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>
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.
|
SBGNBase.Extension, SBGNBase.Notes
Modifier and Type | Field and Description |
---|---|
protected Bbox |
bbox |
protected Glyph.Callout |
callout |
protected java.lang.String |
clazz |
protected Glyph.Clone |
clone |
protected java.lang.Float |
compartmentOrder |
protected java.lang.Object |
compartmentRef |
protected Glyph.Entity |
entity |
protected java.util.List<Glyph> |
glyph |
protected java.lang.String |
id |
protected Label |
label |
protected java.lang.Object |
mapRef |
protected java.lang.String |
orientation |
protected java.util.List<Port> |
port |
protected Glyph.State |
state |
protected java.lang.Object |
tagRef |
Constructor and Description |
---|
Glyph() |
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.
|
java.lang.String |
getClazz()
Gets the value of the clazz property.
|
Glyph.Clone |
getClone()
Gets the value of the clone property.
|
java.lang.Float |
getCompartmentOrder()
Gets the value of the compartmentOrder property.
|
java.lang.Object |
getCompartmentRef()
Gets the value of the compartmentRef property.
|
Glyph.Entity |
getEntity()
Gets the value of the entity property.
|
java.util.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.
|
java.lang.String |
getId()
Gets the value of the id property.
|
Label |
getLabel()
Gets the value of the label property.
|
java.lang.Object |
getMapRef()
Gets the value of the mapRef property.
|
java.lang.String |
getOrientation()
Gets the value of the orientation property.
|
java.util.List<Port> |
getPort()
Gets the value of the port property.
|
Glyph.State |
getState()
Gets the value of the state property.
|
java.lang.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(java.lang.String value)
Sets the value of the clazz property.
|
void |
setClone(Glyph.Clone value)
Sets the value of the clone property.
|
void |
setCompartmentOrder(java.lang.Float value)
Sets the value of the compartmentOrder property.
|
void |
setCompartmentRef(java.lang.Object value)
Sets the value of the compartmentRef property.
|
void |
setEntity(Glyph.Entity value)
Sets the value of the entity property.
|
void |
setId(java.lang.String value)
Sets the value of the id property.
|
void |
setLabel(Label value)
Sets the value of the label property.
|
void |
setMapRef(java.lang.Object value)
Sets the value of the mapRef property.
|
void |
setOrientation(java.lang.String value)
Sets the value of the orientation property.
|
void |
setState(Glyph.State value)
Sets the value of the state property.
|
void |
setTagRef(java.lang.Object value)
Sets the value of the tagRef property.
|
getExtension, getNotes, setExtension, setNotes
protected Label label
protected Glyph.State state
protected Glyph.Clone clone
protected Glyph.Callout callout
protected Glyph.Entity entity
protected Bbox bbox
protected java.util.List<Glyph> glyph
protected java.util.List<Port> port
protected java.lang.String clazz
protected java.lang.String orientation
protected java.lang.String id
protected java.lang.Object compartmentRef
protected java.lang.Float compartmentOrder
protected java.lang.Object mapRef
protected java.lang.Object tagRef
public Label getLabel()
Label
public void setLabel(Label value)
value
- allowed object is
Label
public Glyph.State getState()
Glyph.State
public void setState(Glyph.State value)
value
- allowed object is
Glyph.State
public Glyph.Clone getClone()
Glyph.Clone
public void setClone(Glyph.Clone value)
value
- allowed object is
Glyph.Clone
public Glyph.Callout getCallout()
Glyph.Callout
public void setCallout(Glyph.Callout value)
value
- allowed object is
Glyph.Callout
public Glyph.Entity getEntity()
Glyph.Entity
public void setEntity(Glyph.Entity value)
value
- allowed object is
Glyph.Entity
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>
Bbox
public void setBbox(Bbox value)
value
- allowed object is
Bbox
public java.util.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
public java.util.List<Port> getPort()
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
public java.lang.String getClazz()
String
public void setClazz(java.lang.String value)
value
- allowed object is
String
public java.lang.String getOrientation()
String
public void setOrientation(java.lang.String value)
value
- allowed object is
String
public java.lang.String getId()
String
public void setId(java.lang.String value)
value
- allowed object is
String
public java.lang.Object getCompartmentRef()
Object
public void setCompartmentRef(java.lang.Object value)
value
- allowed object is
Object
public java.lang.Float getCompartmentOrder()
Float
public void setCompartmentOrder(java.lang.Float value)
value
- allowed object is
Float
public java.lang.Object getMapRef()
Object
public void setMapRef(java.lang.Object value)
value
- allowed object is
Object
public java.lang.Object getTagRef()
Object
public void setTagRef(java.lang.Object value)
value
- allowed object is
Object