Index (BioPAX Pattern Search 5.2.2 API)

A B C D E F G H I K L M N O P R S T U V W X
All Classes and Interfaces|All Packages|Serialized Form

A

AbstractSIFMiner - Class in org.biopax.paxtools.pattern.miner: Base class for SIF Miners.
AbstractSIFMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Constructor with interaction type.
AbstractSIFMiner(SIFType, String, String) - Constructor for class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs.
access(PathAccessor, Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).
actChange(boolean, Map<EntityReference, Set<ModificationFeature>>, Map<EntityReference, Set<ModificationFeature>>) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for the activity of an EntityReference is changed through a Conversion.
actionPerformed(ActionEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog: Performs interactive operations.
ACTIVE - Enum constant in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity
ActivityConstraint - Class in org.biopax.paxtools.pattern.constraint: Checks if the PhysicalEntity controls anything.
ActivityConstraint(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.ActivityConstraint: Constructor with the desired activity.
ActivityModificationChangeConstraint - Class in org.biopax.paxtools.pattern.constraint: This is a very specialized constraint that checks if two PhysicalEntity of the same EntityReference have differential features, such that we can predict an activity change based on gain or loss of these features.
ActivityModificationChangeConstraint(boolean, Map<EntityReference, Set<ModificationFeature>>, Map<EntityReference, Set<ModificationFeature>>) - Constructor for class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Constructor with the desired change and maps to activating and inactivating features,
add(Constraint, String...) - Method in class org.biopax.paxtools.pattern.Pattern: Creates a mapped constraint with the given generative constraint and the indexes it applies.
add(Pattern) - Method in class org.biopax.paxtools.pattern.Pattern: Appends the constraints in the parameter pattern to the desired location.
addEntry(String, int, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Adds a new blacklisted ID.
AdjacencyMatrix - Class in org.biopax.paxtools.pattern.util: Adjacency matrix representation of a graph.
AdjacencyMatrix(boolean[][], List<String>) - Constructor for class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Constructor with contents.
AND - Class in org.biopax.paxtools.pattern.constraint: Used for getting logical AND of a set of constraints.
AND(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.AND: Constructor with the mapped constraints.
ANY - Enum constant in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction
ANY - Enum constant in enum class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type
assertIndLength(int[]) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Asserts the size of teh parameter array is equal to the variable size.

B

bindsTo() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds two Protein that appear together in a Complex.
blacklist - Variable in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Blacklist to detect ubiquitous small molecules.
blacklist - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Blacklist for identifying ubiquitous small molecules.
Blacklist - Class in org.biopax.paxtools.pattern.util: A blacklist is used for not using ubiquitous small molecules in patterns.
Blacklist() - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor for a blank blacklist.
Blacklist(InputStream) - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor with resource input stream.
Blacklist(String) - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor with resource file name.
BlacklistGenerator - Class in org.biopax.paxtools.pattern.miner: This class generates a blacklist for the given model.
BlacklistGenerator() - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Default constructor.
BlacklistGenerator(BlacklistGenerator.Decider) - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Constructor with decider.
BlacklistGenerator2 - Class in org.biopax.paxtools.pattern.miner: This class generates a blacklist for the given model.
BlacklistGenerator2() - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator2: Default constructor.
BlacklistGenerator2(BlacklistGenerator2.Decider) - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator2: Constructor with decider.
BlacklistGenerator3 - Class in org.biopax.paxtools.pattern.miner: This class generates a blacklist for the given model.
BlacklistGenerator3() - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator3: Default Constructor.
BlacklistGenerator3(InputStream) - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator3: Constructor.
BOTH - Enum constant in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity
BOTHSIDERS - Enum constant in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction

