com.milaboratory.core.tree

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

java.lang.Object

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

Type Parameters:

S - - key type (must be a sequence)

O - - value type

All Implemented Interfaces:

Serializable

public class SequenceTreeMap<S extends Sequence<S>,O>
extends Object
implements Serializable

Sequence tree map, with fast neighbours search.

Types of mutations:
0 = mismatch,
1 = deletion (excess nucleotide in the reference sequence relative to the target key),
2 = insertion (missing nucleotide in the reference sequence relative to the target key)

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SequenceTreeMap.Node<O>
class	SequenceTreeMap.NodeIterator
class	SequenceTreeMap.NodeOp
class	SequenceTreeMap.ValuesOp

Field Summary

Fields

Modifier and Type	Field and Description
Alphabet<S>	alphabet
SequenceTreeMap.Node<O>	root

Constructor Summary

Constructors

Constructor and Description
SequenceTreeMap(Alphabet<S> alphabet) Creates a tree map for specified Alphabet.

Method Summary

Methods

Modifier and Type	Method and Description
O	createIfAbsent(S sequence, Factory<O> factory)
O	get(S sequence)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, double maxPenalty, double[] penalties, int[] maxErrors, MutationGuide<S> guide)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, int mismatches, int deletions, int insertions)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, int mismatches, int deletions, int insertions, int totalErrors)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, int mismatches, int deletions, int insertions, int totalErrors, MutationGuide<S> guide)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, TreeSearchParameters parameters)
NeighborhoodIterator<S,O>	getNeighborhoodIterator(S reference, TreeSearchParameters parameters, MutationGuide<S> guide)
SequenceTreeMap.Node<O>	getNode(S sequence)
SequenceTreeMap.NodeIterator	nodeIterator()
Iterable<SequenceTreeMap.Node<O>>	nodes()
SequenceTreeMap.NodeOp	nodesOp()
O	put(S sequence, O object)
O	remove(S sequence)
Map<S,O>	toMap()
Iterable<O>	values()
SequenceTreeMap.ValuesOp	valuesOp()

Methods inherited from class java.lang.Object

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

Field Detail

alphabet

public final Alphabet<S extends Sequence<S>> alphabet

root

public final SequenceTreeMap.Node<O> root

Constructor Detail

SequenceTreeMap

public SequenceTreeMap(Alphabet<S> alphabet)

Creates a tree map for specified Alphabet.

Parameters:

alphabet - alphabet

Method Detail

createIfAbsent

public O createIfAbsent(S sequence,
               Factory<O> factory)

put

public O put(S sequence,
    O object)

getNode

public SequenceTreeMap.Node<O> getNode(S sequence)

get

public O get(S sequence)

remove

public O remove(S sequence)

toMap

public Map<S,O> toMap()

nodesOp

public SequenceTreeMap.NodeOp nodesOp()

valuesOp

public SequenceTreeMap.ValuesOp valuesOp()

nodeIterator

public SequenceTreeMap.NodeIterator nodeIterator()

values

public Iterable<O> values()

nodes

public Iterable<SequenceTreeMap.Node<O>> nodes()

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                int mismatches,
                                                int deletions,
                                                int insertions,
                                                int totalErrors)

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                int mismatches,
                                                int deletions,
                                                int insertions,
                                                int totalErrors,
                                                MutationGuide<S> guide)

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                int mismatches,
                                                int deletions,
                                                int insertions)

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                double maxPenalty,
                                                double[] penalties,
                                                int[] maxErrors,
                                                MutationGuide<S> guide)

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                TreeSearchParameters parameters)

getNeighborhoodIterator

public NeighborhoodIterator<S,O> getNeighborhoodIterator(S reference,
                                                TreeSearchParameters parameters,
                                                MutationGuide<S> guide)