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S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic interface SequencePair<S extends Sequence<C>,C extends Compound>
Defines a data structure for the results of pairwise sequence alignment.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile |
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Profile.StringFormat |
Method Summary | |
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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 |
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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 |
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iterator |
Method Detail |
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C getCompoundInQueryAt(int alignmentIndex)
Compound
in query sequence at given column index in alignment.
alignmentIndex
- column index in alignment
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
C getCompoundInTargetAt(int alignmentIndex)
Compound
in target sequence at given column index in alignment.
alignmentIndex
- column index in alignment
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
int getIndexInQueryAt(int alignmentIndex)
alignmentIndex
- column index in alignment
Sequence
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
int getIndexInQueryForTargetAt(int targetIndex)
targetIndex
- index in target Sequence
Sequence
IndexOutOfBoundsException
- if targetIndex < 1 or targetIndex > getTarget()
.getLength()int getIndexInTargetAt(int alignmentIndex)
alignmentIndex
- column index in alignment
Sequence
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Profile.getLength()
int getIndexInTargetForQueryAt(int queryIndex)
queryIndex
- index in query Sequence
Sequence
IndexOutOfBoundsException
- if queryIndex < 1 or queryIndex > getQuery()
.getLength()int getNumIdenticals()
Compound
.
int getNumSimilars()
Compound
.
AlignedSequence<S,C> getQuery()
AlignedSequence
of the pair.
AlignedSequence
of the pairAlignedSequence<S,C> getTarget()
AlignedSequence
of the pair.
AlignedSequence
of the pair
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