Package | Description |
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org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
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org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
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org.biopax.paxtools.pattern |
Main package.
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org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
|
org.biopax.paxtools.pattern.util |
Package for several utility classes.
|
Modifier and Type | Class and Description |
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class |
CovalentBindingFeatureImpl |
class |
ModificationFeatureImpl |
Modifier and Type | Method and Description |
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Class<? extends ModificationFeature> |
ModificationFeatureImpl.getModelInterface() |
Modifier and Type | Interface and Description |
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interface |
CovalentBindingFeature
Definition: An entity feature that represent the covalently bound state of a physical entity.
|
Modifier and Type | Method and Description |
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static Pattern |
PatternBox.actChange(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Pattern for the activity of an EntityReference is changed through a Conversion.
|
static Pattern |
PatternBox.actChange(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Pattern for the activity of an EntityReference is changed through a Conversion.
|
Constructor and Description |
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ActivityModificationChangeConstraint(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Constructor with the desired change and maps to activating and inactivating features,
|
ActivityModificationChangeConstraint(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Constructor with the desired change and maps to activating and inactivating features,
|
Modifier and Type | Method and Description |
---|---|
String |
MinerAdapter.getModificationTerm(ModificationFeature mf)
Gets the String term of the modification feature.
|
String |
MinerAdapter.getPositionInString(ModificationFeature mf)
Gets the position of the modification feature as a String.
|
int |
MinerAdapter.getPositionStart(ModificationFeature mf)
Gets the first position of the modification feature.
|
Modifier and Type | Method and Description |
---|---|
Set<String> |
MinerAdapter.toStringSet(Set<ModificationFeature> set)
Sorts the modifications and gets them in a String.
|
Modifier and Type | Method and Description |
---|---|
Set<ModificationFeature> |
PhysicalEntityChain.getModifications()
Collects modifications from the elements of the chain.
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