C

canGenerate() - Method in interface org.biopax.paxtools.pattern.Constraint: Tells if this constraint is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Specifies if the constraint is generative.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ControlToControllerER: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ConversionSide: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.Empty: Cannot generate
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.OR: Can generate only if all of the wrapped constraints are generative.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.Participant: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.RelatedControl: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.MappedConst: Can generate only if the wrapped constraint is generative.
CATALYSIS_PRECEDES - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
catalysisPrecedes(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for detecting two EntityReferences are controlling consecutive reactions, where output of one reaction is input to the other.
CatalysisPrecedesMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the catalysis-precedes pattern.
CatalysisPrecedesMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner: Constructor that sets name and description.
checkActivityLabel() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if the chain has a member with an activity label.
chemDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher: Set to prefer collecting chemical IDs of such Xrefs where the small molecules db starts with or equals given string, ignoring case.
CHEMICAL_AFFECTS - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
chemicalAffectsProteinThroughBinding(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: A small molecule is in a complex with a protein.
chemicalAffectsProteinThroughControl() - Static method in class org.biopax.paxtools.pattern.PatternBox: A small molecule controls an interaction of which the protein is a participant.
ChemicalAffectsThroughBindingMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the chemical-affects-protein pattern.
ChemicalAffectsThroughBindingMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner: Constructor that sets name and description.
ChemicalAffectsThroughControlMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the chemical-affects-protein pattern.
ChemicalAffectsThroughControlMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner: Constructor that sets name and description.
ChemicalNameNormalizer - Class in org.biopax.paxtools.pattern.util: This class is used for finding a standard name for a small molecule.
ChemicalNameNormalizer(Model) - Constructor for class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer: Constructor that also infers all the mapping.
clone() - Method in class org.biopax.paxtools.pattern.Match: Clones a match.
collectChangedPhosphorylationSites(PhysicalEntity, PhysicalEntity, boolean) - Static method in class org.biopax.paxtools.pattern.util.DifferentialModificationUtil
COMMENTS - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
CommonIDFetcher - Class in org.biopax.paxtools.pattern.miner: Tries to get Gene Symbols or UniProt IDs for genes and - display names for small molecules; This id-fetcher is mainly to use with the BioPAX pathway data from Pathway Commons (PC2) db (normalized and enriched with xrefs).
CommonIDFetcher() - Constructor for class org.biopax.paxtools.pattern.miner.CommonIDFetcher
compareTo(Object) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
complexes() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to its parent Complex recursively.
complexMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex to its members recursively (also getting member of the inner complexes).
compToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex or SimplePhysicalEntity to the related EntityReference.
con1 - Variable in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Generative constraint for first group of generated elements, to use on first mapped element.
con2 - Variable in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Generative constraint for second group of generated elements, to use on second mapped element.
ConBox - Class in org.biopax.paxtools.pattern.constraint: Some predefined constraints.
ConBox() - Constructor for class org.biopax.paxtools.pattern.constraint.ConBox
concat(Set<String>, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Converts the set of string to a single string.
ConfigurableIDFetcher - Class in org.biopax.paxtools.pattern.miner: Tries to get preferred type IDs of an entity reference.
ConfigurableIDFetcher() - Constructor for class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher: Constructor.
Constraint - Interface in org.biopax.paxtools.pattern: A constraint to check if a set of variables satisfy the requirements.
ConstraintAdapter - Class in org.biopax.paxtools.pattern.constraint: This is a base class for a Constraint.
ConstraintAdapter() - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Empty constructor.
ConstraintAdapter(int) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Constructor with size.
ConstraintAdapter(int, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Constructor with size.
ConstraintChain - Class in org.biopax.paxtools.pattern.constraint: Used for using several constraints as a chain.
ConstraintChain(Constraint...) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintChain: Constructor with the chained constraints.
constraints - Variable in class org.biopax.paxtools.pattern.Pattern: List of mapped constraints.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsPhosphorylationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Constructs the pattern to use for mining.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner: Constructs the pattern.
CONSUMPTION_CONTROLLED_BY - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
ConsumptionControlledByMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the consumption-controlled-by pattern.
ConsumptionControlledByMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructor that sets name and description.
ConsumptionControlledByMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructor for extension purposes.
controlled() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Process
controllerPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controller PhysicalEntity
CONTROLS_EXPRESSION_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
CONTROLS_PHOSPHORYLATION_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
CONTROLS_PRODUCTION_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
CONTROLS_STATE_CHANGE_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
CONTROLS_TRANSPORT_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
CONTROLS_TRANSPORT_OF_CHEMICAL - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
controlsConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the controlled Conversion, skipping the middle Control.
controlsDegradationIndirectly() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds cases where protein A changes state of B, and B is then degraded.
ControlsDegradationIndirectMiner - Class in org.biopax.paxtools.pattern.miner: Yet another miner for the controls-degradation pattern.
ControlsDegradationIndirectMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner: Constructor that sets name and description.
ControlsExpressionMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the transcriptional regulation pattern.
ControlsExpressionMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructor that sets name and description.
ControlsExpressionMiner(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructor for extending this class.
controlsExpressionWithConversion() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds the cases where transcription relation is shown using a Conversion instead of a TemplateReaction.
ControlsExpressionWithConvMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the transcriptional regulation pattern, modeled using Conversion.
ControlsExpressionWithConvMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner: Constructor that sets name and description.
controlsExpressionWithTemplateReac() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds transcription factors that trans-activate or trans-inhibit an entity.
controlsInteraction() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the controlled Interaction, skipping the middle Control.
controlsMetabolicCatalysis(Blacklist, boolean) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a Protein controlling a reaction whose participant is a small molecule.
ControlsNotParticipant - Class in org.biopax.paxtools.pattern.constraint: Checks if a controller of this Control is also a participant of the controlled interactions.
ControlsNotParticipant() - Constructor for class org.biopax.paxtools.pattern.constraint.ControlsNotParticipant: Constructor.
controlsPhosphorylation() - Static method in class org.biopax.paxtools.pattern.PatternBox
ControlsPhosphorylationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-phosphorylation pattern.
ControlsPhosphorylationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsPhosphorylationMiner: Constructor that sets the type.
ControlsProductionOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-production-of pattern.
ControlsProductionOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner: Constructor that sets name, description and type.
controlsStateChange() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
controlsStateChangeBothControlAndPart() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
controlsStateChangeButIsParticipant() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
ControlsStateChangeDetailedMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change-detailed pattern.
ControlsStateChangeDetailedMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Constructor that sets name and description.
ControlsStateChangeOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
ControlsStateChangeOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Empty constructor.
ControlsStateChangeOfMiner(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructor for extension purposes.
ControlsStateChangeOfMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructor for extension purposes.
controlsStateChangeThroughBindingSmallMolecule(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
controlsStateChangeThroughControllerSmallMolecule(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
controlsStateChangeThroughDegradation() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds cases where proteins affect their degradation.
controlsTransport() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a ProteinReference has a member PhysicalEntity that is controlling a transportation of another ProteinReference.
ControlsTransportMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-transport pattern.
ControlsTransportMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsTransportMiner: Constructor that sets name and description.
controlsTransportOfChemical(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule.
ControlsTransportOfChemicalMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-transport-of-chemical pattern.
ControlsTransportOfChemicalMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner: Constructor that sets name and description.
ControlToControllerER - Class in org.biopax.paxtools.pattern.constraint: This constraint is used to collect related EntityReference of the controllers of a Control.
ControlToControllerER() - Constructor for class org.biopax.paxtools.pattern.constraint.ControlToControllerER: Constructor.
controlToConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Conversion, traversing downstream Controls recursively.
controlToInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Interaction, traversing downstream Controls recursively.
controlToTempReac() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
ConversionSide - Class in org.biopax.paxtools.pattern.constraint: Given Conversion and its one of the participants (at the left or right), traverses to either the participants at the other side or the same side.
ConversionSide(ConversionSide.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.ConversionSide: Constructor.
ConversionSide(ConversionSide.Type, Blacklist, RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.ConversionSide: Constructor.
ConversionSide.Type - Enum Class in org.biopax.paxtools.pattern.constraint: This enum tells if the user want to traverse towards other side of the conversion or stay at the same side.
convert(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.CustomFormat: Prepares the line in the output file for the given interaction.
convert(SIFInteraction) - Method in interface org.biopax.paxtools.pattern.miner.SIFToText: Creates the textual data corresponding to the given binary interaction.
convertStepDirection(StepDirection) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter
convertToAdjacencyMatrix(Collection<SIFInteraction>, SIFType...) - Static method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Converts the given collection of interactions into an adjacency matrix.
convToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to the upstream Control (and its upstream Control recursively).
convToController() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to the controller of the upstream Control (and its upstream Control recursively).
createSIFInteraction(Match, IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Creates a SIF interaction for the given match.
createSIFInteraction(Match, IDFetcher) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Creates SIF interactions for the given match.
CSCOBothControllerAndParticipantMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOBothControllerAndParticipantMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner: Constructor that sets name and description.
CSCOButIsParticipantMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOButIsParticipantMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner: Constructor that sets name and description.
CSCOThroughBindingSmallMoleculeMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOThroughBindingSmallMoleculeMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner: Constructor that sets name and description.
CSCOThroughControllingSmallMoleculeMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOThroughControllingSmallMoleculeMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner: Constructor that sets name and description.
CSCOThroughDegradationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the degradation pattern.
CSCOThroughDegradationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner: Constructor that sets name and description.
CUSTOM - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
CustomFormat - Class in org.biopax.paxtools.pattern.miner: Used for customizing the columns in the SIF text output.
CustomFormat(String...) - Constructor for class org.biopax.paxtools.pattern.miner.CustomFormat

