org.jscience.ml.sbml
Class Species

java.lang.Object
  extended by org.jscience.ml.sbml.SBase
      extended by org.jscience.ml.sbml.SBaseId
          extended by org.jscience.ml.sbml.Species

public class Species
extends SBaseId

This class represents an entity that takes part in Reactions. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.


Field Summary
 
Fields inherited from class org.jscience.ml.sbml.SBaseId
id, name
 
Constructor Summary
Species()
          Creates a new instance of Species
Species(java.lang.String id, java.lang.String name)
          Creates a new Species object.
 
Method Summary
 java.lang.String getCharge()
          Getter for property charge.
 java.lang.String getCompartment()
          Getter for property compartment.
 boolean getHasOnlySubstanceUnits()
          Getter for property hasOnlySubstanceUnits.
 double getInitialAmount()
          Getter for property initialAmount.
 double getInitialConcentration()
          Getter for property initialConcentration.
 java.lang.String getSpatialSizeUnits()
          Getter for property spatialSizeUnits.
 java.lang.String getSubstanceUnits()
          Getter for property substanceUnits.
 boolean isBoundaryCondition()
          Getter for property boundaryCondition.
 boolean isConstant()
          Getter for property constant.
 void setBoundaryCondition(boolean boundaryCondition)
          Sets whether the species is on the boundary of the reaction system.
 void setCharge(java.lang.String charge)
          Setter for property charge.
 void setCompartment(Compartment ref)
          DOCUMENT ME!
 void setCompartment(java.lang.String compartment)
          Setter for property compartment.
 void setConstant(boolean constant)
          Setter for property constant.
 void setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits)
          Setter for property hasOnlySubstanceUnits.
 void setInitialAmount(double initialAmount)
          Setter for property initialAmount.
 void setInitialConcentration(double initialConcentration)
          Setter for property initialConcentration.
 void setSpatialSizeUnits(java.lang.String spatialSizeUnits)
          Setter for property spatialSizeUnits.
 void setSubstanceUnits(java.lang.String substanceUnits)
          Setter for property substanceUnits.
 java.lang.String toString()
          Get the SBML representation for this class.
 
Methods inherited from class org.jscience.ml.sbml.SBaseId
getId, getName, setId, setName
 
Methods inherited from class org.jscience.ml.sbml.SBase
getAnnotations, getMetaid, getNotes, getRDF, printList, printShortForm, setMetaid, setRDF, setRDF
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Species

public Species(java.lang.String id,
               java.lang.String name)
Creates a new Species object.

Parameters:
id - DOCUMENT ME!
name - DOCUMENT ME!

Species

public Species()
Creates a new instance of Species

Method Detail

getCharge

public java.lang.String getCharge()
Getter for property charge.

Returns:
Value of property charge.

getCompartment

public java.lang.String getCompartment()
Getter for property compartment.

Returns:
Value of property compartment.

getHasOnlySubstanceUnits

public boolean getHasOnlySubstanceUnits()
Getter for property hasOnlySubstanceUnits.

Returns:
Value of property hasOnlySubstanceUnits.

getInitialAmount

public double getInitialAmount()
Getter for property initialAmount.

Returns:
Value of property initialAmount.

getInitialConcentration

public double getInitialConcentration()
Getter for property initialConcentration.

Returns:
Value of property initialConcentration.

getSpatialSizeUnits

public java.lang.String getSpatialSizeUnits()
Getter for property spatialSizeUnits.

Returns:
Value of property spatialSizeUnits.

getSubstanceUnits

public java.lang.String getSubstanceUnits()
Getter for property substanceUnits.

Returns:
Value of property substanceUnits.

isBoundaryCondition

public boolean isBoundaryCondition()
Getter for property boundaryCondition.

Returns:
Value of property boundaryCondition.

isConstant

public boolean isConstant()
Getter for property constant.

Returns:
Value of property constant.

setBoundaryCondition

public void setBoundaryCondition(boolean boundaryCondition)
Sets whether the species is on the boundary of the reaction system.

Parameters:
boundaryCondition - New value of property boundaryCondition.

setCharge

public void setCharge(java.lang.String charge)
Setter for property charge.

Parameters:
charge - New value of property charge.

setCompartment

public void setCompartment(Compartment ref)
DOCUMENT ME!

Parameters:
ref - DOCUMENT ME!

setCompartment

public void setCompartment(java.lang.String compartment)
Setter for property compartment.

Parameters:
compartment - New value of property compartment.

setConstant

public void setConstant(boolean constant)
Setter for property constant.

Parameters:
constant - New value of property constant.

setHasOnlySubstanceUnits

public void setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits)
Setter for property hasOnlySubstanceUnits.

Parameters:
hasOnlySubstanceUnits - New value of property hasOnlySubstanceUnits.

setInitialAmount

public void setInitialAmount(double initialAmount)
Setter for property initialAmount.

Parameters:
initialAmount - New value of property initialAmount.

setInitialConcentration

public void setInitialConcentration(double initialConcentration)
Setter for property initialConcentration.

Parameters:
initialConcentration - New value of property initialConcentration.

setSpatialSizeUnits

public void setSpatialSizeUnits(java.lang.String spatialSizeUnits)
Setter for property spatialSizeUnits.

Parameters:
spatialSizeUnits - New value of property spatialSizeUnits.

setSubstanceUnits

public void setSubstanceUnits(java.lang.String substanceUnits)
Setter for property substanceUnits.

Parameters:
substanceUnits - New value of property substanceUnits.

toString

public java.lang.String toString()
Get the SBML representation for this class.

Overrides:
toString in class SBase
Returns:
The class's SBML representation