Package | Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractTraverser
This is an all-in-one Traverser/Visitor combination
to use when deep recursive visiting is required.
|
class |
Cloner
Specifically "Clones" the BioPAX elements set
(traverses to obtain dependent elements),
puts them to the new model using the visitor and traverser framework;
ignores elements that are not in the source list (compare to
Fetcher ) |
class |
Completer
This class is used for getting a valid subgraph from a set of BioPAX elements.
|
class |
Merger
Utility class to merge multiple biopax models into one.
|
class |
ShallowCopy
"Clones" a BioPAX element - using direct properties and dependent children only.
|
Modifier and Type | Field and Description |
---|---|
protected Visitor |
Traverser.visitor |
Modifier and Type | Method and Description |
---|---|
Visitor |
Traverser.getVisitor() |
Modifier and Type | Method and Description |
---|---|
void |
Traverser.setVisitor(Visitor visitor) |
Constructor and Description |
---|
Traverser(EditorMap editorMap,
Visitor visitor,
Filter<PropertyEditor>... filters)
The full constructor.
|
TraverserBilinked(EditorMap editorMap,
Visitor visitor,
PropertyFilterBilinked... filters)
Constructor.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelUpgrader
Upgrades BioPAX L1 and L2 to Level 3.
|
Modifier and Type | Class and Description |
---|---|
class |
PathwayGenesExtractor
Prints all the genes (aka proteins) in the L2 pathway
and sub-pathways (*conditions apply), and also - trace
where they come from.
|
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