- getAboutId() - Method in class org.sbgn.schematron.Issue
-
identifier of the element that this issue is about.
- getAny() - Method in class org.sbgn.bindings.SBGNBase.Extension
-
Gets the value of the any property.
- getAny() - Method in class org.sbgn.bindings.SBGNBase.Notes
-
Gets the value of the any property.
- getArc() - Method in class org.sbgn.bindings.Arcgroup
-
<?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">
An arcgroup can have multiple arcs.
- getArc() - Method in class org.sbgn.bindings.Map
-
Gets the value of the arc property.
- getArcgroup() - Method in class org.sbgn.bindings.Map
-
Gets the value of the arcgroup property.
- getBbox() - Method in class org.sbgn.bindings.Glyph
-
<?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.
- getBbox() - Method in class org.sbgn.bindings.Label
-
Gets the value of the bbox property.
- getBbox() - Method in class org.sbgn.bindings.Map
-
<?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 on a map is not mandatory, it allows the
application to define a canvas, and at the same time
define a whitespace margin around the glyphs.
- getCallout() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the callout property.
- getClazz() - Method in enum org.sbgn.ArcClazz
-
- getClazz() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the clazz property.
- getClazz() - Method in class org.sbgn.bindings.Arcgroup
-
Gets the value of the clazz property.
- getClazz() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the clazz property.
- getClazz() - Method in enum org.sbgn.GlyphClazz
-
- getClone() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the clone property.
- getCompartmentOrder() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the compartmentOrder property.
- getCompartmentRef() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the compartmentRef property.
- getEnd() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the end property.
- getEntity() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the entity property.
- getExtension() - Method in class org.sbgn.bindings.SBGNBase
-
Gets the value of the extension property.
- getGlyph() - Method in class org.sbgn.bindings.Arc
-
<?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 PD, an arc can contain a single optional sub-glyph.
- getGlyph() - Method in class org.sbgn.bindings.Arcgroup
-
<?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">
An arcgroup can contain glyphs.
- getGlyph() - Method in class org.sbgn.bindings.Glyph
-
<?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.
- getGlyph() - Method in class org.sbgn.bindings.Map
-
Gets the value of the glyph property.
- getH() - Method in class org.sbgn.bindings.Bbox
-
Gets the value of the h property.
- getId() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the id property.
- getId() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the id property.
- getId() - Method in class org.sbgn.bindings.Map
-
Gets the value of the id property.
- getId() - Method in class org.sbgn.bindings.Port
-
Gets the value of the id property.
- getLabel() - Method in class org.sbgn.bindings.Glyph.Clone
-
Gets the value of the label property.
- getLabel() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the label property.
- getLanguage() - Method in class org.sbgn.bindings.Map
-
Gets the value of the language property.
- getLanguage(File) - Static method in class org.sbgn.SbgnVersionFinder
-
- getMap() - Method in class org.sbgn.bindings.Sbgn
-
Gets the value of the map property.
- getMapRef() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the mapRef property.
- getName() - Method in class org.sbgn.bindings.Glyph.Entity
-
Gets the value of the name property.
- getName() - Method in enum org.sbgn.Language
-
String representation, suitable for use on the language attribute of the map element in SBGN-ML.
- getNext() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the next property.
- getNotes() - Method in class org.sbgn.bindings.SBGNBase
-
Gets the value of the notes property.
- getOrientation() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the orientation property.
- getPoint() - Method in class org.sbgn.bindings.Arc.End
-
Gets the value of the point property.
- getPoint() - Method in class org.sbgn.bindings.Arc.Next
-
Gets the value of the point property.
- getPoint() - Method in class org.sbgn.bindings.Glyph.Callout
-
Gets the value of the point property.
- getPort() - Method in class org.sbgn.bindings.Arc
-
<?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">
Ports are only allowed in ER.
- getPort() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the port property.
- getResource(String) - Static method in class org.sbgn.SbgnUtil
-
Gets the resource.
- getRuleDescription() - Method in class org.sbgn.schematron.Issue
-
Human readable description of the issue.
- getRuleId() - Method in class org.sbgn.schematron.Issue
-
identifier of the issue.
- getSeverity() - Method in class org.sbgn.schematron.Issue
-
Severity of the issue, i.e.: is it an error, or a warning?