D

DeltaFeatureExtractor - Class in org.biopax.paxtools.pattern.example: This class goes over the state change pattern results and writes down the gained and lost modifications through these directed relations.
DeltaFeatureExtractor() - Constructor for class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
description - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Description of the miner.
Dialog - Class in org.biopax.paxtools.pattern.miner: This is the user interface with GUI for selecting a model, a pattern miner, and an output file.
Dialog(Miner...) - Constructor for class org.biopax.paxtools.pattern.miner.Dialog: Constructor for the dialog.
differentialActivity(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an activity.
DifferentialModificationUtil - Class in org.biopax.paxtools.pattern.util: THis class is used for comparing modification features of two PhysicalEntity objects of same EntityReference.
DifferentialModificationUtil() - Constructor for class org.biopax.paxtools.pattern.util.DifferentialModificationUtil
DirectedRelationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the directed relations between proteins.
DirectedRelationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Constructor that sets name and description.

E

Empty - Class in org.biopax.paxtools.pattern.constraint: Checks if the parameter constraint cannot generate any candidate.
Empty(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.Empty: Constructor with the generative Constraint.
EMPTY - Static variable in class org.biopax.paxtools.pattern.constraint.Field: Possible parameter value indicating user desire the field to be empty.
enrichWithCM(Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets parent complexes or complex members recursively according to the type of the linkage.
enrichWithGenerics(Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets the linked homologies and then switches to complex-relationship mode.
equal(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
EQUAL - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Size.Type
Equality - Class in org.biopax.paxtools.pattern.constraint: Checks identity of two elements.
Equality(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Equality: Constructor with the desired output.
equals(Object) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
erToPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From EntityReference to the member PhysicalEntity
ExtendedSIFWriter - Class in org.biopax.paxtools.pattern.miner: This class is used for writing the binary interactions to a text output stream in the so called Pathway Commons EXTENDED_BINARY_SIF format.
ExtendedSIFWriter() - Constructor for class org.biopax.paxtools.pattern.miner.ExtendedSIFWriter
extractModifNames(Map) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Extracts the modification terms from the moficiation features.
extractModifNames(Set) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Extracts terms of the modification features.

F

featureSubstring - Variable in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Partial names of the features to be considered.
fetchID(BioPAXElement) - Method in class org.biopax.paxtools.pattern.miner.CommonIDFetcher
fetchID(BioPAXElement) - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher
fetchID(BioPAXElement) - Method in interface org.biopax.paxtools.pattern.miner.IDFetcher: Finds a String ID for the given element.
fetchID(BioPAXElement) - Method in class org.biopax.paxtools.pattern.miner.SimpleIDFetcher
fetchIDs(BioPAXElement, IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
Field - Class in org.biopax.paxtools.pattern.constraint: Checks if an element has or has not a specific value for a field, or the field value of another element.
Field(String, String, Field.Operation) - Constructor for class org.biopax.paxtools.pattern.constraint.Field: Constructor with accessor strings for the field value of the element and the desired value that will be reached from the second element.
Field(String, Field.Operation, Object) - Constructor for class org.biopax.paxtools.pattern.constraint.Field: Constructor with accessor string for the field value of the element and the desired value.
Field.Operation - Enum Class in org.biopax.paxtools.pattern.constraint
FieldOfMultiple - Class in org.biopax.paxtools.pattern.constraint: Checks if generated elements has or has not a specific value for a field, or the field value of another set of generated elements.
FieldOfMultiple(MappedConst, String, Field.Operation, Object) - Constructor for class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Constructor with accessor string for the field value of the element and the desired value.
FieldOfMultiple(MappedConst, String, MappedConst, String, Field.Operation) - Constructor for class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Constructor with accessor strings for the field value of the element and the desired value that will be reached from the second element.
fillArray(PhysicalEntity, PhysicalEntity, int, int) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Creates the chain that links the given endpoints.
findDirectionInCatalysis(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Searches the controlling catalysis for possible direction of the conversion.
findDirectionInPathways(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Searches pathways that contains this conversion for the possible directions.

