Package org.snpeff.reactome
Class Reactome
java.lang.Object
org.snpeff.reactome.Reactome
Load reactome data from TXT files
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final double
static final double
static final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add an entity <-> geneIditerator()
void
protected void
Load catalyst activity to molecule mappingprotected void
Load complexesprotected void
Load objects table (populate objectType and objectName maps)void
loadGeneIds
(String geneIdsFile) Load Gene IDs data, then map geneIDs <-> Entitiesprotected void
Load a two-column file into a Hashprotected void
Load pathway eventsprotected void
Load compartment informationprotected void
Load reaction catalystprotected void
Load reaction inputsprotected void
Load reaction outputsprotected void
Load reaction regulationstatic void
Mainvoid
reset()
Reset all nodes in the circuitboolean
run
(GtexExperiment gtexExperiment) Run some simulationsboolean
Run all experiments on gtexvoid
setMonitorTrace
(Monitor monitorTrace) void
setVerbose
(boolean verbose) toString()
Show detailsMethods 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
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Field Details
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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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EPSILON
public static final double EPSILON- See Also:
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MAX_CONVERGENCE_DIFFERENCE
public static final double MAX_CONVERGENCE_DIFFERENCE- See Also:
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MAX_ITERATIONS
public static final int MAX_ITERATIONS- See Also:
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Constructor Details
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Reactome
public Reactome()
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Method Details
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main
Main- Parameters:
args
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add
Add an entity <-> geneId- Parameters:
entity
-geneId
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getMonitor
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getMonitorTrace
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iterator
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load
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loadCatalystActivity
protected void loadCatalystActivity()Load catalyst activity to molecule mapping -
loadComplex2HasComponent
protected void loadComplex2HasComponent()Load complexes- Parameters:
name
-fileName
-map
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loadDatabaseObjects
protected void loadDatabaseObjects()Load objects table (populate objectType and objectName maps) -
loadGeneIds
Load Gene IDs data, then map geneIDs <-> Entities- Parameters:
geneIdsFile
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loadMap
Load a two-column file into a Hash- Parameters:
name
-fileName
-map
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loadPathway2HasEvent
protected void loadPathway2HasEvent()Load pathway events- Parameters:
name
-fileName
-map
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loadPhysicalEntity2Compartment
protected void loadPhysicalEntity2Compartment()Load compartment information- Parameters:
name
-fileName
-map
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loadReactionlikeEvent2CatalystActivity
protected void loadReactionlikeEvent2CatalystActivity()Load reaction catalyst- Parameters:
name
-fileName
-map
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loadReactionlikeEvent2Input
protected void loadReactionlikeEvent2Input()Load reaction inputs- Parameters:
name
-fileName
-map
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loadReactionlikeEvent2Output
protected void loadReactionlikeEvent2Output()Load reaction outputs- Parameters:
name
-fileName
-map
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loadRegulation
protected void loadRegulation()Load reaction regulation- Parameters:
name
-fileName
-map
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reset
public void reset()Reset all nodes in the circuit -
run
Run all experiments on gtex- Parameters:
gtex
-- Returns:
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run
Run some simulations- Parameters:
gtex
-gtexExperiment
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setMonitorTrace
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setVerbose
public void setVerbose(boolean verbose) -
toString
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toStringDetails
Show details- Returns:
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