Package | Description |
---|---|
org.biopax.paxtools.command |
This package contains classes for implementing undoable editing the model.
|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.converter |
This package contains a tools for upgrading BioPAX L1 and L2 to L3.
|
org.biopax.paxtools.examples |
This package contains several examples that uses Paxtools to demonstrate basic functionality.
|
org.biopax.paxtools.io |
This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
|
org.biopax.paxtools.io.jena |
This package contains a Jena bases reader/writer for reading BioPAX files.
|
Modifier and Type | Method and Description |
---|---|
void |
CommandManager.addProperty(BioPAXElement bpe,
PropertyEditor editor,
Object value) |
void |
CommandManager.removeProperty(BioPAXElement bpe,
PropertyEditor editor,
Object value) |
Modifier and Type | Interface and Description |
---|---|
interface |
DataPropertyEditor<D extends BioPAXElement,R>
Created by igor on 13/08/15.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractPropertyEditor<D extends BioPAXElement,R>
This is the base class for all property editors.
|
class |
EnumeratedPropertyEditor<D extends BioPAXElement,R extends Enum>
Provides an ENUM class compatible editor by extending the
PropertyEditor . |
class |
ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement>
Provides an editor for all object value types, e.g.
|
class |
PrimitivePropertyEditor<D extends BioPAXElement,R>
Provides a primitive (int, float, double) class compatible editor by extending the
PropertyEditor . |
class |
StringPropertyEditor<D extends BioPAXElement>
Provides an String class compatible editor by extending the
PropertyEditor . |
Modifier and Type | Field and Description |
---|---|
protected Map<Class<? extends BioPAXElement>,Map<String,PropertyEditor>> |
EditorMapImpl.classToEditorMap
A map from classes to their registered editors.
|
protected Map<Class<? extends BioPAXElement>,Set<PropertyEditor>> |
EditorMapImpl.classToEditorSet
Another map to keep editors as a set rather than a map.
|
static Filter<PropertyEditor> |
Fetcher.evidenceFilter
A property filter to ignore 'evidence' ('EVIDENCE' in L2) property
(it can eventually lead to other organism, experimental entities)
|
static Filter<PropertyEditor> |
Fetcher.nextStepFilter
This property filter can be used to ignore 'nextStep' ('NEXT-STEP' in L2)
property when fetching a sub-graph of child biopax elements, because
using this property can eventually lead outside current pathway context
into peer pathways, etc.
|
static Filter<PropertyEditor> |
Fetcher.objectPropertiesOnlyFilter
A property filter to visit only biopax object type properties.
|
protected Map<String,Set<PropertyEditor>> |
EditorMapImpl.propertyToEditorMap
A map from property names to actual property editors.
|
Modifier and Type | Method and Description |
---|---|
protected PropertyEditor |
EditorMapImpl.createAndRegisterBeanEditor(String pName,
Class domain,
Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> rRestrictions) |
static <D extends BioPAXElement,R> |
AbstractPropertyEditor.createPropertyEditor(Class<D> domain,
String property)
This method creates a property reflecting on the domain and property.
|
<D extends BioPAXElement> |
SimpleEditorMap.getEditorForProperty(String property,
Class<D> javaClass) |
<D extends BioPAXElement> |
EditorMapImpl.getEditorForProperty(String property,
Class<D> javaClass) |
<D extends BioPAXElement> |
EditorMap.getEditorForProperty(String property,
Class<D> javaClass)
This method returns the editor intended to handle
property named property of a class (javaClass).
|
Modifier and Type | Method and Description |
---|---|
Set<PropertyEditor> |
SimpleEditorMap.getEditorsForProperty(String property) |
Set<PropertyEditor> |
EditorMapImpl.getEditorsForProperty(String property) |
Set<PropertyEditor> |
EditorMap.getEditorsForProperty(String property)
This method returns the set of editors intended to handle
property named property.
