Package | Description |
---|---|
org.biopax.paxtools.pattern |
Main package.
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org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
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Modifier and Type | Method and Description |
---|---|
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.bindsTo()
Finds two Protein that appear together in a Complex.
|
static Pattern |
PatternBox.catalysisPrecedes(Blacklist blacklist)
Pattern for detecting two EntityReferences are controlling consecutive reactions, where
output of one reaction is input to the other.
|
static Pattern |
PatternBox.chemicalAffectsProteinThroughBinding(Blacklist blacklist)
A small molecule is in a complex with a protein.
|
static Pattern |
PatternBox.chemicalAffectsProteinThroughControl()
A small molecule controls an interaction of which the protein is a participant.
|
static Pattern |
PatternBox.controlsDegradationIndirectly()
Finds cases where protein A changes state of B, and B is then degraded.
|
static Pattern |
PatternBox.controlsExpressionWithConversion()
Finds the cases where transcription relation is shown using a Conversion instead of a
TemplateReaction.
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static Pattern |
PatternBox.controlsExpressionWithTemplateReac()
Finds transcription factors that trans-activate or trans-inhibit an entity.
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static Pattern |
PatternBox.controlsMetabolicCatalysis(Blacklist blacklist,
boolean consumption)
Pattern for a Protein controlling a reaction whose participant is a small molecule.
|
static Pattern |
PatternBox.controlsPhosphorylation() |
static Pattern |
PatternBox.controlsStateChange()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
|
static Pattern |
PatternBox.controlsStateChangeBothControlAndPart()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
|
static Pattern |
PatternBox.controlsStateChangeButIsParticipant()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
|
static Pattern |
PatternBox.controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist)
Pattern for an entity is producing a small molecule, and the small molecule controls state
change of another molecule.
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static Pattern |
PatternBox.controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist)
Pattern for an entity is producing a small molecule, and the small molecule controls state
change of another molecule.
|
static Pattern |
PatternBox.controlsStateChangeThroughDegradation()
Finds cases where proteins affect their degradation.
|
static Pattern |
PatternBox.controlsTransport()
Pattern for a ProteinReference has a member PhysicalEntity that is controlling a
transportation of another ProteinReference.
|
static Pattern |
PatternBox.controlsTransportOfChemical(Blacklist blacklist)
Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction
that changes cellular location of a small molecule.
|
static Pattern |
PatternBox.hasNonSelfEffect()
Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not
associated with the EntityReference of the initial PhysicalEntity.
|
static Pattern |
PatternBox.inComplexWith()
Two proteins have states that are members of the same complex.
|
static Pattern |
PatternBox.inSameActiveComplex()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex has an activity.
|
static Pattern |
PatternBox.inSameComplex()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
|
static Pattern |
PatternBox.inSameComplexEffectingConversion()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex is controlling a Conversion.
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static Pattern |
PatternBox.inSameComplexHavingTransActivity()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex has transcriptional activity.
|
static Pattern |
PatternBox.modifiedPESimple()
Pattern for an EntityReference has distinct PhysicalEntities associated with both left and
right of a Conversion.
|
static Pattern |
PatternBox.modifierConv()
Pattern for finding Conversions that an EntityReference is participating.
|
static Pattern |
PatternBox.molecularInteraction()
Constructs a pattern where first and last molecules are participants of a
MolecularInteraction.
|
static Pattern |
PatternBox.neighborOf()
Constructs a pattern where first and last proteins are related through an interaction.
|
static Pattern |
PatternBox.peInOut() |
static Pattern |
PatternBox.reactsWith(Blacklist blacklist)
Constructs a pattern where first and last small molecules are substrates to the same
biochemical reaction.
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static Pattern |
PatternBox.relatedProteinRefOfInter(Class<? extends Interaction>... seedType)
Finds ProteinsReference related to an interaction.
|
static Pattern |
PatternBox.stateChange(Pattern p,
String ctrlLabel)
Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that
belongs to the same EntityReference.
|
static Pattern |
PatternBox.usedToProduce(Blacklist blacklist)
Constructs a pattern where first small molecule is an input a biochemical reaction that
produces the second small molecule.
|
Modifier and Type | Method and Description |
---|---|
void |
Pattern.add(Pattern p)
Appends the constraints in the parameter pattern to the desired location.
|
List<BioPAXElement> |
Match.get(String[] label,
Pattern p)
Gets elements corresponding to the given labels in the pattern.
