com.compomics.util.experiment.identification.protein_inference.proteintree

Class Node

java.lang.Object

com.compomics.util.experiment.identification.protein_inference.proteintree.Node

All Implemented Interfaces:

Serializable

public class Node
extends Object
implements Serializable

A node of the protein tree.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	proteinBatchSize The number of proteins which should be imported at a time.

Constructor Summary

Constructors

Constructor and Description
Node(int depth) Constructor.
Node(int depth, HashMap<String,ArrayList<Integer>> accessions) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addAccession(String accession, ArrayList<Integer> indexes) Adds an accession to the node.
void	clearAccessions() Clears the accessions of this node.
HashMap<String,ArrayList<Integer>>	getAccessions() Returns the accessions attribute.
HashMap<String,ArrayList<Integer>>	getAllMappings() Returns all the protein mapping of the node.
int	getDepth() Returns the depth of the node in the tree.
HashMap<String,HashMap<String,ArrayList<Integer>>>	getProteinMapping(AminoAcidPattern query, String currentSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance, boolean limitXs) Returns the protein mappings for the given peptide sequence.
long	getSize() Returns the size of the node in accession*tag.
Node	getSubNode(String sequence) Returns the subnode associated to an amino acid sequence.
HashMap<Character,Node>	getSubtree() Returns the subtree.
HashMap<String,ArrayList<Integer>>	getTermini() Returns the terminal mappings (they are not in the subtree).
boolean	isEmpty() Indicates whether the node is empty.
boolean	splitNode(int maxNodeSize, int maxDepth) Splits the node into subnode if its size is larger than the maxNodeSize and does the same for every sub node.

Methods inherited from class java.lang.Object

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

Field Detail

proteinBatchSize

public static final int proteinBatchSize

The number of proteins which should be imported at a time.

See Also:

Constant Field Values

Constructor Detail

Node

public Node(int depth)

Constructor.

Parameters:

depth - the depth of the node

Node

public Node(int depth,
    HashMap<String,ArrayList<Integer>> accessions)

Constructor.

Parameters:

depth - the depth of the node

accessions - the accessions of the node

Method Detail

getProteinMapping

public HashMap<String,HashMap<String,ArrayList<Integer>>> getProteinMapping(AminoAcidPattern query,
                                                                   String currentSequence,
                                                                   AminoAcidPattern.MatchingType matchingType,
                                                                   Double massTolerance,
                                                                   boolean limitXs)
                                                                     throws IOException,
                                                                            InterruptedException,
                                                                            ClassNotFoundException

Returns the protein mappings for the given peptide sequence. peptide sequence -> protein accession -> index in the protein. An empty map if not found.

Parameters:

query - the given amino acid pattern to query the tree

currentSequence - the sequence found until now

matchingType - the matching type

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

limitXs - if true the share of Xs in the peptide sequences will be limited in order to increase sequencing speed.

Returns:

the protein mapping for the given peptide sequence

Throws:

IOException

InterruptedException

ClassNotFoundException

splitNode

public boolean splitNode(int maxNodeSize,
                int maxDepth)
                  throws IOException,
                         IllegalArgumentException,
                         InterruptedException,
                         ClassNotFoundException

Splits the node into subnode if its size is larger than the maxNodeSize and does the same for every sub node.

Parameters:

maxNodeSize - the maximal node size allowed when splitting

maxDepth - the maximum depth

Returns:

returns true if the node was actually splitted and thus needs to be saved in indexed mode

Throws:

IOException

IllegalArgumentException

InterruptedException

ClassNotFoundException

addAccession

public void addAccession(String accession,
                ArrayList<Integer> indexes)

Adds an accession to the node.

Parameters:

accession - the accession to add

indexes - the indexes in this accession where the key can be found. Any prior entry will be silently overwritten

getSize

public long getSize()

Returns the size of the node in accession*tag.

Returns:

the size of the node

getAccessions

public HashMap<String,ArrayList<Integer>> getAccessions()

Returns the accessions attribute.

Returns:

the accessions attribute

getTermini

public HashMap<String,ArrayList<Integer>> getTermini()

Returns the terminal mappings (they are not in the subtree).

Returns:

the terminal mappings

getSubtree

public HashMap<Character,Node> getSubtree()

Returns the subtree. Null if end of the tree.

Returns:

the subtree

clearAccessions

public void clearAccessions()

Clears the accessions of this node.

isEmpty

public boolean isEmpty()

Indicates whether the node is empty.

Returns:

whether the node is empty

getDepth

public int getDepth()

Returns the depth of the node in the tree.

Returns:

the depth of the node in the tree

getAllMappings

public HashMap<String,ArrayList<Integer>> getAllMappings()
                                                  throws IOException

Returns all the protein mapping of the node.

Returns:

all the protein mappings of the node

Throws:

IOException

getSubNode

public Node getSubNode(String sequence)

Returns the subnode associated to an amino acid sequence.

Parameters:

sequence - the amino acid sequence

Returns:

the corresponding subnode