|
Set<PropertyEditor> |
SimpleEditorMap.getEditorsOf(BioPAXElement bpe) |
Set<PropertyEditor> |
EditorMapImpl.getEditorsOf(BioPAXElement bpe) |
Set<PropertyEditor> |
EditorMap.getEditorsOf(BioPAXElement bpe)
This method returns the set of editors whose domain
subsumes the class of given BioPAX element.
|
Set<PropertyEditor> |
SimpleEditorMap.getEditorsOf(Class<? extends BioPAXElement> domain) |
Set<PropertyEditor> |
EditorMapImpl.getEditorsOf(Class<? extends BioPAXElement> domain) |
Set<PropertyEditor> |
EditorMap.getEditorsOf(Class<? extends BioPAXElement> domain)
This method returns the set of editors whose domain
subsumes the given class
|
<D extends BioPAXElement> |
SimpleEditorMap.getSubclassEditorsForProperty(String property,
Class<D> domain) |
<D extends BioPAXElement> |
EditorMapImpl.getSubclassEditorsForProperty(String property,
Class<D> domain) |
<D extends BioPAXElement> |
EditorMap.getSubclassEditorsForProperty(String property,
Class<D> domain)
This method returns the set of editors intended to handle
property named property.
|
Iterator<PropertyEditor> |
SimpleEditorMap.iterator() |
Iterator<PropertyEditor> |
EditorMapImpl.iterator() |
Iterator<PropertyEditor> |
EditorMap.iterator() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
Traverser.filter(PropertyEditor<?,?> editor) |
protected boolean |
TraverserBilinked.filterInverse(PropertyEditor editor) |
boolean |
PropertyFilterBilinked.filterInverse(PropertyEditor editor) |
protected void |
EditorMapImpl.registerEditorsWithSubClasses(PropertyEditor editor,
Class<? extends BioPAXElement> domain)
This method registers an editor with sub classes - i.e.
|
protected void |
Traverser.traverseElements(BioPAXElement element,
Model model,
PropertyEditor<?,?> editor,
Set<?> valueSet) |
void |
ShallowCopy.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor editor)
An implementation of this method should perform a BioPAX element
and editor dependent operation on the model.
|
void |
Merger.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor editor)
Checks whether model contains bpe element, and if it does, then it updates the
value of the equivalent element for bpe by using the specific editor.
|
void |
Completer.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor editor) |
void |
Cloner.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor editor) |
void |
Visitor.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor<?,?> editor)
An implementation of this method should perform a BioPAX element
and editor dependent operation on the model.
|
void |
AbstractTraverser.visit(BioPAXElement domain,
Object range,
Model model,
PropertyEditor<?,?> editor)
Calls the protected abstract method visit that is to be
implemented in subclasses of this abstract class.
|
protected abstract void |
AbstractTraverser.visit(Object range,
BioPAXElement domain,
Model model,
PropertyEditor<?,?> editor)
This is to implement a real action here:
do something, return or even to continue (traverse)
into the child (range) element's properties if it's a BioPAX object.
|
Modifier and Type | Method and Description |
---|---|
protected void |
LevelUpgrader.visit(Object value,
BioPAXElement parent,
Model newModel,
PropertyEditor editor) |
Modifier and Type | Method and Description |
---|---|
void |
PathwayGenesExtractor.visit(BioPAXElement domain1,
Object range,
Model model,
PropertyEditor editor) |
Modifier and Type | Method and Description |
---|---|
protected void |
BioPAXIOHandlerAdapter.bindValue(String valueString,
PropertyEditor editor,
BioPAXElement bpe,
Model model)
This method binds the value to the bpe.
|
protected BioPAXElement |
BioPAXIOHandlerAdapter.L1ToL2Fixes(PropertyEditor editor,
BioPAXElement bpe,
Model model,
String value)
Deprecated.
BioPAX Level 1 exports are extremely rare and obsolete.
|
Modifier and Type | Method and Description |
---|---|
com.hp.hpl.jena.datatypes.xsd.XSDDatatype |
JenaEditorMap.getDataTypeFor(PropertyEditor editor) |
Copyright © 2015 BioPAX. All rights reserved.