Species (cd2sbgnml 0.4.2 API)

java.lang.Object
- org.sbml._2001.ns.celldesigner.Species

public class Species
extends Object

Species inside complexes.

Java class for species complex type.

The following schema fragment specifies the expected content contained within this class.

 <complexType name="species">
   <complexContent>
     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
       <sequence>
         <element name="notes" type="{http://www.sbml.org/2001/ns/celldesigner}notes" minOccurs="0"/>
         <element name="annotation">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <choice>
                     <element ref="{http://www.sbml.org/2001/ns/celldesigner}positionToCompartment"/>
                     <element ref="{http://www.sbml.org/2001/ns/celldesigner}complexSpecies"/>
                   </choice>
                   <element name="speciesIdentity" type="{http://www.sbml.org/2001/ns/celldesigner}speciesIdentity"/>
                   <element name="listOfCatalyzedReactions" type="{http://www.sbml.org/2001/ns/celldesigner}listOfCatalyzedReactions" minOccurs="0"/>
                 </sequence>
               </restriction>
             </complexContent>
           </complexType>
         </element>
       </sequence>
       <attribute name="id" use="required" type="{http://www.sbml.org/2001/ns/celldesigner}SId" />
       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="compartment" type="{http://www.sbml.org/2001/ns/celldesigner}SId" />
       <attribute name="initialAmount" type="{http://www.w3.org/2001/XMLSchema}double" />
       <attribute name="initialConcentration" type="{http://www.w3.org/2001/XMLSchema}double" />
       <attribute name="substanceUnits" type="{http://www.sbml.org/2001/ns/celldesigner}SId" />
       <attribute name="spatialSizeUnits" type="{http://www.sbml.org/2001/ns/celldesigner}SId" />
       <attribute name="hasOnlySubstanceUnits" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
       <attribute name="boundaryCondition" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
       <attribute name="charge" type="{http://www.w3.org/2001/XMLSchema}integer" />
       <attribute name="constant" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     </restriction>
   </complexContent>
 </complexType>

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Species.Annotation
Java class for anonymous complex type.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Species.Annotation` Java class for anonymous complex type.

Field Summary

Fields
Modifier and Type	Field and Description
`protected Species.Annotation`	`annotation`
`protected Boolean`	`boundaryCondition`
`protected BigInteger`	`charge`
`protected String`	`compartment`
`protected Boolean`	`constant`
`protected Boolean`	`hasOnlySubstanceUnits`
`protected String`	`id`
`protected Double`	`initialAmount`
`protected Double`	`initialConcentration`
`protected String`	`name`
`protected Notes`	`notes`
`protected String`	`spatialSizeUnits`
`protected String`	`substanceUnits`

Constructor Summary

Constructors
Constructor and Description

Species()

Constructors
Constructor and Description
`Species()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Species.Annotation`	`getAnnotation()` Gets the value of the annotation property.
`BigInteger`	`getCharge()` Gets the value of the charge property.
`String`	`getCompartment()` Gets the value of the compartment property.
`String`	`getId()` Gets the value of the id property.
`Double`	`getInitialAmount()` Gets the value of the initialAmount property.
`Double`	`getInitialConcentration()` Gets the value of the initialConcentration property.
`String`	`getName()` Gets the value of the name property.
`Notes`	`getNotes()` Gets the value of the notes property.
`String`	`getSpatialSizeUnits()` Gets the value of the spatialSizeUnits property.
`String`	`getSubstanceUnits()` Gets the value of the substanceUnits property.
`boolean`	`isBoundaryCondition()` Gets the value of the boundaryCondition property.
`boolean`	`isConstant()` Gets the value of the constant property.
`boolean`	`isHasOnlySubstanceUnits()` Gets the value of the hasOnlySubstanceUnits property.
`void`	`setAnnotation(Species.Annotation value)` Sets the value of the annotation property.
`void`	`setBoundaryCondition(Boolean value)` Sets the value of the boundaryCondition property.
`void`	`setCharge(BigInteger value)` Sets the value of the charge property.
`void`	`setCompartment(String value)` Sets the value of the compartment property.
`void`	`setConstant(Boolean value)` Sets the value of the constant property.
`void`	`setHasOnlySubstanceUnits(Boolean value)` Sets the value of the hasOnlySubstanceUnits property.
`void`	`setId(String value)` Sets the value of the id property.
`void`	`setInitialAmount(Double value)` Sets the value of the initialAmount property.
`void`	`setInitialConcentration(Double value)` Sets the value of the initialConcentration property.
`void`	`setName(String value)` Sets the value of the name property.
`void`	`setNotes(Notes value)` Sets the value of the notes property.
`void`	`setSpatialSizeUnits(String value)` Sets the value of the spatialSizeUnits property.
`void`	`setSubstanceUnits(String value)` Sets the value of the substanceUnits property.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - notes
```
protected Notes notes
```
  - annotation
```
protected Species.Annotation annotation
```
  - id
```
protected String id
```
  - name
```
protected String name
```
  - compartment
```
protected String compartment
```
  - initialAmount
```
protected Double initialAmount
```
  - initialConcentration
```
protected Double initialConcentration
```
  - substanceUnits
```
protected String substanceUnits
```
  - spatialSizeUnits
```
protected String spatialSizeUnits
```
  - hasOnlySubstanceUnits
```
protected Boolean hasOnlySubstanceUnits
```
  - boundaryCondition
```
protected Boolean boundaryCondition
```
  - charge
```
protected BigInteger charge
```
  - constant
```
protected Boolean constant
```
- Constructor Detail
  - Species
```
public Species()
```
- Method Detail
  - getNotes
```
public Notes getNotes()
```
    Gets the value of the notes property.
    