G

GAIN - Enum constant in enum class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type
general - Static variable in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Some general modification sub-strings to use if exact terms are not conclusive.
generate(Conversion, InterToPartER.Direction, Set<Entity>) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Gets the related entity references of the given interaction,
generate(Interaction, Set<Entity>) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Gets the related entity references of the given interaction.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.AND: Gets intersection of the generated elements by the member constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: This method has to be overridden by generative constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintChain: Chains the member constraints and returns the output of the last constraint.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ControlToControllerER: Navigates to the related ERs of the controllers of the given Control.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConversionSide: Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.
generate(Match, int...) - Method in interface org.biopax.paxtools.pattern.Constraint: Generates candidate values for the variable to be generated.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Iterated over non-taboo participants and collectes related ER.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets to the linked PhysicalEntity.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.OR: Gets the intersection of the generated values of wrapped constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Participant: Identifies the conversion direction and gets the related participants.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Identifies the conversion direction and gets the related participants.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: Uses the encapsulated PAthAccessor to generate satisfying elements.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.RelatedControl: According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Gets the first mapped element along with the generated elements of wrapped constraint.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.XOR: Gets xor of the generated elements by the member constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.MappedConst: Calls generate method of the constraint with index translation.
generateBlacklist(Model) - Method in class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Generates the blacklist.
generateBlacklist(Model) - Method in class org.biopax.paxtools.pattern.miner.BlacklistGenerator2: Generates the blacklist.
generateBlacklist(Model) - Method in class org.biopax.paxtools.pattern.miner.BlacklistGenerator3: Generates the blacklist.
genericEquiv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to its generic equivalents, i.e.
get(int) - Method in class org.biopax.paxtools.pattern.Match: Gets element at the index.
get(String[], Pattern) - Method in class org.biopax.paxtools.pattern.Match: Gets elements corresponding to the given labels in the pattern.
get(String, Pattern) - Method in class org.biopax.paxtools.pattern.Match: Gets element corresponding to the given label in the pattern.
getAName(BioPAXElement) - Method in class org.biopax.paxtools.pattern.Match: Finds a name for the variable.
getCatalysisDirection(Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control, if exists.
getCellularLocations() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Retrieves the cellular location of the PhysicalEntity.
getCellularLocations(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets cellular locations of the given elements in a string set.
getCellularLocationsOfSource() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects cellular location terms of source objects.
getCellularLocationsOfTarget() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects cellular location terms of target objects.
getChain(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
getChangedModifications(PhysicalEntity, PhysicalEntity) - Static method in class org.biopax.paxtools.pattern.util.DifferentialModificationUtil: Gets the differential features.
getChemDbStartsWithOrEquals() - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher
getColumnValue(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.OutputColumn: Get the string to write in the output file.
getCompoundName(SmallMoleculeReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the name of the small molecule to use in SIF.
getConstr() - Method in class org.biopax.paxtools.pattern.MappedConst: Getter for the constraint.
getConstraints() - Method in class org.biopax.paxtools.pattern.Pattern: Getter for the constraint list.
getContext(String) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the context of the ubiquity of the ID.
getControlChain(Control, Interaction) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the chain of Control, staring from the given Control, leading to the given Interaction.
getConvParticipants(Conversion, RelType) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets input ot output participants of the Conversion.
getDataSources() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects data source names (Provenance display names) of mediators.
getDeltaCompartments(Match, String, String, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets delta compartments of the given two PE chains.
getDeltaModifications(Match, String, String, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets delta modifications of the given elements in string sets.
getDescription() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets description of the miner.
getDescription() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the description of the miner.
getDescription() - Method in enum class org.biopax.paxtools.pattern.miner.SIFEnum: Gets the description of the SIF type.
getDescription() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Gets the description of the SIF type.
getDirection(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter
getDirection(Conversion, Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getDirection(Conversion, Pathway) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getDirection(Conversion, Pathway, Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getFirst() - Method in class org.biopax.paxtools.pattern.Match: Gets first element of the match
getGeneSymbol(ProteinReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the gene symbol of the given EntityReference.
getGeneSymbol(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the gene symbol of the given EntityReference.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Gets the header of the result file.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Sets header of the output.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the first line of the result file.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Gets header of the result file.
getIdentifiers(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Uses uniprot name or gene symbol as identifier.
getIdMap() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
getInds() - Method in class org.biopax.paxtools.pattern.MappedConst: Getter for the mapped indices.
getLast() - Method in class org.biopax.paxtools.pattern.Match: Gets last element of the match.
getLinkedElements(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE
getListed() - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the IDs of the blacklisted molecules.
getMaxInd() - Method in class org.biopax.paxtools.pattern.MappedConst: Gets the maximum index.
getMediatorComments() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects comments strings of mediator objects.
getMediatorIDs() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects IDs of mediators.
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which essential BioPAX elements mediated this relation, then they need to override this method and pass the labels of elements.
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getMediatorsInString() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Gets the mediator IDs in a String with a space between each ID.
getMiners() - Method in enum class org.biopax.paxtools.pattern.miner.SIFEnum
getMiners() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Gets the list of SIFMiner classes that can search this type of SIF edge in a BioPAX model.
getModifications() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Collects modifications from the elements of the chain.
getModifications(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets modifications of the given element in a string.
getModifications(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets modifications of the given elements in a string set.
getModificationTerm(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the String term of the modification feature.
getName() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets name of the miner.
getName() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the name of the miner.
getName(SmallMoleculeReference) - Method in class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer: Gets the standard name of the small molecule.
getNonUbiqueObjects(Set) - Method in class org.biopax.paxtools.pattern.util.Blacklist
getNonUbiques(Set<PhysicalEntity>, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the non-ubiquitous physical entities in the given set and in the given context.
getPathwayNames() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects the names of the related pathways.
getPathways() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects Pathway objects that the Interactions among the mediators are members.
getPathwayUris() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects the related pathway URIs.
getPattern() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets the pattern to use for mining the graph.
getPattern() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the pattern, constructs if null.
getPositionInString(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the position of the modification feature as a String.
getPositionStart(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the first position of the modification feature.
getPublicationIDs(boolean) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects Pubmed or PMC ids
getRelatedERs(Control) - Method in class org.biopax.paxtools.pattern.constraint.ControlToControllerER
getRelatedERs(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.constraint.ControlToControllerER
getRelationType() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if the relation captured by match has a type.
getSeqDbStartsWithOrEquals() - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher
getSIFType() - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner
getSIFType() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the type of the interaction.
getSortedGeneNames(Collection<SIFInteraction>, SIFType...) - Static method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects and sorts sourceID and targetID of the given collection of sif interactions.
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getSourceLabel() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the label of the source node.
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getStartingClass() - Method in class org.biopax.paxtools.pattern.Pattern: Gets the type of the initial element.
getSymbol(String) - Static method in class org.biopax.paxtools.pattern.util.HGNC
getTag() - Method in enum class org.biopax.paxtools.pattern.miner.SIFEnum: Tag of a SIF type is derived from the enum name.
getTag() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Tag of a SIF type is derived from the enum name.
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getTargetLabel() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the label of the target node.
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getType(String) - Static method in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
getUbiques(Set<PhysicalEntity>, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the ubiquitous small molecules among the given set and in the given context.
getUniprotNameForHuman(ProteinReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the uniprot name of the given human EntityReference.
getUniprotNameForHuman(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the uniprot name of the given human EntityReference.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Creates values for the result file columns.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method has to be overridden if writeResultDetailed method is used.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Gets the ids of the small molecule reference and its physical entities.
getVariables() - Method in class org.biopax.paxtools.pattern.Match: Getter for the element array.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the variable size of the constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.Empty: Variable size is one less than the wrapped Constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Size of this constraint is one less than con1 if con2 is null, otherwise it is two less than the total of size of con1 and con2.
getVariableSize() - Method in interface org.biopax.paxtools.pattern.Constraint: Number of variables to check consistency.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.HasAnID: Returns 1.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.IDConstraint: Returns 1.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.NOT: Size is equal to the of the negated constraint
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.OR: Checks the inner mapping of the wrapped constraints and figures the size.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Returns size of the wrapped constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.Size: Size is one less than the size of wrapped constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.MappedConst: Gets variable size of the wrapped constraint.
GREATER - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Size.Type
GREATER_OR_EQUAL - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Size.Type