- getSource() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the source property.
- getStart() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the start property.
- getState() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the state property.
- getTagRef() - Method in class org.sbgn.bindings.Glyph
-
Gets the value of the tagRef property.
- getTarget() - Method in class org.sbgn.bindings.Arc
-
Gets the value of the target property.
- getTarget() - Method in class org.sbgn.bindings.Glyph.Callout
-
Gets the value of the target property.
- getText() - Method in class org.sbgn.bindings.Label
-
Gets the value of the text property.
- getValue() - Method in class org.sbgn.bindings.Glyph.State
-
Gets the value of the value property.
- getVariable() - Method in class org.sbgn.bindings.Glyph.State
-
Gets the value of the variable property.
- getVersion() - Method in class org.sbgn.bindings.Map
-
Gets the value of the version property.
- getVersion(File) - Static method in class org.sbgn.SbgnVersionFinder
-
- getW() - Method in class org.sbgn.bindings.Bbox
-
Gets the value of the w property.
- getX() - Method in class org.sbgn.bindings.Arc.End
-
Gets the value of the x property.
- getX() - Method in class org.sbgn.bindings.Arc.Next
-
Gets the value of the x property.
- getX() - Method in class org.sbgn.bindings.Arc.Start
-
Gets the value of the x property.
- getX() - Method in class org.sbgn.bindings.Bbox
-
Gets the value of the x property.
- getX() - Method in class org.sbgn.bindings.Point
-
Gets the value of the x property.
- getX() - Method in class org.sbgn.bindings.Port
-
Gets the value of the x property.
- getY() - Method in class org.sbgn.bindings.Arc.End
-
Gets the value of the y property.
- getY() - Method in class org.sbgn.bindings.Arc.Next
-
Gets the value of the y property.
- getY() - Method in class org.sbgn.bindings.Arc.Start
-
Gets the value of the y property.
- getY() - Method in class org.sbgn.bindings.Bbox
-
Gets the value of the y property.
- getY() - Method in class org.sbgn.bindings.Point
-
Gets the value of the y property.
- getY() - Method in class org.sbgn.bindings.Port
-
Gets the value of the y property.
- glyph - Variable in class org.sbgn.bindings.Arc
-
- glyph - Variable in class org.sbgn.bindings.Arcgroup
-
- Glyph - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- Glyph() - Constructor for class org.sbgn.bindings.Glyph
-
- glyph - Variable in class org.sbgn.bindings.Glyph
-
- glyph - Variable in class org.sbgn.bindings.Map
-
- Glyph.Callout - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- Glyph.Clone - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- Glyph.Entity - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- Glyph.State - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- GlyphClazz - Enum in org.sbgn
-
Enumeration with all possible values for the class attribute of Glyphs in SBGN-ML.
- Sbgn - Class in org.sbgn.bindings
-
Java class for anonymous complex type.
- Sbgn() - Constructor for class org.sbgn.bindings.Sbgn
-
- SBGNBase - Class in org.sbgn.bindings
-
<?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 SBGNBase type is the base type of all main components in SBGN.
- SBGNBase() - Constructor for class org.sbgn.bindings.SBGNBase
-
- SBGNBase.Extension - Class in org.sbgn.bindings
-
<?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 extension element stores extension information like
render information, metadata or annotations.
- SBGNBase.Notes - Class in org.sbgn.bindings
-
<?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 notes element stores notes.
- SbgnUtil - Class in org.sbgn
-
- SbgnUtil() - Constructor for class org.sbgn.SbgnUtil
-
- SbgnVersionFinder - Class in org.sbgn
-
- SbgnVersionFinder() - Constructor for class org.sbgn.SbgnVersionFinder
-
- SchematronValidator - Class in org.sbgn.schematron
-
- setBbox(Bbox) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the bbox property.
- setBbox(Bbox) - Method in class org.sbgn.bindings.Label
-
Sets the value of the bbox property.
- setBbox(Bbox) - Method in class org.sbgn.bindings.Map
-
Sets the value of the bbox property.
- setCallout(Glyph.Callout) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the callout property.
- setClazz(String) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the clazz property.
- setClazz(String) - Method in class org.sbgn.bindings.Arcgroup
-
Sets the value of the clazz property.