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BioPAXElement |
Match.get(String label,
Pattern p)
Gets element corresponding to the given label in the pattern.
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boolean |
Searcher.hasSolution(Pattern p,
BioPAXElement... ele)
Checks if there is any match for the given pattern if search starts from the given element.
|
static List<Match> |
Searcher.search(BioPAXElement ele,
Pattern pattern)
Searches the pattern starting from the given element.
|
static Map<BioPAXElement,List<Match>> |
Searcher.search(Collection<? extends BioPAXElement> eles,
Pattern pattern)
Searches the given pattern starting from the given elements.
|
static List<Match> |
Searcher.search(Match m,
Pattern pattern)
Searches the pattern starting from the given match.
|
static Map<BioPAXElement,List<Match>> |
Searcher.search(Model model,
Pattern pattern)
Searches the given pattern in the given model.
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static Map<BioPAXElement,List<Match>> |
Searcher.search(Model model,
Pattern pattern,
ProgressWatcher prg)
Searches the given pattern in the given model.
|
static <T extends BioPAXElement> |
Searcher.searchAndCollect(BioPAXElement ele,
Pattern pattern,
int index,
Class<T> c)
Searches the given pattern starting from the given element, then collects the specified
elements of the matches and returns.
|
static <T extends BioPAXElement> |
Searcher.searchAndCollect(Collection<? extends BioPAXElement> eles,
Pattern pattern,
int index,
Class<T> c)
Searches the given pattern starting from the given elements, then collects the specified
elements of the matches and returns.
|
static <T extends BioPAXElement> |
Searcher.searchAndCollect(Model model,
Pattern pattern,
int index,
Class<T> c)
Searches a model for the given pattern, then collects the specified elements of the matches
and returns.
|
static void |
Searcher.searchInFile(Pattern p,
String inFile,
String outFile)
Searches a pattern reading the model from the given file, and creates another model that is
excised using the matching patterns.
|
static void |
Searcher.searchInFile(Pattern p,
String inFile,
String outFile,
int seedLimit,
int graphPerSeed)
Searches a pattern reading the model from the given file, and creates another model that is
excised using the matching patterns.
|
static List<Match> |
Searcher.searchPlain(Collection<? extends BioPAXElement> eles,
Pattern pattern)
Searches the pattern starting from given elements, but instead of a match map, returns all
matches in a list.
|
static List<Match> |
Searcher.searchPlain(Model model,
Pattern pattern)
Searches the pattern in a given model, but instead of a match map, returns all matches in a
list.
|
static Pattern |
PatternBox.stateChange(Pattern p,
String ctrlLabel)
Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that
belongs to the same EntityReference.
|
Modifier and Type | Field and Description |
---|---|
protected Pattern |
MinerAdapter.pattern
Pattern to use for mining.
|
Modifier and Type | Method and Description |
---|---|
Pattern |
UsedToProduceMiner.constructPattern()
Constructs the pattern.
|
Pattern |
UbiquitousIDMiner.constructPattern()
Constructs the pattern.
|
Pattern |
RelatedGenesOfInteractionsMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ReactsWithMiner.constructPattern()
Constructs the pattern.
|
Pattern |
NeighborOfMiner.constructPattern()
Constructs the pattern.
|
abstract Pattern |
MinerAdapter.constructPattern()
Constructs the pattern to use for mining.
|
Pattern |
InteractsWithMiner.constructPattern()
Constructs the pattern.
|
Pattern |
InComplexWithMiner.constructPattern()
Constructs the pattern.
|
Pattern |
DirectedRelationMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CSCOThroughDegradationMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CSCOThroughControllingSmallMoleculeMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CSCOThroughBindingSmallMoleculeMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CSCOButIsParticipantMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CSCOBothControllerAndParticipantMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsTransportOfChemicalMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsTransportMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsStateChangeOfMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsStateChangeDetailedMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsProductionOfMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsPhosphorylationMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsExpressionWithConvMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsExpressionMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ControlsDegradationIndirectMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ConsumptionControlledByMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ChemicalAffectsThroughControlMiner.constructPattern()
Constructs the pattern.
|
Pattern |
ChemicalAffectsThroughBindingMiner.constructPattern()
Constructs the pattern.
|
Pattern |
CatalysisPrecedesMiner.constructPattern()
Constructs the pattern.
|
Pattern |
MinerAdapter.getPattern()
Gets the pattern, constructs if null.
|
Pattern |
Miner.getPattern()
Gets the pattern to use for mining the graph.
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Copyright © 2015 BioPAX. All rights reserved.