H

HasAnID - Class in org.biopax.paxtools.pattern.constraint: Checks if the element has a valid ID.
HasAnID(IDFetcher, Map<BioPAXElement, Set<String>>) - Constructor for class org.biopax.paxtools.pattern.constraint.HasAnID: Constructor with the ID fetcher.
hasDifferentCompartments() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if two physical entities have non-empty and different compartments.
hashCode() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
hasIDs() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
hasLabel(int) - Method in class org.biopax.paxtools.pattern.Pattern: Checks if the given location has a label.
hasLabel(String) - Method in class org.biopax.paxtools.pattern.Pattern: Checks if the label is already in use.
hasNonSelfEffect() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not associated with the EntityReference of the initial PhysicalEntity.
hasProvenance(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the object is associated with a Provenance with the given name.
hasSolution(Pattern, BioPAXElement...) - Method in class org.biopax.paxtools.pattern.Searcher: Checks if there is any match for the given pattern if search starts from the given element.
hasXref(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the object has an Xref with the given ID.
HGNC - Class in org.biopax.paxtools.pattern.util: This class provides a mapping between HGNC IDs and Symbols.
HGNC() - Constructor for class org.biopax.paxtools.pattern.util.HGNC

I

IDConstraint - Class in org.biopax.paxtools.pattern.constraint: Checks if the element has the desired ID.
IDConstraint(Set<String>) - Constructor for class org.biopax.paxtools.pattern.constraint.IDConstraint: Constructor with desired IDs.
idFetcher - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: ID fetcher is used for skipping objects that cannot generate a valid ID during the search.
IDFetcher - Interface in org.biopax.paxtools.pattern.miner
idMap - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Memory for object IDs.
IN_COMPLEX_WITH - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
INACTIVE - Enum constant in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity
inComplexWith() - Static method in class org.biopax.paxtools.pattern.PatternBox: Two proteins have states that are members of the same complex.
InComplexWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the degradation pattern.
InComplexWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.InComplexWithMiner: Constructor that sets edge type.
indexOf(String) - Method in class org.biopax.paxtools.pattern.Pattern: Gets the index of the given label.
INPUT - Enum constant in enum class org.biopax.paxtools.pattern.util.RelType
inSameActiveComplex() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has an activity.
inSameComplex() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
inSameComplexEffectingConversion() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex is controlling a Conversion.
inSameComplexHavingTransActivity() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has transcriptional activity.
inSamePathway() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the two interactions are members of the same pathway.
insertPointConstraint(Constraint, int...) - Method in class org.biopax.paxtools.pattern.Pattern: A point constraint deals with only one element in a match, checks its validity.
INTERACTS_WITH - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
InteractsWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "interacts-with" relation.
InteractsWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.InteractsWithMiner: Constructor that sets sif type.
INTERSECT - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Field.Operation
intersects(PhysicalEntityChain) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if two chains intersect without ignoring endpoint intersection.
intersects(PhysicalEntityChain, boolean) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if two chains intersect.
interToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the upstream Control (and its upstream Control recursively).
interToController() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the controlling Controls recursively, and their controller PEs.
InterToPartER - Class in org.biopax.paxtools.pattern.constraint: This constraint is used to collect related EntityReference of the participant physical entities.
InterToPartER() - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor without parameters.
InterToPartER(int) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with parameters.
InterToPartER(InterToPartER.Direction) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with direction.
InterToPartER(InterToPartER.Direction, int) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with parameters.
InterToPartER.Direction - Enum Class in org.biopax.paxtools.pattern.constraint
interToPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the related PhysicalEntity.
isBait() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if the molecule is a bait of a Y2H experiment.
isDirected() - Method in enum class org.biopax.paxtools.pattern.miner.SIFEnum: Asks if the edge is directed.
isDirected() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Asks if the edge is directed.
isHuman() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the EntityReference or the PhysicalEntity belongs to human.
isInhibition(Control) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if the type of a Control is inhibition.
isPrey() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if the molecule is a prey of a Y2H experiment.
isUbique(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted in at least one context.
isUbique(PhysicalEntity, Conversion, ConversionDirectionType, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted for the given Conversion assuming the Conversion flows towards the given direction, and the entity is in given context.
isUbiqueInBothContexts(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted in both context together.

K

keyPressed(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog
keyReleased(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog
keyTyped(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog: Listens key pressing events.

L

label(String, int) - Method in class org.biopax.paxtools.pattern.Pattern: Puts the given label for the given index.
labeledInactive(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if a PE chain is labeled as inactive.
labelMap - Variable in class org.biopax.paxtools.pattern.Pattern: Indexes in a pattern can be labeled using this map.
lastIndex - Variable in class org.biopax.paxtools.pattern.Pattern: How many elements are there in a pattern match.
left() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to its left participants.
LEFT - Enum constant in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction
LESS - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Size.Type
LESS_OR_EQUAL - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Size.Type
linkedER(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox
LinkedPE - Class in org.biopax.paxtools.pattern.constraint: Many times we want to link PhysicalEntities (PE) while traversing a relation.
LinkedPE(LinkedPE.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.LinkedPE: Constructor with the linking type.
LinkedPE(LinkedPE.Type, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.LinkedPE: Constructor with the linking type.
LinkedPE.Type - Enum Class in org.biopax.paxtools.pattern.constraint: Two type of linking between PhysicalEntity.
linkToComplex() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
linkToComplex(Blacklist) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
linkToSimple(Blacklist) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
linkToSpecific() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
LOSS - Enum constant in enum class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type

