be.svlandeg.diffany.study.osmotic.arabidopsis

Class KinaseData

java.lang.Object

be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData

public class KinaseData
extends Object

This class defines and analyses the data retrieved for Arabidopsis thaliana.

Author:

Sofie Van Landeghem

Field Summary

Fields

Modifier and Type	Field and Description
static int	hubPhos

Constructor Summary

Constructors

Constructor and Description
KinaseData(GenePrinter gp) Constructor: defines the gene printer that can deal with gene synonymy etc.

Method Summary

Modifier and Type	Method and Description
protected URI	getKinaseInteractions() Retrieve the URI of the kinase interaction data
protected URI	getKinases() Retrieve the URI of the kinase activity data
protected URI	getPhosphat() Retrieve the URI of the Phosphat data
Set<Edge>	readAllKinaseInteractions(boolean includeSelfInteractions) Construct a set of kinase-target edges, reading input from a specified URI.
Set<Edge>	readKinaseInteractionsByLocustags(Set<Node> source_incl, Set<Node> source_excl, Set<Node> target_incl, Set<Node> target_excl, boolean includeSelfInteractions) Construct a set of kinase interaction edges from a certain input set of nodes, and reading input from a specified URI.
Set<String>	readKinaseLocusTags() Read a list of (lower-case) locus tags with kinase activity.
Set<String>	readPhosphorylationLocusTags(boolean includePredicted) Read a list of (lower-case) locus tags with phosphorylation sites.

Methods inherited from class java.lang.Object

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

Field Detail

hubPhos

public static final int hubPhos

See Also:

Constant Field Values

Constructor Detail

KinaseData

public KinaseData(GenePrinter gp)

Constructor: defines the gene printer that can deal with gene synonymy etc.

Parameters:

gp - the gene printer object

Method Detail

getPhosphat

protected URI getPhosphat()

Retrieve the URI of the Phosphat data

Returns:

the URI of the Phosphat data, or null if the resource could not be located

getKinases

protected URI getKinases()

Retrieve the URI of the kinase activity data

Returns:

the URI of the kinase activity data, or null if the resource could not be located

getKinaseInteractions

protected URI getKinaseInteractions()

Retrieve the URI of the kinase interaction data

Returns:

the URI of the kinase interaction data, or null if the resource could not be located

readAllKinaseInteractions

public Set<Edge> readAllKinaseInteractions(boolean includeSelfInteractions)
                                    throws URISyntaxException,
                                           IOException

Construct a set of kinase-target edges, reading input from a specified URI. This method imposes asymmetry of the read edges.

Parameters:

includeSelfInteractions - whether or not to include self interactions

Returns:

the set of PPI edges read from the input file

Throws:

URISyntaxException - when the regulation datafile can not be read properly

IOException - when the regulation datafile can not be read properly

readKinaseInteractionsByLocustags

public Set<Edge> readKinaseInteractionsByLocustags(Set<Node> source_incl,
                                                   Set<Node> source_excl,
                                                   Set<Node> target_incl,
                                                   Set<Node> target_excl,
                                                   boolean includeSelfInteractions)
                                            throws URISyntaxException,
                                                   IOException

Construct a set of kinase interaction edges from a certain input set of nodes, and reading input from a specified URI. This method can either only include regulations between the nodes themselves, or also include neighbours, or put a cutoff on minimal number of neighbours to avoid including outliers in the networks.

Parameters:

source_incl - the source nodes (can be null, in which case any node will qualify, except those in source_excl)

source_excl - the source nodes that are excluded (can be null, in which case any node in source_incl will qualify)

target_incl - the target nodes (can be null, in which case any node will qualify, except those in target_excl)

target_excl - the target nodes that are excluded (can be null, in which case any node in target_incl will qualify)

includeSelfInteractions - whether or not to include self interactions

Returns:

the corresponding set of regulation edges

Throws:

URISyntaxException - when the regulation datafile can not be read properly

IOException - when the regulation datafile can not be read properly

readPhosphorylationLocusTags

public Set<String> readPhosphorylationLocusTags(boolean includePredicted)
                                         throws URISyntaxException,
                                                IOException

Read a list of (lower-case) locus tags with phosphorylation sites. Either include all, or only those that are experimentally verified. Those are apparent from the data by the usage of (pS), (pT) or (pY) in the modified peptide string.

Parameters:

includePredicted - whether or not to include predicted sites

Returns:

the corresponding set of locus tags with phosphorylation sites

Throws:

URISyntaxException - when the phosphorylation datafile can not be read properly

IOException - when the phosphorylation datafile can not be read properly

readKinaseLocusTags

public Set<String> readKinaseLocusTags()
                                throws URISyntaxException,
                                       IOException

Read a list of (lower-case) locus tags with kinase activity. The file, downloaded from Gene Ontology, contains all types of annotations and evidence codes, and is currently not filtered further.

Returns:

the corresponding set of locus tags with kinase activity

Throws:

URISyntaxException - when the kinase activity datafile can not be read properly

IOException - when the kinase activity datafile can not be read properly