A B C E G H I M O P R S T V W

A

ActivityNetworkAnalyzer - Class in org.biopax.paxtools.io.sif.level3

Deprecated.

ActivityNetworkAnalyzer() - Constructor for class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

add(SimpleInteraction) - Method in class org.biopax.paxtools.io.sif.InteractionSet

If the interaction already exists, mediators are updated with merging.

addMediator(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Adds a mediator to the interaction.

addMember(EntityReference) - Method in class org.biopax.paxtools.io.sif.level3.Group

addSubgroup(Group) - Method in class org.biopax.paxtools.io.sif.level3.Group

AffectsRule - Class in org.biopax.paxtools.io.sif.level2

This is an experimental rule that mines ACTIVATES and INHIBITS relations between molecules.

AffectsRule() - Constructor for class org.biopax.paxtools.io.sif.level2.AffectsRule

analyzeStates(Model) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

Given a model this method will analyze the states and populate the stateChangeMap and extendedControls maps.

B

BinaryInteractionType - Enum in org.biopax.paxtools.io.sif

This class holds the description, tag (used in SIF file), the information if the interaction is directed for the relevant binary interaction types.

BINDING - Static variable in enum org.biopax.paxtools.io.sif.level3.ChangeType

Special static entity feature used as a 'hack' to capture complex membership.

C

changedFrom(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

changedInto(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

ChangeType - Enum in org.biopax.paxtools.io.sif.level3

This enum handles types of modifications and contains utility methods for extracting them.

checkOption(Object, Object, Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Checks if the options map has the given option with the given value.

collectEntities(Set<PhysicalEntity>, InteractionSetL3) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

ComponentRule - Class in org.biopax.paxtools.io.sif.level2

Component.InSame: A and B are components of same flattened complex structure, A and B are simple.

ComponentRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule

Constructor with default values.

ComponentRule(int) - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule

Constructor with threshold

ComponentRule(int, boolean) - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule

Constructor with threshold and exception suppressing option.

ComponentRule - Class in org.biopax.paxtools.io.sif.level3

This rule class mines complex membership relations.

ComponentRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ComponentRule

ConsecutiveCatalysisRule - Class in org.biopax.paxtools.io.sif.level2

This class creates an interaction between two entities if they are catalyzing consecutive conversions.

ConsecutiveCatalysisRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule

ConsecutiveCatalysisRule - Class in org.biopax.paxtools.io.sif.level3

This class creates an interaction between two entities if they are catalyzing consecutive conversions.

ConsecutiveCatalysisRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule

ControlRule - Class in org.biopax.paxtools.io.sif.level2

A controls a conversion which B is at left or right or both.

ControlRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ControlRule

ControlRule - Class in org.biopax.paxtools.io.sif.level3

A controls a conversion which B is at left or right or both.

ControlRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ControlRule

ControlsTogetherRule - Class in org.biopax.paxtools.io.sif.level2

Implements Co-Control rule, which means A and B have a control over the same interaction.

ControlsTogetherRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule

ControlsTogetherRule - Class in org.biopax.paxtools.io.sif.level3

Implements Co-Control rule, which means A and B have a control over the same interaction.

ControlsTogetherRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule

convertGroupsToInteractions() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3

Creates membership links between group nodes and members in the generated SIF graph.

createAndAdd(BioPAXElement, BioPAXElement, InteractionSetL3, BinaryInteractionType, BioPAXElement...) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Creates the binary interaction and adds to the inferred interaction list.

createClique(InteractionSetL3, List<BioPAXElement>, BinaryInteractionType, BioPAXElement...) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Creates an interactions between every ordered pair of components.

E

entityHasAChange(BioPAXElement, Conversion, GroupMap, Set<PEStateChange>, Map<Conversion, Set<EntityReference>>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify

entityHasAChange(BioPAXElement, Conversion, GroupMap, Set<PEStateChange>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify

equals(Object) - Method in class org.biopax.paxtools.io.sif.level3.Group

equals(Object) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

equals(Object) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

This method checks for source, target and type equality.

equivalenceCode() - Method in class org.biopax.paxtools.io.sif.level3.Group

EXISTENCE - Static variable in enum org.biopax.paxtools.io.sif.level3.ChangeType

Special static entity feature used for representing changes that effect existence of protein -i.e.

expandGroups() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3

This method iteratively replaces groups with BioPAX elements

ExpressionRule - Class in org.biopax.paxtools.io.sif.level3

This rule mines the transctivation and transinhibition relations between entities.

ExpressionRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ExpressionRule

G

getAllSimpleMembers() - Method in class org.biopax.paxtools.io.sif.level3.Group

getAllStates(EntityReference) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

getANameForSIF(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

This method is used when we want to use readable names in the simple SIF format instead of IDs.

getAnnotations() - Method in class org.biopax.paxtools.io.sif.level3.Group

getControllersAsString() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getConv() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getDeltaControls() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getDeltaFeatures(PhysicalEntity, PhysicalEntity, PhysicalEntity, PhysicalEntity) - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType

This method returns the features that are "changed" between the left and right physical entities.

getDeltaFeatures() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getDescription() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType

Returns the description of the binary interaction as a string.

getEntityReferenceOrGroup(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.level3.GroupMap

getGroupMap() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3

Getter for the groupMap

getLeft() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getLeftRoot() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getMap() - Method in class org.biopax.paxtools.io.sif.level3.GroupMap

getMediators() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Gets other related elements of the interaction.

getPrecedingStates(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

getRDFId() - Method in class org.biopax.paxtools.io.sif.level3.Group

getRelatedEntrezGeneID(XReferrable) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Searches for the Entrez Gene ID in the references.

getRight() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getRightRoot() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

getRules(BioPAXLevel) - Static method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Gets all available interaction rules for the given level.

getRuleTypes() - Method in interface org.biopax.paxtools.io.sif.InteractionRule

Gets a list of the rule types that this class implements.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.AffectsRule

Gets supported interactions types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ControlRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ControlRule

Gets supported interaction types.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ExpressionRule

Gets a list of the rule types that this class implements.

getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule

Gets supported interaction types.

getSimpleMembers(PhysicalEntity, Set<SimplePhysicalEntity>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify

getSource() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Gets source element.

getSucceedingStates(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

getTag() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType

Returns the tag of the binary interaction.

getTarget() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Gets target element.

getType() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Gets the type of the interaction.

Group - Class in org.biopax.paxtools.io.sif.level3

This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.

Grouper - Class in org.biopax.paxtools.io.sif.level3

Grouper() - Constructor for class org.biopax.paxtools.io.sif.level3.Grouper

GroupMap - Class in org.biopax.paxtools.io.sif.level3

GroupMap(Map<BioPAXElement, Group>) - Constructor for class org.biopax.paxtools.io.sif.level3.GroupMap

groupTypeToString() - Method in class org.biopax.paxtools.io.sif.level3.Group

H

hashCode() - Method in class org.biopax.paxtools.io.sif.level3.Group

hashCode() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

hashCode() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

This method returns a hashcode based on the source, target and types hashcodes.

I

inferGroups(Model) - Static method in class org.biopax.paxtools.io.sif.level3.Grouper

inferInteractions(InteractionSet, BioPAXElement, Model) - Method in interface org.biopax.paxtools.io.sif.InteractionRule

This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

inferInteractions(InteractionSet, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

Uses physicalEntity as source of the interaction.

inferInteractions(InteractionSet, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Selects only PhysicalEntity as seed.

inferInteractions(Model) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Infers simple interactions from the interactions found in the model for every interaction rule given; and returns this inferred simple interactions.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.AffectsRule

Infers interactions using the given physicalEntity as seed.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule

Infer starting from the given physicalEntity.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule

Infers using the given physicalEntity as source.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ControlRule

When options map is null, then all rules are generated.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule

Infers interactions using A as source.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in interface org.biopax.paxtools.io.sif.level2.InteractionRuleL2

This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule

Infer using given physicalEntity as source.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule

Infer interactions where A = the given PhysicalEntity.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule

Infers interactions using the given PhysicalEntity as seed.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ControlRule

When options map is null, then all rules are generated.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ExpressionRule

Searches the transcriptional relations using the pattern, then decides the interaction type according to the type of the Control.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in interface org.biopax.paxtools.io.sif.level3.InteractionRuleL3

This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule

Infers interactions starting from the given PhysicalEntity.

initOptions(Map) - Method in interface org.biopax.paxtools.io.sif.InteractionRule

Uses the parameter map as options for the rule.

initOptions(Map) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

Initializes options.

initOptions(Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Initializes the options.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule

Initializes options.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ControlRule

Initializes option.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

Does nothing here.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule

Initializes options.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule

Initializes options.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ControlRule

Initializes options.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

Does nothing for this class.

initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule

Initializes options.