M

main(String[]) - Static method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
main(String[]) - Static method in class org.biopax.paxtools.pattern.miner.Dialog: Runs the program showing the dialog.
main(String[]) - Static method in class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer
MappedConst - Class in org.biopax.paxtools.pattern: This is a mapping from a constraint to the elements in a match.
MappedConst(Constraint, int...) - Constructor for class org.biopax.paxtools.pattern.MappedConst: Constructor with the constraint and the index mapping.
Match - Class in org.biopax.paxtools.pattern: A pattern match is an array of biopax elements that satisfies the list of mapped constraints in a pattern.
Match(int) - Constructor for class org.biopax.paxtools.pattern.Match: Constructor with size.
matrix - Variable in class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Edges matrix.
max(int[]) - Method in class org.biopax.paxtools.pattern.constraint.OR: Gets the max value.
maxDegree(int) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the participant degree (number of Conversions that this is a participant) of the PhysicalEntity is less than or equal to the parameter.
MEDIATOR - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
mediators - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
mergeWith(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Merges publications of the parameter equivalent sif with this one.
mineAndCollect(Model) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
Miner - Interface in org.biopax.paxtools.pattern.miner: A miner provides a pattern to mine, and knows how to use the result set to prepare the text output.
MinerAdapter - Class in org.biopax.paxtools.pattern.miner: Adapter class for a miner.
MinerAdapter(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.MinerAdapter: Constructor with name and description.
ModificationChangeConstraint - Class in org.biopax.paxtools.pattern.constraint: This class checks if there exists a desired type of modification change among two PhysicalEntity.
ModificationChangeConstraint(ModificationChangeConstraint.Type, String...) - Constructor for class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Constructor with the desired change and maps to activating and inactivating features.
ModificationChangeConstraint.Type - Enum Class in org.biopax.paxtools.pattern.constraint
modificationConstraint(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity or any linked PE contains the modification term.
modifiedPESimple() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an EntityReference has distinct PhysicalEntities associated with both left and right of a Conversion.
modifierConv() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for finding Conversions that an EntityReference is participating.
molecularInteraction() - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last molecules are participants of a MolecularInteraction.
moreControllerThanParticipant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity is controlling more reactions than it participates (excluding complex assembly).
MultiPathConstraint - Class in org.biopax.paxtools.pattern.constraint: Logical OR of several PathConstraints.
MultiPathConstraint(String...) - Constructor for class org.biopax.paxtools.pattern.constraint.MultiPathConstraint: Constructor with specifier string of the path constraints.

N

name - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Name of the miner.
nameEquals(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Filters Named to contain a specific name.
nameEquals(String...) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Filters Named to contain a name from the input set.
names - Variable in class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Unique node names.
NEIGHBOR_OF - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
neighborOf() - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last proteins are related through an interaction.
NeighborOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "neighbor-of" relation.
NeighborOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.NeighborOfMiner: Constructor that sets sif type.
nextInteraction() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Starts from an Interaction and gets next Interactions in temporal order, if ever defined in a Pathway.
NONE - Enum constant in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity
NonUbique - Class in org.biopax.paxtools.pattern.constraint: This is a non-generative constraint that checks if the small molecule is ubiquitous in any context.
NonUbique(Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.NonUbique
NOT - Class in org.biopax.paxtools.pattern.constraint: Negation of a constraint.
NOT(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.NOT: Constructor with the wrapped constraint.
NOT_EMPTY_AND_NOT_INTERSECT - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Field.Operation
NOT_INTERSECT - Enum constant in enum class org.biopax.paxtools.pattern.constraint.Field.Operation
notAParticipant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the second element (PhysicalEntity) is not a participant of the first element (Interaction).
notControlled() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the Interaction has no Control
notControlsThis() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the second element (Control) is not a controller to the first element (Interaction).
notGeneric() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity do not have member physical entities..
notLabeledInactive() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not labeled as inactive.

O

ONESIDERS - Enum constant in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction
optimizeConstraintOrder() - Method in class org.biopax.paxtools.pattern.Pattern
OR - Class in org.biopax.paxtools.pattern.constraint: Logical OR of several constraints.
OR(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.OR: Constructor with the array of mapped constraints.
org.biopax.paxtools.pattern - package org.biopax.paxtools.pattern: Main package.
org.biopax.paxtools.pattern.constraint - package org.biopax.paxtools.pattern.constraint: Package for constraints.
org.biopax.paxtools.pattern.example - package org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner - package org.biopax.paxtools.pattern.miner: Package for pattern miner utility.
org.biopax.paxtools.pattern.util - package org.biopax.paxtools.pattern.util: Package for several utility classes.
OTHER_SIDE - Enum constant in enum class org.biopax.paxtools.pattern.constraint.ConversionSide.Type
OUTPUT - Enum constant in enum class org.biopax.paxtools.pattern.util.RelType
OutputColumn - Class in org.biopax.paxtools.pattern.miner: This class is used for defining a custom column in the te
OutputColumn(String) - Constructor for class org.biopax.paxtools.pattern.miner.OutputColumn: Constructor with output type.
OutputColumn.Type - Enum Class in org.biopax.paxtools.pattern.miner: Type of the output column.

P

participant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to its PhysicalEntity participants.
Participant - Class in org.biopax.paxtools.pattern.constraint: Gets input or output participants of a Conversion.
Participant(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, Blacklist, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, Blacklist, boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
participantER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the related EntityReference of its participants.
participatesInConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the Conversion that it participates.
ParticipatesInConv - Class in org.biopax.paxtools.pattern.constraint: Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired.
ParticipatesInConv(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Constructor with parameters.
ParticipatesInConv(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Constructor with parameters.
participatesInInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the Interaction that it participates.
PathConstraint - Class in org.biopax.paxtools.pattern.constraint: PathConstraint encapsulates PathAccessor of Paxtools.
PathConstraint(String) - Constructor for class org.biopax.paxtools.pattern.constraint.PathConstraint: Constructor with the constructor String of PathAccessor.
PATHWAY - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
PATHWAY_URI - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
Pattern - Class in org.biopax.paxtools.pattern: A pattern is a list of mapped constraints.
Pattern(Class<? extends BioPAXElement>, String) - Constructor for class org.biopax.paxtools.pattern.Pattern: Constructor with a label for the element at index 0.
Pattern(Class<? extends BioPAXElement>, Constraint, String...) - Constructor for class org.biopax.paxtools.pattern.Pattern: Constructor with the first constraint and labels it uses.
PatternBox - Class in org.biopax.paxtools.pattern: This class contains several pattern samples.
PatternBox() - Constructor for class org.biopax.paxtools.pattern.PatternBox
PE2FEAT - Static variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Accessor to the modification term.
PE2TERM - Static variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Accessor to the modification term.
PEChainsIntersect - Class in org.biopax.paxtools.pattern.constraint: This constraint checks if two chains of linked physical entities are intersecting or not.
PEChainsIntersect(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Constructor with the desired result.
PEChainsIntersect(boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Constructor with the desired result and endpoint ignore option.
peInOut() - Static method in class org.biopax.paxtools.pattern.PatternBox
peNotRelatedToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the given physical entity is not related to the entity reference.
pes - Variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Array that links two ends of the chain.
peToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Control
peToControlledConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Conversion.
peToControlledInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Interaction.
peToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From SimplePhysicalEntity to its EntityReference.
peToInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the related Interaction.
PhysicalEntityChain - Class in org.biopax.paxtools.pattern.util: This class takes two PhysicalEntity objects linked with generic or complex member relationships, and prepares an array of PEs that link those.
PhysicalEntityChain(PhysicalEntity, PhysicalEntity) - Constructor for class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Constructor with endpoints.
PhysicalEntityChain.Activity - Enum Class in org.biopax.paxtools.pattern.util: Values for activity.
PMC - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
product() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From TemplateReaction to its products.
ProgressWatcher - Interface in org.biopax.paxtools.pattern.util: This interface is to use for tracking progress of a process.
PUBMED - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type

