Glyph (libsbgn 2.1.0 API)

java.lang.Object
- org.sbgn.bindings.SBGNBase
- - org.sbgn.bindings.Glyph

public class Glyph
extends SBGNBase

Java class for anonymous complex type.

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

 <complexType>
   <complexContent>
     <extension base="{http://sbgn.org/libsbgn/0.3}SBGNBase">
       <sequence>
         <choice>
           <element ref="{http://sbgn.org/libsbgn/0.3}label" minOccurs="0"/>
           <element name="state" minOccurs="0">
             <complexType>
               <complexContent>
                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                   <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
                   <attribute name="variable" type="{http://www.w3.org/2001/XMLSchema}string" />
                 </restriction>
               </complexContent>
             </complexType>
           </element>
         </choice>
         <element name="clone" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element ref="{http://sbgn.org/libsbgn/0.3}label" minOccurs="0"/>
                 </sequence>
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="callout" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <sequence>
                   <element ref="{http://sbgn.org/libsbgn/0.3}point"/>
                 </sequence>
                 <attribute name="target" type="{http://www.w3.org/2001/XMLSchema}IDREF" />
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element name="entity" minOccurs="0">
           <complexType>
             <complexContent>
               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                 <attribute name="name" use="required">
                   <simpleType>
                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                       <enumeration value="unspecified entity"/>
                       <enumeration value="simple chemical"/>
                       <enumeration value="macromolecule"/>
                       <enumeration value="nucleic acid feature"/>
                       <enumeration value="complex"/>
                       <enumeration value="perturbation"/>
                     </restriction>
                   </simpleType>
                 </attribute>
               </restriction>
             </complexContent>
           </complexType>
         </element>
         <element ref="{http://sbgn.org/libsbgn/0.3}bbox"/>
         <element ref="{http://sbgn.org/libsbgn/0.3}glyph" maxOccurs="unbounded" minOccurs="0"/>
         <element ref="{http://sbgn.org/libsbgn/0.3}port" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="class" use="required">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
             <enumeration value="unspecified entity"/>
             <enumeration value="simple chemical"/>
             <enumeration value="macromolecule"/>
             <enumeration value="nucleic acid feature"/>
             <enumeration value="simple chemical multimer"/>
             <enumeration value="macromolecule multimer"/>
             <enumeration value="nucleic acid feature multimer"/>
             <enumeration value="complex"/>
             <enumeration value="complex multimer"/>
             <enumeration value="source and sink"/>
             <enumeration value="perturbation"/>
             <enumeration value="biological activity"/>
             <enumeration value="perturbing agent"/>
             <enumeration value="compartment"/>
             <enumeration value="submap"/>
             <enumeration value="tag"/>
             <enumeration value="terminal"/>
             <enumeration value="process"/>
             <enumeration value="omitted process"/>
             <enumeration value="uncertain process"/>
             <enumeration value="association"/>
             <enumeration value="dissociation"/>
             <enumeration value="phenotype"/>
             <enumeration value="and"/>
             <enumeration value="or"/>
             <enumeration value="not"/>
             <enumeration value="state variable"/>
             <enumeration value="unit of information"/>
             <enumeration value="entity"/>
             <enumeration value="outcome"/>
             <enumeration value="interaction"/>
             <enumeration value="influence target"/>
             <enumeration value="annotation"/>
             <enumeration value="variable value"/>
             <enumeration value="implicit xor"/>
             <enumeration value="delay"/>
             <enumeration value="existence"/>
             <enumeration value="location"/>
             <enumeration value="cardinality"/>
             <enumeration value="observable"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="orientation" default="horizontal">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
             <enumeration value="horizontal"/>
             <enumeration value="vertical"/>
             <enumeration value="left"/>
             <enumeration value="right"/>
             <enumeration value="up"/>
             <enumeration value="down"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}ID" />
       <attribute name="compartmentRef" type="{http://www.w3.org/2001/XMLSchema}IDREF" />
       <attribute name="compartmentOrder" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="mapRef" type="{http://www.w3.org/2001/XMLSchema}IDREF" />
       <attribute name="tagRef" type="{http://www.w3.org/2001/XMLSchema}IDREF" />
     </extension>
   </complexContent>
 </complexType>

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`Glyph.Callout` Java class for anonymous complex type.
`static class`	`Glyph.Clone` Java class for anonymous complex type.
`static class`	`Glyph.Entity` Java class for anonymous complex type.
`static class`	`Glyph.State` Java class for anonymous complex type.

