Package org.snpeff.reactome
Class Entity
java.lang.Object
org.snpeff.reactome.Entity
- All Implemented Interfaces:
Comparable<Entity>
- Direct Known Subclasses:
Compartment
,Event
A reactome basic entity (e.g. anything in reactome database derives fro this object)
- Author:
- pcingola
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic double
protected Compartment
static boolean
protected double
protected int
protected String
protected double
static Entity.TransferFunction
protected double
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a geneIddouble
calc()
double
Calculate entities.int
int
getId()
getName()
double
double
boolean
boolean
isFixed()
boolean
void
reset()
void
setCompartment
(Compartment compartment) void
setFixedOutput
(double fixedOutput) void
setWeight
(double weight) toString()
protected double
transferFunction
(double x) Transfer function
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Field Details
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debug
public static boolean debug -
TRANSFER_FUNCTION
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BETA
public static double BETA -
id
protected int id -
name
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compartment
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output
protected double output -
weight
protected double weight -
fixedOutput
protected double fixedOutput -
geneIds
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Constructor Details
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Entity
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Method Details
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addGeneId
Add a geneId- Parameters:
geneId
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calc
public double calc() -
calc
Calculate entities. Make sure we don't calculate twice (keep 'doneEntities' set up to date)- Parameters:
doneEntities
-- Returns:
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compareTo
- Specified by:
compareTo
in interfaceComparable<Entity>
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getCompartment
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getGeneIds
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getId
public int getId() -
getName
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getOutput
public double getOutput() -
getWeight
public double getWeight() -
hasOutput
public boolean hasOutput() -
isFixed
public boolean isFixed() -
isReaction
public boolean isReaction() -
reset
public void reset() -
setCompartment
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setFixedOutput
public void setFixedOutput(double fixedOutput) -
setWeight
public void setWeight(double weight) -
toString
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toString
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toStringSimple
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transferFunction
protected double transferFunction(double x) Transfer function- Parameters:
x
-- Returns:
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