R

REACTS_WITH - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
reactsWith(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last small molecules are substrates to the same biochemical reaction.
ReactsWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "reacts-with" relation.
ReactsWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ReactsWithMiner: Constructor that sets sif type.
RelatedControl - Class in org.biopax.paxtools.pattern.constraint: After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to the Control.
RelatedControl(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.RelatedControl: Constructor with the relation type between PhysicalEntity and Conversion.
RelatedControl(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.RelatedControl: Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.
RelatedGenesOfInteractionsMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the related genes (participant or controller) of interactions.
RelatedGenesOfInteractionsMiner() - Constructor for class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Constructor that sets name and description.
relatedProteinRefOfInter(Class<? extends Interaction>...) - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds ProteinsReference related to an interaction.
RelType - Enum Class in org.biopax.paxtools.pattern.util: Distinguishes between input and output.
removeCommon(Set<String>, Set<String>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
removeLastConstraint() - Method in class org.biopax.paxtools.pattern.Pattern: Removes the last constraint added to the pattern.
RESOURCE - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
right() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to its right participants.
RIGHT - Enum constant in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction

S

SAME_SIDE - Enum constant in enum class org.biopax.paxtools.pattern.constraint.ConversionSide.Type
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ActivityConstraint: Checks if the PhysicalEntity controls anything.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Checks the gained and and lost features to predict the activity change is the desired change.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.AND: Checks if all the constraints satisfy.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Use this method only if constraint canGenerate, and satisfaction criteria is that simple.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ControlsNotParticipant: Checks if the controlled Interaction contains a controller as a participant.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Empty: Checks if the wrapped Constraint can generate any elements.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Equality: Checks if the two elements are identical or not identical as desired.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Field: Checks if the element in the first index has the desired value.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: 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.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.HasAnID: Checks if the element has one of the desired IDs.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.IDConstraint: Checks if the element has one of the desired IDs.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Checks the any of the changed modifications match to any of the desired modifications.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.NonUbique
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.NOT: Negates the satisfies value of the wrapped constraint.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.OR: Checks if any of the wrapped constraints satisfy.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: Checks if the PathAccessor is generating the second mapped element.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Creates two PhysicalEntity chains with the given endpoints, and checks if they are intersecting.
satisfies(Match, int...) - Method in interface org.biopax.paxtools.pattern.Constraint: Checks if the variables in the Match satisfies this constraint.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Checks if the last index is either generated or equal to the first element.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Size: Checks if generated element size is in limits.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Type: Checks if the element is assignable to a variable of the desired type.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.XOR: Checks if constraints satisfy in xor pattern.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.MappedConst: Directs to satisfies method of the wrapped constraint with index translation.
search(Collection<? extends BioPAXElement>, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given elements.
search(BioPAXElement, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from the given element.
search(Model, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern in the given model.
search(Model, Pattern, ProgressWatcher) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern in the given model.
search(Match, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from the given match.
searchAndCollect(Collection<? extends BioPAXElement>, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
searchAndCollect(BioPAXElement, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
searchAndCollect(Model, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a model for the given pattern, then collects the specified elements of the matches and returns.
Searcher - Class in org.biopax.paxtools.pattern: Searcher for searching a given pattern in a model.
Searcher() - Constructor for class org.biopax.paxtools.pattern.Searcher
searchInFile(Pattern, String, String) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
searchInFile(Pattern, String, String, int, int) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
searchPlain(Collection<? extends BioPAXElement>, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.
searchPlain(Model, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern in a given model, but instead of a match map, returns all matches in a list.
searchRecursive(Match, List<MappedConst>, int) - Static method in class org.biopax.paxtools.pattern.Searcher: Continues searching with the mapped constraint at the given index.
searchSIF(Model) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIF(Model, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIF(Model, OutputStream, SIFToText) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIFGetMatrix(Model) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
SelfOrThis - Class in org.biopax.paxtools.pattern.constraint: When a constraint excludes the origin element, but it is needed to be among them, use this constraint.
SelfOrThis(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.SelfOrThis: Constructor with the wrapped constraint.
SelfOrThis(Constraint, int) - Constructor for class org.biopax.paxtools.pattern.constraint.SelfOrThis: Constructor with the wrapped constraint and index of self.
seqDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher: Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case.
set(BioPAXElement, int) - Method in class org.biopax.paxtools.pattern.Match: Sets the given element to the given index.
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sets the blacklist to use during SIF search.
setBlacklist(Blacklist) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Sets the blacklist that can be used during the search.
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Sets the blacklist that manages IDs of ubique molecules.
setContainsGeneralTerm(Set<String>, String) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Checks if any element in the set contains the term.
setDescription(String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
setIDFetcher(IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sets the ID fetcher to use during SIF search.
setIDFetcher(IDFetcher) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Sets the idFetcher that helps to fasten the search.
setIdMap(Map<BioPAXElement, Set<String>>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
setName(String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
setSize(int) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Sets the size of the constraint.
setTotalTicks(int) - Method in interface org.biopax.paxtools.pattern.util.ProgressWatcher: Sets how many ticks are there in total.
setType(SIFType) - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Sets the SIF type
setUseUniprotIDs(boolean) - Method in class org.biopax.paxtools.pattern.miner.CommonIDFetcher
SIFEnum - Enum Class in org.biopax.paxtools.pattern.miner: Enum for representing supported SIF edge types.
SIFInteraction - Class in org.biopax.paxtools.pattern.miner
SIFInteraction(String, String, BioPAXElement, BioPAXElement, SIFType, Set<BioPAXElement>, Set<BioPAXElement>, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.pattern.miner.SIFInteraction
SIFMiner - Interface in org.biopax.paxtools.pattern.miner: This interface tells that the miner supports SIF output.
SIFSearcher - Class in org.biopax.paxtools.pattern.miner: Searches a model and generates SIF network using the pattern matches.
SIFSearcher(IDFetcher, SIFMiner...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with ID fetcher and miners.
SIFSearcher(IDFetcher, SIFType...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with ID fetcher and binary interaction types.
SIFSearcher(SIFMiner...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with miners.
SIFSearcher(SIFType...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with binary interaction types.
SIFToText - Interface in org.biopax.paxtools.pattern.miner: An interface for converting a SIF interaction to text.
SIFType - Interface in org.biopax.paxtools.pattern.miner
sign(Control) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Identifies negative and positive controls.
sign(Match, String...) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks the cumulative sign of the chained controls.
SimpleIDFetcher - Class in org.biopax.paxtools.pattern.miner: Simple gets the URI (of an entity reference);
SimpleIDFetcher() - Constructor for class org.biopax.paxtools.pattern.miner.SimpleIDFetcher
simpleMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From complex to its simple members (members which are of type SimplePhysicalEntity) recursively.
simplePEToConv(RelType) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From simple PhysicalEntity to related Conversion.
size - Variable in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Size of the constraint.
size() - Method in class org.biopax.paxtools.pattern.Pattern: Gets the element size of the pattern.
Size - Class in org.biopax.paxtools.pattern.constraint: Checks the size of the generated elements of the wrapped constraint.
Size(Constraint, int, Size.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.Size: Constructor with parameters.
Size.Type - Enum Class in org.biopax.paxtools.pattern.constraint: Type of the (in)equality.
source(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox
SOURCE_LOC - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
sourceERs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
sourceID - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
sourcePEs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
startingClass - Variable in class org.biopax.paxtools.pattern.Pattern: Class of the first elements to match with this pattern.
stateChange(Pattern, String) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.

T

TARGET_LOC - Enum constant in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type
targetERs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
targetID - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
targetPEs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
tick(int) - Method in interface org.biopax.paxtools.pattern.util.ProgressWatcher: Ticks the progress watcher.
TO_GENERAL - Enum constant in enum class org.biopax.paxtools.pattern.constraint.LinkedPE.Type
TO_SPECIFIC - Enum constant in enum class org.biopax.paxtools.pattern.constraint.LinkedPE.Type
toString() - Method in class org.biopax.paxtools.pattern.Match: Gets name of variables.
toString() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Uses the name as sting representation of the miner.
toString() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
toString() - Method in class org.biopax.paxtools.pattern.util.AdjacencyMatrix
toStringSet(Set<ModificationFeature>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sorts the modifications and gets them in a String.
translate(int[]) - Method in class org.biopax.paxtools.pattern.MappedConst: This methods translates the indexes of outer constraint, to this inner constraint.
type - Variable in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Gain or loss?
type - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
type(Class<? extends BioPAXElement>) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Creates an element type constraint.
Type - Class in org.biopax.paxtools.pattern.constraint: Checks if a variable is a specific type or its subclass.
Type(Class<? extends BioPAXElement>) - Constructor for class org.biopax.paxtools.pattern.constraint.Type: Constructor with the desired class.
typeOf(String) - Static method in enum class org.biopax.paxtools.pattern.miner.SIFEnum

U

UbiquitousIDMiner - Class in org.biopax.paxtools.pattern.miner: Miner for getting ubiquitous small molecules in a model.
UbiquitousIDMiner() - Constructor for class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Constructor that sets name and description.
updateLabel(String, String) - Method in class org.biopax.paxtools.pattern.Pattern: Changes a label.
USE_SECOND_ARG - Static variable in class org.biopax.paxtools.pattern.constraint.Field: Possible parameter value indicating the desired value will be given as the second element to the constraint.
USED_TO_PRODUCE - Enum constant in enum class org.biopax.paxtools.pattern.miner.SIFEnum
usedToProduce(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
UsedToProduceMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "used-for-production-of" relation.
UsedToProduceMiner() - Constructor for class org.biopax.paxtools.pattern.miner.UsedToProduceMiner: Constructor that sets sif type.
useNameWhenNoDbMatch(boolean) - Method in class org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher: Set the flag to use the entity reference's names when no desired ID type can be found (none of xref.db matched before, or there're no xrefs at all).

V

valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.ConversionSide.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.Field.Operation: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.LinkedPE.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.constraint.Size.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.miner.SIFEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biopax.paxtools.pattern.util.RelType: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.ConversionSide.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.Field.Operation: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.InterToPartER.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.LinkedPE.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.constraint.Size.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.miner.OutputColumn.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.miner.SIFEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biopax.paxtools.pattern.util.RelType: Returns an array containing the constants of this enum class, in the order they are declared.
varSize() - Method in class org.biopax.paxtools.pattern.Match: Gets the array size.
varsPresent(int...) - Method in class org.biopax.paxtools.pattern.Match: Checks if all given indices are assigned.

W

withComplexes() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to parent Complex recursively, or to itself.
withComplexMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex to its members, or the complex itself.
withSimpleMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From complex to its simple members recursively, or the Complex itself
write(OutputStream) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Dumps data to the given output stream.
write(String) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Dumps data to the given file.
write(Set<SIFInteraction>, OutputStream) - Static method in class org.biopax.paxtools.pattern.miner.ExtendedSIFWriter: Writes down the given inferred binary interactions into the output stream using the Pathway Commons one-file EXTENDED_BINARY_SIF format, where edges (interactions) are written first, followed by a single blank line, followed by the nodes section (participant details and annotations).
writeInteractions(Set<SIFInteraction>, OutputStream) - Static method in class org.biopax.paxtools.pattern.miner.ExtendedSIFWriter: Writes down the given interactions into the given "edges" output stream.
writeParticipants(Set<SIFInteraction>, OutputStream) - Static method in class org.biopax.paxtools.pattern.miner.ExtendedSIFWriter: Writes down the interaction participants' (nodes) details to the given output stream.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: 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.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in interface org.biopax.paxtools.pattern.miner.Miner: Writes the text output to the given stream.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Writes the IDs of interaction, then gene symbols of related proteins in a line.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
writeResultAsSIF(Map<BioPAXElement, List<Match>>, OutputStream, boolean, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method writes the output as pairs of gene symbols of the given two ProteinReference.
writeResultDetailed(Map<BioPAXElement, List<Match>>, OutputStream, int) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Writes the result as a tab delimited format, where the column values are customized.
writeResults(String) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
writeSIFsUsingSIFFramework(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method writes the output as pairs of gene symbols of the given two ProteinReference.

X

XOR - Class in org.biopax.paxtools.pattern.constraint: Used for getting logical XOR of a set of constraints.
XOR(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.XOR: Constructor with the mapped constraints.

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