Package org.snpeff.reactome

Class Reactome

java.lang.Object

org.snpeff.reactome.Reactome

All Implemented Interfaces:

java.lang.Iterable<Entity>

public class Reactome
extends java.lang.Object
implements java.lang.Iterable<Entity>

Load reactome data from TXT files

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static double	EPSILON
static double	MAX_CONVERGENCE_DIFFERENCE
static int	MAX_ITERATIONS
static int	SHOW_EVERY

Constructor Summary

Constructors

Constructor	Description
Reactome()

Method Summary

Modifier and Type	Method	Description
void	add(Entity entity, java.lang.String geneId)	Add an entity <-> geneId
Monitor	getMonitor()
Monitor	getMonitorTrace()
java.util.Iterator<Entity>	iterator()
void	load(java.lang.String dirName, java.lang.String geneIdsFile)
protected void	loadCatalystActivity()	Load catalyst activity to molecule mapping
protected void	loadComplex2HasComponent()	Load complexes
protected void	loadDatabaseObjects()	Load objects table (populate objectType and objectName maps)
void	loadGeneIds(java.lang.String geneIdsFile)	Load Gene IDs data, then map geneIDs <-> Entities
protected void	loadMap(java.lang.String name, java.lang.String fileName, java.util.HashMap<java.lang.String,java.lang.String> map)	Load a two-column file into a Hash
protected void	loadPathway2HasEvent()	Load pathway events
protected void	loadPhysicalEntity2Compartment()	Load compartment information
protected void	loadReactionlikeEvent2CatalystActivity()	Load reaction catalyst
protected void	loadReactionlikeEvent2Input()	Load reaction inputs
protected void	loadReactionlikeEvent2Output()	Load reaction outputs
protected void	loadRegulation()	Load reaction regulation
static void	main(java.lang.String[] args)	Main
void	reset()	Reset all nodes in the circuit
boolean	run(GtexExperiment gtexExperiment)	Run some simulations
boolean	run(Gtex gtex, java.lang.String nameMatch)	Run all experiments on gtex
void	setMonitorTrace(Monitor monitorTrace)
void	setVerbose(boolean verbose)
java.lang.String	toString()
java.lang.String	toStringDetails()	Show details

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

SHOW_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

EPSILON

public static final double EPSILON

See Also:

Constant Field Values

MAX_CONVERGENCE_DIFFERENCE

public static final double MAX_CONVERGENCE_DIFFERENCE

See Also:

Constant Field Values

MAX_ITERATIONS

public static final int MAX_ITERATIONS

See Also:

Constant Field Values

Constructor Detail

Reactome

public Reactome()

Method Detail

main

public static void main(java.lang.String[] args)

Main

Parameters:

args -

add

public void add(Entity entity,
                java.lang.String geneId)

Add an entity <-> geneId

Parameters:

entity -

geneId -

getMonitor

public Monitor getMonitor()

getMonitorTrace

public Monitor getMonitorTrace()

iterator

public java.util.Iterator<Entity> iterator()

Specified by:

iterator in interface java.lang.Iterable<Entity>

load

public void load(java.lang.String dirName,
                 java.lang.String geneIdsFile)

loadCatalystActivity

protected void loadCatalystActivity()

Load catalyst activity to molecule mapping

loadComplex2HasComponent

protected void loadComplex2HasComponent()

Load complexes

Parameters:

name -

fileName -

map -

loadDatabaseObjects

protected void loadDatabaseObjects()

Load objects table (populate objectType and objectName maps)

loadGeneIds

public void loadGeneIds(java.lang.String geneIdsFile)

Load Gene IDs data, then map geneIDs <-> Entities

Parameters:

geneIdsFile -

loadMap

protected void loadMap(java.lang.String name,
                       java.lang.String fileName,
                       java.util.HashMap<java.lang.String,java.lang.String> map)

Load a two-column file into a Hash

Parameters:

name -

fileName -

map -

loadPathway2HasEvent

protected void loadPathway2HasEvent()

Load pathway events

Parameters:

name -

fileName -

map -

loadPhysicalEntity2Compartment

protected void loadPhysicalEntity2Compartment()

Load compartment information

Parameters:

name -

fileName -

map -

loadReactionlikeEvent2CatalystActivity

protected void loadReactionlikeEvent2CatalystActivity()

Load reaction catalyst

Parameters:

name -

fileName -

map -

loadReactionlikeEvent2Input

protected void loadReactionlikeEvent2Input()

Load reaction inputs

Parameters:

name -

fileName -

map -

loadReactionlikeEvent2Output

protected void loadReactionlikeEvent2Output()

Load reaction outputs

Parameters:

name -

fileName -

map -

loadRegulation

protected void loadRegulation()

Load reaction regulation

Parameters:

name -

fileName -

map -

reset

public void reset()

Reset all nodes in the circuit

run

public boolean run(Gtex gtex,
                   java.lang.String nameMatch)

Run all experiments on gtex

Parameters:

gtex -

Returns:

run

public boolean run(GtexExperiment gtexExperiment)

Run some simulations

Parameters:

gtex -

gtexExperiment -

setMonitorTrace

public void setMonitorTrace(Monitor monitorTrace)

setVerbose

public void setVerbose(boolean verbose)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringDetails

public java.lang.String toStringDetails()

Show details

Returns: