Package | Description |
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org.biopax.paxtools.pattern |
Main package.
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org.biopax.paxtools.pattern.constraint |
Package for constraints.
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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 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.
|
static Map<BioPAXElement,List<Match>> |
Searcher.search(Model model,
Pattern pattern,
ProgressWatcher prg)
Searches the given pattern in the given model.
|
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.
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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.
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static List<Match> |
Searcher.searchRecursive(Match match,
List<MappedConst> mc,
int index)
Continues searching with the mapped constraint at the given index.
|
Modifier and Type | Method and Description |
---|---|
Collection<BioPAXElement> |
MappedConst.generate(Match match,
int... outer)
Calls generate method of the constraint with index translation.
|
Collection<BioPAXElement> |
Constraint.generate(Match match,
int... ind)
Generates candidate values for the variable to be generated.
|
boolean |
MappedConst.satisfies(Match match,
int... outer)
Directs to satisfies method of the wrapped constraint with index translation.
|
boolean |
Constraint.satisfies(Match match,
int... ind)
Checks if the variables in the Match satisfies this constraint.
|
static List<Match> |
Searcher.search(Match m,
Pattern pattern)
Searches the pattern starting from the given match.
|
static List<Match> |
Searcher.searchRecursive(Match match,
List<MappedConst> mc,
int index)
Continues searching with the mapped constraint at the given index.
|
Modifier and Type | Method and Description |
---|---|
Collection<BioPAXElement> |
XOR.generate(Match match,
int... ind)
Gets xor of the generated elements by the member constraints.
|
Collection<BioPAXElement> |
SelfOrThis.generate(Match match,
int... ind)
Gets the first mapped element along with the generated elements of wrapped constraint.
|
Collection<BioPAXElement> |
RelatedControl.generate(Match match,
int... ind)
According to the relation between PhysicalEntity and the Conversion, checks of the Control is
relevant.
|
Collection<BioPAXElement> |
PathConstraint.generate(Match match,
int... ind)
Uses the encapsulated PAthAccessor to generate satisfying elements.
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Collection<BioPAXElement> |
ParticipatingPE.generate(Match match,
int... ind)
Deprecated.
First evaluates the direction that the Control is affecting the Conversion, then gets the
related participants.
|
Collection<BioPAXElement> |
ParticipatesInConv.generate(Match match,
int... ind)
Identifies the conversion direction and gets the related participants.
|
Collection<BioPAXElement> |
Participant.generate(Match match,
int... ind)
Identifies the conversion direction and gets the related participants.
|
Collection<BioPAXElement> |
OtherSide.generate(Match match,
int... ind)
Deprecated.
Checks which side is the first PhysicalEntity, and gathers participants on the other side.
|
Collection<BioPAXElement> |
OR.generate(Match match,
int... ind)
Gets the intersection of the generated values of wrapped constraints.
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Collection<BioPAXElement> |
LinkedPE.generate(Match match,
int... ind)
Gets to the linked PhysicalEntity.
|
Collection<BioPAXElement> |
InterToPartER.generate(Match match,
int... ind)
Iterated over non-taboo participants and collectes related ER.
|
Collection<BioPAXElement> |
ConversionSide.generate(Match match,
int... ind)
Checks which side is the first PhysicalEntity, and gathers participants on either the other
side or the same side.
|
Collection<BioPAXElement> |
ConstraintChain.generate(Match match,
int... ind)
Chains the member constraints and returns the output of the last constraint.
|
Collection<BioPAXElement> |
ConstraintAdapter.generate(Match match,
int... ind)
This method has to be overridden by generative constraints.
|
Collection<BioPAXElement> |
AND.generate(Match match,
int... ind)
Gets intersection of the generated elements by the member constraints.
|
boolean |
XOR.satisfies(Match match,
int... ind)
Checks if constraints satisfy in xor pattern.
|
boolean |
Type.satisfies(Match match,
int... ind)
Checks if the element is assignable to a variable of the desired type.
|
boolean |
Size.satisfies(Match match,
int... ind)
Checks if generated element size is in limits.
|
boolean |
SelfOrThis.satisfies(Match match,
int... ind)
Checks if the last index is either generated or equal to the first element.
|
boolean |
PEChainsIntersect.satisfies(Match match,
int... ind)
Creates two PhysicalEntity chains with the given endpoints, and checks if they are
intersecting.
|
boolean |
PathConstraint.satisfies(Match match,
int... ind)
Checks if the PathAccessor is generating the second mapped element.
|
boolean |
OR.satisfies(Match match,
int... ind)
Checks if any of the wrapped constraints satisfy.
|
boolean |
NOT.satisfies(Match match,
int... ind)
Negates the satisfies value of the wrapped constraint.
|
boolean |
NonUbique.satisfies(Match match,
int... ind) |
boolean |
ModificationChangeConstraint.satisfies(Match match,
int... ind)
Checks the any of the changed modifications match to any of the desired modifications.
|
boolean |
IDConstraint.satisfies(Match match,
int... ind)
Checks if the element has one of the desired IDs.
