org.broadinstitute.hellbender.tools.spark.pathseq

Class PSTree

java.lang.Object

org.broadinstitute.hellbender.tools.spark.pathseq.PSTree

public class PSTree
extends java.lang.Object

Represents a taxonomic tree with nodes assigned a name and taxonomic rank (e.g. order, family, genus, species, etc.) Nodes are stored in a HashMap and keyed by a String id. Tree keeps track of each node's children as well as its parent for efficient traversals top-down and bottom-up.

Designed to be constructed on-the-fly while parsing the NCBI taxonomy dump, which specifies each node and its parent. As a result, invalid trees may be constructed (e.g. multiple roots or cycles). Use checkStructure() to confirm its validity.

Note the tree root is initialized in the constructor and cannot be modified (except adding children with addNode()).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PSTree.Serializer

Field Summary

Fields

Modifier and Type	Field and Description
static int	NULL_NODE

Constructor Summary

Constructors

Modifier	Constructor and Description
	PSTree(int rootId)
protected	PSTree(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input input)

Method Summary

Modifier and Type	Method and Description
void	addNode(int id, java.lang.String name, int parent, long length, java.lang.String rank) Adds a node to the tree.
void	checkStructure() Because of the piecemeal way we allow the tree to be constructed, we can end up with invalid tree structures.
boolean	equals(java.lang.Object o)
java.util.Collection<java.lang.Integer>	getChildrenOf(int id)
int	getLCA(java.util.Collection<java.lang.Integer> nodes) Get lowest common ancester of the set of given nodes.
long	getLengthOf(int id)
java.lang.String	getNameOf(int id)
java.util.Set<java.lang.Integer>	getNodeIDs()
int	getParentOf(int id)
java.util.List<java.lang.Integer>	getPathOf(int id) Returns path of node id's from the input id to the root.
java.lang.String	getRankOf(int id)
int	hashCode()
boolean	hasNode(int id)
java.util.Set<java.lang.Integer>	removeUnreachableNodes() Deletes nodes unreachable from the root and returns the set of deleted nodes.
void	retainNodes(java.util.Set<java.lang.Integer> idsToKeep) Removes all nodes not in the given set
protected void	serialize(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
void	setLengthOf(int id, long length)
void	setNameOf(int id, java.lang.String name)
void	setRankOf(int id, java.lang.String rank)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

NULL_NODE

public static final int NULL_NODE

See Also:

Constant Field Values

Constructor Detail

PSTree

public PSTree(int rootId)

PSTree

protected PSTree(com.esotericsoftware.kryo.Kryo kryo,
                 com.esotericsoftware.kryo.io.Input input)

Method Detail

serialize

protected void serialize(com.esotericsoftware.kryo.Kryo kryo,
                         com.esotericsoftware.kryo.io.Output output)

addNode

public void addNode(int id,
                    java.lang.String name,
                    int parent,
                    long length,
                    java.lang.String rank)

Adds a node to the tree. ID must be unique, and all arguments must be non-null. If the node exists, its properties are modified

removeUnreachableNodes

public java.util.Set<java.lang.Integer> removeUnreachableNodes()

Deletes nodes unreachable from the root and returns the set of deleted nodes.

checkStructure

public void checkStructure()

Because of the piecemeal way we allow the tree to be constructed, we can end up with invalid tree structures. Check that tree structure contains valid pointers and is connected.

getLCA

public int getLCA(java.util.Collection<java.lang.Integer> nodes)

Get lowest common ancester of the set of given nodes. Takes the intersection of node-to-root paths of all the nodes and finding the lowest one in the tree.

getChildrenOf

public java.util.Collection<java.lang.Integer> getChildrenOf(int id)

getNodeIDs

public java.util.Set<java.lang.Integer> getNodeIDs()

getNameOf

public java.lang.String getNameOf(int id)

getParentOf

public int getParentOf(int id)

getLengthOf

public long getLengthOf(int id)

getRankOf

public java.lang.String getRankOf(int id)

hasNode

public boolean hasNode(int id)

retainNodes

public void retainNodes(java.util.Set<java.lang.Integer> idsToKeep)

Removes all nodes not in the given set

setNameOf

public void setNameOf(int id,
                      java.lang.String name)

setRankOf

public void setRankOf(int id,
                      java.lang.String rank)

setLengthOf

public void setLengthOf(int id,
                        long length)

getPathOf

public java.util.List<java.lang.Integer> getPathOf(int id)

Returns path of node id's from the input id to the root.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object