| Constructor and Description |
|---|
NeighborhoodIterator(S reference,
TreeSearchParameters parameters,
MutationGuide guide,
SequenceTreeMap.Node<O> root)
Constrictor for root NeighborhoodIterator iterator.
|
| Modifier and Type | Method and Description |
|---|---|
byte |
getCode(int i) |
Alignment<S> |
getCurrentAlignment() |
Alignment<S> |
getCurrentAlignment(LinearGapAlignmentScoring<S> scoring) |
byte[] |
getCurrentBranchingSequence() |
Mutations<S> |
getCurrentMutations() |
int |
getDeletions() |
int |
getInsertions() |
int[] |
getIntroducedDifferences() |
int |
getMismatches() |
int |
getMutationsCount() |
double |
getPenalty() |
int |
getPosition(int i) |
byte |
getType(int i) |
Iterable<O> |
it() |
O |
next() |
SequenceTreeMap.Node<O> |
nextNode() |
List<O> |
toList() |
SequenceTreeMap.Node<O> |
traverseToTheEnd(SequenceTreeMap.Node<O> node,
int position) |
public NeighborhoodIterator(S reference, TreeSearchParameters parameters, MutationGuide guide, SequenceTreeMap.Node<O> root)
reference - reference sequenceroot - root node of the treepublic O next()
public SequenceTreeMap.Node<O> nextNode()
public SequenceTreeMap.Node<O> traverseToTheEnd(SequenceTreeMap.Node<O> node, int position)
public byte[] getCurrentBranchingSequence()
public int getMutationsCount()
public byte getType(int i)
public Alignment<S> getCurrentAlignment(LinearGapAlignmentScoring<S> scoring)
public int getPosition(int i)
public byte getCode(int i)
public int getMismatches()
public int getDeletions()
public int getInsertions()
public int[] getIntroducedDifferences()
public double getPenalty()
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