- setClazz(String) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the clazz property.
- setClone(Glyph.Clone) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the clone property.
- setCompartmentOrder(Float) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the compartmentOrder property.
- setCompartmentRef(Object) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the compartmentRef property.
- setEnd(Arc.End) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the end property.
- setEntity(Glyph.Entity) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the entity property.
- setExtension(SBGNBase.Extension) - Method in class org.sbgn.bindings.SBGNBase
-
Sets the value of the extension property.
- setH(float) - Method in class org.sbgn.bindings.Bbox
-
Sets the value of the h property.
- setId(String) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the id property.
- setId(String) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the id property.
- setId(String) - Method in class org.sbgn.bindings.Map
-
Sets the value of the id property.
- setId(String) - Method in class org.sbgn.bindings.Port
-
Sets the value of the id property.
- setLabel(Label) - Method in class org.sbgn.bindings.Glyph.Clone
-
Sets the value of the label property.
- setLabel(Label) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the label property.
- setLanguage(String) - Method in class org.sbgn.bindings.Map
-
Sets the value of the language property.
- setMapRef(Object) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the mapRef property.
- setName(String) - Method in class org.sbgn.bindings.Glyph.Entity
-
Sets the value of the name property.
- setNotes(SBGNBase.Notes) - Method in class org.sbgn.bindings.SBGNBase
-
Sets the value of the notes property.
- setOrientation(String) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the orientation property.
- setPoint(Point) - Method in class org.sbgn.bindings.Glyph.Callout
-
Sets the value of the point property.
- setSource(Object) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the source property.
- setStart(Arc.Start) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the start property.
- setState(Glyph.State) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the state property.
- setSvrlDump(boolean) - Static method in class org.sbgn.schematron.SchematronValidator
-
Dump validation report to file
- setTagRef(Object) - Method in class org.sbgn.bindings.Glyph
-
Sets the value of the tagRef property.
- setTarget(Object) - Method in class org.sbgn.bindings.Arc
-
Sets the value of the target property.
- setTarget(Object) - Method in class org.sbgn.bindings.Glyph.Callout
-
Sets the value of the target property.
- setText(String) - Method in class org.sbgn.bindings.Label
-
Sets the value of the text property.
- setValue(String) - Method in class org.sbgn.bindings.Glyph.State
-
Sets the value of the value property.
- setVariable(String) - Method in class org.sbgn.bindings.Glyph.State
-
Sets the value of the variable property.
- setVersion(String) - Method in class org.sbgn.bindings.Map
-
Sets the value of the version property.
- setW(float) - Method in class org.sbgn.bindings.Bbox
-
Sets the value of the w property.
- setX(float) - Method in class org.sbgn.bindings.Arc.End
-
Sets the value of the x property.
- setX(float) - Method in class org.sbgn.bindings.Arc.Next
-
Sets the value of the x property.
- setX(float) - Method in class org.sbgn.bindings.Arc.Start
-
Sets the value of the x property.
- setX(float) - Method in class org.sbgn.bindings.Bbox
-
Sets the value of the x property.
- setX(float) - Method in class org.sbgn.bindings.Point
-
Sets the value of the x property.
- setX(float) - Method in class org.sbgn.bindings.Port
-
Sets the value of the x property.
- setY(float) - Method in class org.sbgn.bindings.Arc.End
-
Sets the value of the y property.
- setY(float) - Method in class org.sbgn.bindings.Arc.Next
-
Sets the value of the y property.
- setY(float) - Method in class org.sbgn.bindings.Arc.Start
-
Sets the value of the y property.
- setY(float) - Method in class org.sbgn.bindings.Bbox
-
Sets the value of the y property.
- setY(float) - Method in class org.sbgn.bindings.Point
-
Sets the value of the y property.
- setY(float) - Method in class org.sbgn.bindings.Port
-
Sets the value of the y property.
- source - Variable in class org.sbgn.bindings.Arc
-
- start - Variable in class org.sbgn.bindings.Arc
-
- Start() - Constructor for class org.sbgn.bindings.Arc.Start
-
- state - Variable in class org.sbgn.bindings.Glyph
-
- State() - Constructor for class org.sbgn.bindings.Glyph.State
-