of type S
C - each element of an AlignedSequence is a Compound of type C
All Implemented Interfaces:
Iterable<AlignedSequence<S,C>>, Profile<S,C>, ProfilePair<S,C>

public class SimpleProfilePair<S extends Sequence<C>,C extends Compound>
extends SimpleProfile<S,C>
implements ProfilePair<S,C>

Implements a data structure for the results of the alignment of a pair of Profiles.

Author:
Mark Chapman

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile
Profile.StringFormat
 
Field Summary
 
Fields inherited from class org.biojava3.alignment.SimpleProfile
matrix
 
Constructor Summary
SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
          Creates a pair profile for the given profiles.
 
Method Summary
 Profile<S,C> getQuery()
          Returns the first Profile of the pair.
 Profile<S,C> getTarget()
          Returns the second Profile of the pair.
 
Methods inherited from class org.biojava3.alignment.SimpleProfile
getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, iterator, toString, toString, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
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
 

Constructor Detail

SimpleProfilePair

public SimpleProfilePair(Profile<S,C> query,
                         Profile<S,C> target,
                         List<AlignedSequence.Step> sx,
                         List<AlignedSequence.Step> sy)
Creates a pair profile for the given profiles.

Parameters:
query - the first profile of the pair
target - the second profile of the pair
sx - lists whether the query profile aligns a Compound or gap at each index of the alignment
sy - lists whether the target profile aligns a Compound or gap at each index of the alignment
Throws:
IllegalArgumentException - if alignments differ in size or given profiles do not fit in alignments
Method Detail

getQuery

public Profile<S,C> getQuery()
Description copied from interface: ProfilePair
Returns the first Profile of the pair.

Specified by:
getQuery in interface ProfilePair<S extends Sequence<C>,C extends Compound>
Returns:
the first Profile of the pair

getTarget

public Profile<S,C> getTarget()
Description copied from interface: ProfilePair
Returns the second Profile of the pair.

Specified by:
getTarget in interface ProfilePair<S extends Sequence<C>,C extends Compound>
Returns:
the second Profile of the pair