org.biojava3.alignment
Class SimpleProfilePair<S extends Sequence<C>,C extends Compound>
java.lang.Object
org.biojava3.alignment.SimpleProfile<S,C>
org.biojava3.alignment.SimpleProfilePair<S,C>
- Type Parameters:
S
- each element of an alignment Profile
is of type SC
- 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 Profile
s.
- Author:
- Mark Chapman
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 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 |
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 pairtarget
- the second profile of the pairsx
- lists whether the query profile aligns a Compound
or gap at each index of the alignmentsy
- 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
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