    Returns:
    
    possible object is Notes
  - setNotes
```
public void setNotes(Notes value)
```
    Sets the value of the notes property.
    
    Parameters:
    
    value - allowed object is Notes
  - getAnnotation
```
public Species.Annotation getAnnotation()
```
    Gets the value of the annotation property.
    
    Returns:
    
    possible object is Species.Annotation
  - setAnnotation
```
public void setAnnotation(Species.Annotation value)
```
    Sets the value of the annotation property.
    
    Parameters:
    
    value - allowed object is Species.Annotation
  - getId
```
public String getId()
```
    Gets the value of the id property.
    
    Returns:
    
    possible object is String
  - setId
```
public void setId(String value)
```
    Sets the value of the id property.
    
    Parameters:
    
    value - allowed object is String
  - getName
```
public String getName()
```
    Gets the value of the name property.
    
    Returns:
    
    possible object is String
  - setName
```
public void setName(String value)
```
    Sets the value of the name property.
    
    Parameters:
    
    value - allowed object is String
  - getCompartment
```
public String getCompartment()
```
    Gets the value of the compartment property.
    
    Returns:
    
    possible object is String
  - setCompartment
```
public void setCompartment(String value)
```
    Sets the value of the compartment property.
    
    Parameters:
    
    value - allowed object is String
  - getInitialAmount
```
public Double getInitialAmount()
```
    Gets the value of the initialAmount property.
    
    Returns:
    
    possible object is Double
  - setInitialAmount
```
public void setInitialAmount(Double value)
```
    Sets the value of the initialAmount property.
    
    Parameters:
    
    value - allowed object is Double
  - getInitialConcentration
```
public Double getInitialConcentration()
```
    Gets the value of the initialConcentration property.
    
    Returns:
    
    possible object is Double
  - setInitialConcentration
```
public void setInitialConcentration(Double value)
```
    Sets the value of the initialConcentration property.
    
    Parameters:
    
    value - allowed object is Double
  - getSubstanceUnits
```
public String getSubstanceUnits()
```
    Gets the value of the substanceUnits property.
    
    Returns:
    
    possible object is String
  - setSubstanceUnits
```
public void setSubstanceUnits(String value)
```
    Sets the value of the substanceUnits property.
    
    Parameters:
    
    value - allowed object is String
  - getSpatialSizeUnits
```
public String getSpatialSizeUnits()
```
    Gets the value of the spatialSizeUnits property.
    
    Returns:
    
    possible object is String
  - setSpatialSizeUnits
```
public void setSpatialSizeUnits(String value)
```
    Sets the value of the spatialSizeUnits property.
    
    Parameters:
    
    value - allowed object is String
  - isHasOnlySubstanceUnits
```
public boolean isHasOnlySubstanceUnits()
```
    Gets the value of the hasOnlySubstanceUnits property.
    
    Returns:
    
    possible object is Boolean
  - setHasOnlySubstanceUnits
```
public void setHasOnlySubstanceUnits(Boolean value)
```
    Sets the value of the hasOnlySubstanceUnits property.
    
    Parameters:
    
    value - allowed object is Boolean
  - isBoundaryCondition
```
public boolean isBoundaryCondition()
```
    Gets the value of the boundaryCondition property.
    
    Returns:
    
    possible object is Boolean
  - setBoundaryCondition
```
public void setBoundaryCondition(Boolean value)
```
    Sets the value of the boundaryCondition property.
    
    Parameters:
    
    value - allowed object is Boolean
  - getCharge
```
public BigInteger getCharge()
```
    Gets the value of the charge property.
    
    Returns:
    
    possible object is BigInteger
  - setCharge
```
public void setCharge(BigInteger value)
```
    Sets the value of the charge property.
    
    Parameters:
    
    value - allowed object is BigInteger
  - isConstant
```
public boolean isConstant()
```
    Gets the value of the constant property.
    
    Returns:
    
    possible object is Boolean
  - setConstant
```
public void setConstant(Boolean value)
```
    Sets the value of the constant property.
    
    Parameters:
    
    value - allowed object is Boolean

Class Species

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

notes

annotation

id

name

compartment

initialAmount

initialConcentration

substanceUnits

spatialSizeUnits

hasOnlySubstanceUnits

boundaryCondition

charge

constant

Constructor Detail

Species

Method Detail

getNotes

setNotes

getAnnotation

setAnnotation

getId

setId

getName

setName

getCompartment

setCompartment

getInitialAmount

setInitialAmount

getInitialConcentration

setInitialConcentration

getSubstanceUnits

setSubstanceUnits

getSpatialSizeUnits

setSpatialSizeUnits

isHasOnlySubstanceUnits

setHasOnlySubstanceUnits

isBoundaryCondition

setBoundaryCondition

getCharge

setCharge

isConstant

setConstant