|
boolean |
HasAnID.satisfies(Match match,
int... ind)
Checks if the element has one of the desired IDs.
|
boolean |
FieldOfMultiple.satisfies(Match match,
int... ind)
Checks if the generated elements from the first mapped element has either the desired value,
or has some value in common with the elements generated from second mapped element.
|
boolean |
Field.satisfies(Match match,
int... ind)
Checks if the element in the first index has the desired value.
|
boolean |
Equality.satisfies(Match match,
int... ind)
Checks if the two elements are identical or not identical as desired.
|
boolean |
Empty.satisfies(Match match,
int... ind)
Checks if the wrapped Constraint can generate any elements.
|
boolean |
ControlsNotParticipant.satisfies(Match match,
int... ind)
Checks if the controlled Interaction contains a controller as a participant.
|
boolean |
ConstraintAdapter.satisfies(Match match,
int... ind)
Use this method only if constraint canGenerate, and satisfaction criteria is that simple.
|
boolean |
AND.satisfies(Match match,
int... ind)
Checks if all the constraints satisfy.
|
boolean |
ActivityModificationChangeConstraint.satisfies(Match match,
int... ind)
Checks the gained and and lost features to predict the activity change is the desired change.
|
boolean |
ActivityConstraint.satisfies(Match match,
int... ind)
Checks if the PhysicalEntity controls anything.
|
Modifier and Type | Method and Description |
---|---|
Set<SIFInteraction> |
SIFMiner.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates SIF interactions for the given match.
|
Set<SIFInteraction> |
MinerAdapter.createSIFInteraction(Match m,
IDFetcher fetcher)
Creates a SIF interaction for the given match.
|
protected Set<String> |
MinerAdapter.getCellularLocations(Match m,
String memLabel,
String comLabel)
Gets cellular locations of the given elements in a string set.
|
protected PhysicalEntityChain |
MinerAdapter.getChain(Match m,
String memLabel,
String comLabel) |
protected Set<String>[] |
MinerAdapter.getDeltaCompartments(Match m,
String memLabel1,
String comLabel1,
String memLabel2,
String comLabel2)
Gets delta compartments of the given two PE chains.
|
protected Set<String>[] |
MinerAdapter.getDeltaModifications(Match m,
String memLabel1,
String comLabel1,
String memLabel2,
String comLabel2)
Gets delta modifications of the given elements in string sets.
|
protected String |
MinerAdapter.getGeneSymbol(Match m,
String label)
Searches for the gene symbol of the given EntityReference.
|
Set<String> |
MinerAdapter.getIdentifiers(Match m,
String label)
Uses uniprot name or gene symbol as identifier.
|
protected Set<String> |
MinerAdapter.getModifications(Match m,
String label)
Gets modifications of the given element in a string.
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protected Set<String> |
MinerAdapter.getModifications(Match m,
String memLabel,
String comLabel)
Gets modifications of the given elements in a string set.
|
protected String |
MinerAdapter.getUniprotNameForHuman(Match m,
String label)
Searches for the uniprot name of the given human EntityReference.
|
String |
UbiquitousIDMiner.getValue(Match m,
int col)
Gets the ids of the small molecule reference and its physical entities.
|
String |
MinerAdapter.getValue(Match m,
int col)
This method has to be overridden if
writeResultDetailed method is used. |
String |
ControlsStateChangeDetailedMiner.getValue(Match m,
int col)
Creates values for the result file columns.
|
protected boolean |
MinerAdapter.labeledInactive(Match m,
String simpleLabel,
String complexLabel)
Checks if a PE chain is labeled as inactive.
|
protected int |
MinerAdapter.sign(Match m,
String... ctrlLabel)
Checks the cumulative sign of the chained controls.
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Modifier and Type | Method and Description |
---|---|
void |
UbiquitousIDMiner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
|
void |
RelatedGenesOfInteractionsMiner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the IDs of interaction, then gene symbols of related proteins in a line.
|
void |
Miner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the text output to the given stream.
|
void |
DirectedRelationMiner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
|
void |
ControlsStateChangeDetailedMiner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the result as "A modifications-of-A B gains-of-B loss-of-B", where A and B are gene
symbols, and whitespace is tab.
|
void |
AbstractSIFMiner.writeResult(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
Writes the result as "A used-for-production-of B", where A and B are small molecule names,
and whitespace is tab.
|
void |
MinerAdapter.writeResultAsSIF(Map<BioPAXElement,List<Match>> matches,
OutputStream out,
boolean directed,
String label1,
String label2)
This method writes the output as pairs of gene symbols of the given two ProteinReference.
|
void |
MinerAdapter.writeResultDetailed(Map<BioPAXElement,List<Match>> matches,
OutputStream out,
int columns)
Writes the result as a tab delimited format, where the column values are customized.
|
void |
MinerAdapter.writeSIFsUsingSIFFramework(Map<BioPAXElement,List<Match>> matches,
OutputStream out)
This method writes the output as pairs of gene symbols of the given two ProteinReference.
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Copyright © 2015 BioPAX. All rights reserved.