Nested classes/interfaces inherited from class org.sbgn.bindings.SBGNBase
SBGNBase.Extension, SBGNBase.Notes

Field Summary

Fields
Modifier and Type	Field and Description
`protected Bbox`	`bbox`
`protected Glyph.Callout`	`callout`
`protected String`	`clazz`
`protected Glyph.Clone`	`clone`
`protected Float`	`compartmentOrder`
`protected Object`	`compartmentRef`
`protected Glyph.Entity`	`entity`
`protected List<Glyph>`	`glyph`
`protected String`	`id`
`protected Label`	`label`
`protected Object`	`mapRef`
`protected String`	`orientation`
`protected List<Port>`	`port`
`protected Glyph.State`	`state`
`protected Object`	`tagRef`

Fields inherited from class org.sbgn.bindings.SBGNBase
extension, notes

Constructor Summary

Constructors
Constructor and Description

Glyph()

Constructors
Constructor and Description
`Glyph()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Bbox`	`getBbox()` <?xml version="1.0" encoding="UTF-8"?><p xmlns="http://sbgn.org/libsbgn/0.3" xmlns:sbgn="http://sbgn.org/libsbgn/0.3" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> The bbox element is mandatory and unique: exactly one per glyph.
`Glyph.Callout`	`getCallout()` Gets the value of the callout property.
`String`	`getClazz()` Gets the value of the clazz property.
`Glyph.Clone`	`getClone()` Gets the value of the clone property.
`Float`	`getCompartmentOrder()` Gets the value of the compartmentOrder property.
`Object`	`getCompartmentRef()` Gets the value of the compartmentRef property.
`Glyph.Entity`	`getEntity()` Gets the value of the entity property.
`List<Glyph>`	`getGlyph()` <?xml version="1.0" encoding="UTF-8"?><p xmlns="http://sbgn.org/libsbgn/0.3" xmlns:sbgn="http://sbgn.org/libsbgn/0.3" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> A glyph element can contain any number of children glyph elements.
`String`	`getId()` Gets the value of the id property.
`Label`	`getLabel()` Gets the value of the label property.
`Object`	`getMapRef()` Gets the value of the mapRef property.
`String`	`getOrientation()` Gets the value of the orientation property.
`List<Port>`	`getPort()` Gets the value of the port property.
`Glyph.State`	`getState()` Gets the value of the state property.
`Object`	`getTagRef()` Gets the value of the tagRef property.
`void`	`setBbox(Bbox value)` Sets the value of the bbox property.
`void`	`setCallout(Glyph.Callout value)` Sets the value of the callout property.
`void`	`setClazz(String value)` Sets the value of the clazz property.
`void`	`setClone(Glyph.Clone value)` Sets the value of the clone property.
`void`	`setCompartmentOrder(Float value)` Sets the value of the compartmentOrder property.
`void`	`setCompartmentRef(Object value)` Sets the value of the compartmentRef property.
`void`	`setEntity(Glyph.Entity value)` Sets the value of the entity property.
`void`	`setId(String value)` Sets the value of the id property.
`void`	`setLabel(Label value)` Sets the value of the label property.
`void`	`setMapRef(Object value)` Sets the value of the mapRef property.
`void`	`setOrientation(String value)` Sets the value of the orientation property.
`void`	`setState(Glyph.State value)` Sets the value of the state property.
`void`	`setTagRef(Object value)` Sets the value of the tagRef property.

Methods inherited from class org.sbgn.bindings.SBGNBase
getExtension, getNotes, setExtension, setNotes

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

Field Detail

label
```
protected Label label
```

state
```
protected Glyph.State state
```

clone
```
protected Glyph.Clone clone
```

callout
```
protected Glyph.Callout callout
```

entity
```
protected Glyph.Entity entity
```

bbox
```
protected Bbox bbox
```

glyph
```
protected List<Glyph> glyph
```

port
```
protected List<Port> port
```

clazz
```
protected String clazz
```

orientation
```
protected String orientation
```

id
```
protected String id
```

compartmentRef
```
protected Object compartmentRef
```

compartmentOrder
```
protected Float compartmentOrder
```

mapRef
```
protected Object mapRef
```

tagRef
```
protected Object tagRef
```

Constructor Detail
- Glyph
```
public Glyph()
```

Method Detail

getLabel
```
public Label getLabel()
```
Gets the value of the label property.

Returns:

possible object is Label

setLabel
```
public void setLabel(Label value)
```
Sets the value of the label property.

Parameters:

value - allowed object is Label

getState
```
public Glyph.State getState()
```
Gets the value of the state property.

Returns:

possible object is Glyph.State

setState
```
public void setState(Glyph.State value)
```
Sets the value of the state property.

Parameters:

value - allowed object is Glyph.State

getClone
```
public Glyph.Clone getClone()
```
Gets the value of the clone property.

Returns:

possible object is Glyph.Clone

setClone
```
public void setClone(Glyph.Clone value)
```
Sets the value of the clone property.

Parameters:

value - allowed object is Glyph.Clone

getCallout
```
public Glyph.Callout getCallout()
```
Gets the value of the callout property.

Returns:

possible object is Glyph.Callout

setCallout
```
public void setCallout(Glyph.Callout value)
```
Sets the value of the callout property.

Parameters:

value - allowed object is Glyph.Callout

getEntity
```
public Glyph.Entity getEntity()
```
Gets the value of the entity property.

