Package org.snpeff.reactome
Class Reactome
- java.lang.Object
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- org.snpeff.reactome.Reactome
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Field Summary
Fields Modifier and Type Field Description static double
EPSILON
static double
MAX_CONVERGENCE_DIFFERENCE
static int
MAX_ITERATIONS
static int
SHOW_EVERY
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Constructor Summary
Constructors Constructor Description Reactome()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(Entity entity, java.lang.String geneId)
Add an entity <-> geneIdMonitor
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 mappingprotected void
loadComplex2HasComponent()
Load complexesprotected void
loadDatabaseObjects()
Load objects table (populate objectType and objectName maps)void
loadGeneIds(java.lang.String geneIdsFile)
Load Gene IDs data, then map geneIDs <-> Entitiesprotected 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 Hashprotected void
loadPathway2HasEvent()
Load pathway eventsprotected void
loadPhysicalEntity2Compartment()
Load compartment informationprotected void
loadReactionlikeEvent2CatalystActivity()
Load reaction catalystprotected void
loadReactionlikeEvent2Input()
Load reaction inputsprotected void
loadReactionlikeEvent2Output()
Load reaction outputsprotected void
loadRegulation()
Load reaction regulationstatic void
main(java.lang.String[] args)
Mainvoid
reset()
Reset all nodes in the circuitboolean
run(GtexExperiment gtexExperiment)
Run some simulationsboolean
run(Gtex gtex, java.lang.String nameMatch)
Run all experiments on gtexvoid
setMonitorTrace(Monitor monitorTrace)
void
setVerbose(boolean verbose)
java.lang.String
toString()
java.lang.String
toStringDetails()
Show details
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Field Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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EPSILON
public static final double EPSILON
- See Also:
- Constant Field Values
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MAX_CONVERGENCE_DIFFERENCE
public static final double MAX_CONVERGENCE_DIFFERENCE
- See Also:
- Constant Field Values
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MAX_ITERATIONS
public static final int MAX_ITERATIONS
- See Also:
- Constant Field Values
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Method Detail
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main
public static void main(java.lang.String[] args)
Main- Parameters:
args
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add
public void add(Entity entity, java.lang.String geneId)
Add an entity <-> geneId- Parameters:
entity
-geneId
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getMonitor
public Monitor getMonitor()
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getMonitorTrace
public Monitor getMonitorTrace()
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iterator
public java.util.Iterator<Entity> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<Entity>
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load
public void load(java.lang.String dirName, java.lang.String geneIdsFile)
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loadCatalystActivity
protected void loadCatalystActivity()
Load catalyst activity to molecule mapping
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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)
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loadGeneIds
public void loadGeneIds(java.lang.String geneIdsFile)
Load Gene IDs data, then map geneIDs <-> Entities- Parameters:
geneIdsFile
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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
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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
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run
public boolean run(Gtex gtex, java.lang.String nameMatch)
Run all experiments on gtex- Parameters:
gtex
-- Returns:
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run
public boolean run(GtexExperiment gtexExperiment)
Run some simulations- Parameters:
gtex
-gtexExperiment
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setMonitorTrace
public void setMonitorTrace(Monitor monitorTrace)
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringDetails
public java.lang.String toStringDetails()
Show details- Returns:
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