Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.util |
This package contains various collections and utilities that is used by the other packages and modules of paxtools.
|
Modifier and Type | Interface and Description |
---|---|
interface |
PropertyFilterBilinked
A generic interface for bidirectional property filter
|
Modifier and Type | Field and Description |
---|---|
static Filter<PropertyEditor> |
Fetcher.evidenceFilter
A property filter to ignore 'evidence' ('EVIDENCE' in L2) property
(it can eventually lead to other organism, experimental entities)
|
protected Filter<PropertyEditor>[] |
Traverser.filters |
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.
|
Modifier and Type | Method and Description |
---|---|
static Model |
ModelUtils.getAllChildren(BioPAXElement bpe,
Filter<PropertyEditor>... filters)
Gets all the child BioPAX elements of a given BioPAX element
(using the "tuned"
Fetcher ) and adds them to a
new model. |
static Set<String> |
ModelUtils.getKeywords(BioPAXElement biopaxElement,
int depth,
Filter<DataPropertyEditor>... dataPropertyFilters)
Collects data type (not object) property
values (can be then used for full-text indexing).
|
Constructor and Description |
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AbstractTraverser(EditorMap editorMap,
Filter<PropertyEditor>... filters) |
Fetcher(EditorMap editorMap,
Filter<PropertyEditor>... filters)
Constructor.
|
SimpleMerger(EditorMap map,
Filter<BioPAXElement> mergeObjPropOf) |
Traverser(EditorMap editorMap,
Visitor visitor,
Filter<PropertyEditor>... filters)
The full constructor.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractFilterSet<F,E>
Base class for implementing various filter sets.
|
class |
ClassFilterSet<E,F extends E>
A FilterSet that filters based on the class.
|
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