Returns:

possible object is Glyph.Entity

setEntity
```
public void setEntity(Glyph.Entity value)
```
Sets the value of the entity property.

Parameters:

value - allowed object is Glyph.Entity

getBbox

public Bbox getBbox()

 <?xml version="1.0" encoding="UTF-8"?><p xmlns="http://sbgn.org/libsbgn/0.3" xmlns:sbgn="http://sbgn.org/libsbgn/0.3" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
                                         The bbox element is mandatory and unique: exactly one per
                                         glyph.
                                         It defines the outer bounding box of the glyph.
                                         The actual shape of the glyph can be irregular
                                         (for instance in the case of some compartments)
                                     </p>

 <?xml version="1.0" encoding="UTF-8"?><p xmlns="http://sbgn.org/libsbgn/0.3" xmlns:sbgn="http://sbgn.org/libsbgn/0.3" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
                                         In the case of process nodes, the bounding box only concerns the
                                         central glyph (square, or circle):
                                         the input/output ports are not included, and neither are the lines
                                         connecting them to the central glyph.
                                     </p>

Returns:: possible object is Bbox

setBbox
```
public void setBbox(Bbox value)
```
Sets the value of the bbox property.

Parameters:

value - allowed object is Bbox

getGlyph

public List<Glyph> getGlyph()

 <?xml version="1.0" encoding="UTF-8"?><p xmlns="http://sbgn.org/libsbgn/0.3" xmlns:sbgn="http://sbgn.org/libsbgn/0.3" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
                                         A glyph element can contain any number of children glyph
                                         elements.
                                         In practice, this should only happen in the following cases:
                                         <ul>
                                             <li>a compartment with unit of information children,</li>
                                             <li>
                                                 an EPN with states variables and/or unit of information
                                                 children,
                                             </li>
                                             <li>
                                                 a complex, with state variables, unit of info, and/or EPN
                                                 children.
                                             </li>
                                         </ul>
                                     </p>

Gets the value of the glyph property.

This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the glyph property.

For example, to add a new item, do as follows:

    getGlyph().add(newItem);

Objects of the following type(s) are allowed in the list Glyph

getPort
```
public List<Port> getPort()
```
Gets the value of the port property.
This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the port property.
For example, to add a new item, do as follows:
```
    getPort().add(newItem);
 
```
Objects of the following type(s) are allowed in the list Port

getClazz
```
public String getClazz()
```
Gets the value of the clazz property.

Returns:

possible object is String

setClazz
```
public void setClazz(String value)
```
Sets the value of the clazz property.

Parameters:

value - allowed object is String

getOrientation
```
public String getOrientation()
```
Gets the value of the orientation property.

Returns:

possible object is String

setOrientation
```
public void setOrientation(String value)
```
Sets the value of the orientation property.

Parameters:

value - allowed object is String

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

getCompartmentRef
```
public Object getCompartmentRef()
```
Gets the value of the compartmentRef property.

Returns:

possible object is Object

setCompartmentRef
```
public void setCompartmentRef(Object value)
```
Sets the value of the compartmentRef property.

Parameters:

value - allowed object is Object

getCompartmentOrder
```
public Float getCompartmentOrder()
```
Gets the value of the compartmentOrder property.

Returns:

possible object is Float

setCompartmentOrder
```
public void setCompartmentOrder(Float value)
```
Sets the value of the compartmentOrder property.

Parameters:

value - allowed object is Float

getMapRef
```
public Object getMapRef()
```
Gets the value of the mapRef property.

Returns:

possible object is Object

setMapRef
```
public void setMapRef(Object value)
```
Sets the value of the mapRef property.

Parameters:

value - allowed object is Object

getTagRef
```
public Object getTagRef()
```
Gets the value of the tagRef property.

Returns:

possible object is Object

setTagRef
```
public void setTagRef(Object value)
```
Sets the value of the tagRef property.

Parameters:

value - allowed object is Object

Class Glyph

Nested Class Summary

Nested classes/interfaces inherited from class org.sbgn.bindings.SBGNBase

Field Summary

Fields inherited from class org.sbgn.bindings.SBGNBase

Constructor Summary

Method Summary

Methods inherited from class org.sbgn.bindings.SBGNBase

Methods inherited from class java.lang.Object

Field Detail

label

state

clone

callout

entity

bbox

glyph

port

clazz

orientation

id

compartmentRef

compartmentOrder

mapRef

tagRef

Constructor Detail

Glyph

Method Detail

getLabel

setLabel

getState

setState

getClone

setClone

getCallout

setCallout

getEntity

setEntity

getBbox

setBbox

getGlyph

getPort

getClazz

setClazz

getOrientation

setOrientation

getId

setId

getCompartmentRef

setCompartmentRef

getCompartmentOrder

setCompartmentOrder

getMapRef

setMapRef

getTagRef

setTagRef