com.milaboratory.core.tree

Class NeighborhoodIterator<S extends Sequence<S>,O>

java.lang.Object

com.milaboratory.core.tree.NeighborhoodIterator<S,O>

public final class NeighborhoodIterator<S extends Sequence<S>,O>
extends Object

Created by dbolotin on 25/06/14.

Constructor Summary

Constructors

Constructor and Description
NeighborhoodIterator(S reference, TreeSearchParameters parameters, MutationGuide guide, SequenceTreeMap.Node<O> root) Constrictor for root NeighborhoodIterator iterator.

Method Summary

Methods

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NeighborhoodIterator

public NeighborhoodIterator(S reference,
                    TreeSearchParameters parameters,
                    MutationGuide guide,
                    SequenceTreeMap.Node<O> root)

Constrictor for root NeighborhoodIterator iterator.

Parameters:

reference - reference sequence

root - root node of the tree

Method Detail

next

public O next()

nextNode

public SequenceTreeMap.Node<O> nextNode()

traverseToTheEnd

public SequenceTreeMap.Node<O> traverseToTheEnd(SequenceTreeMap.Node<O> node,
                                       int position)

getCurrentBranchingSequence

public byte[] getCurrentBranchingSequence()

getMutationsCount

public int getMutationsCount()

getType

public byte getType(int i)

getCurrentMutations

public Mutations<S> getCurrentMutations()

getCurrentAlignment

public Alignment<S> getCurrentAlignment()

getCurrentAlignment

public Alignment<S> getCurrentAlignment(LinearGapAlignmentScoring<S> scoring)

getPosition

public int getPosition(int i)

getCode

public byte getCode(int i)

getMismatches

public int getMismatches()

getDeletions

public int getDeletions()

getInsertions

public int getInsertions()

getIntroducedDifferences

public int[] getIntroducedDifferences()

getPenalty

public double getPenalty()

it

public Iterable<O> it()

toList

public List<O> toList()