InteractionRule - Interface in org.biopax.paxtools.io.sif

This interface defines a rule which can be run on BioPAX model to derive simple interactions.

InteractionRuleL2 - Interface in org.biopax.paxtools.io.sif.level2

This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.

InteractionRuleL2Adaptor - Class in org.biopax.paxtools.io.sif.level2

Base class for level 2 rules.

InteractionRuleL2Adaptor() - Constructor for class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

InteractionRuleL3 - Interface in org.biopax.paxtools.io.sif.level3

This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.

InteractionRuleL3Adaptor - Class in org.biopax.paxtools.io.sif.level3

Base class for level 3 interactions rules.

InteractionRuleL3Adaptor() - Constructor for class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

InteractionSet - Class in org.biopax.paxtools.io.sif

This is a set of binary interactions.

InteractionSet() - Constructor for class org.biopax.paxtools.io.sif.InteractionSet

InteractionSetL3 - Class in org.biopax.paxtools.io.sif.level3

Set of inferred interactions.

InteractionSetL3(Model) - Constructor for class org.biopax.paxtools.io.sif.level3.InteractionSetL3

Constructor with the model.

isComplex() - Method in class org.biopax.paxtools.io.sif.level3.Group

isDirected() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType

Returns true, if the interaction is directed.

isEmpty() - Method in class org.biopax.paxtools.io.sif.level3.Group

isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.level3.Group

M

MaximumInteractionThresholdExceedException - Exception in org.biopax.paxtools.io.sif

This exception is thrown when there are more than a maximum number of interactions generated.

MaximumInteractionThresholdExceedException(String) - Constructor for exception org.biopax.paxtools.io.sif.MaximumInteractionThresholdExceedException

Constructor with the message.

O

org.biopax.paxtools.io.sif - package org.biopax.paxtools.io.sif

This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.

org.biopax.paxtools.io.sif.level2 - package org.biopax.paxtools.io.sif.level2

org.biopax.paxtools.io.sif.level3 - package org.biopax.paxtools.io.sif.level3

This package contains the SIF rules for BioPAX Level 3.

P

ParticipatesRule - Class in org.biopax.paxtools.io.sif.level2

Finds pairs of molecules that are participants of the same interaction.

ParticipatesRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule

Constructor with default values.

ParticipatesRule(int) - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule

Constructor with participant number threshold.

ParticipatesRule(int, boolean) - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule

Constructor with participant number threshold and option to suppress exceptions.

ParticipatesRule - Class in org.biopax.paxtools.io.sif.level3

Finds pairs of molecules that are participants of the same interaction for the INTERACTS_WITH type, and participants of the same Conversion for the REACTS_WITH type.

ParticipatesRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ParticipatesRule

PEStateChange - Class in org.biopax.paxtools.io.sif.level3

This experimental class is used by Activity Network Analyzer to capture state change events.

PEStateChange(SimplePhysicalEntity, SimplePhysicalEntity, PhysicalEntity, PhysicalEntity, BioPAXElement, Conversion) - Constructor for class org.biopax.paxtools.io.sif.level3.PEStateChange

R

REDUCE_COMPLEXES - Static variable in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Option to reduce complexes or use them as they are in interactions.

REDUCE_GENERICS - Static variable in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Option to reduce complexes or use them as they are in interactions.

removeInteractionsWithBlackListMolecules(Set<SimpleInteraction>, Set<String>) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Filters out interactions whose source or target are in black list.

S

setSource(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Sets source element.

setTarget(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Sets target element.

setType(BinaryInteractionType) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Sets the type of the interaction.

SimpleInteraction - Class in org.biopax.paxtools.io.sif

This class implements a directed binary interaction between two entities.

SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction

Constructor with parameters, without mediators.

SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType, BioPAXElement...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction

Constructor with parameters, with mediators.

SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType, Collection<BioPAXElement>) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction

Constructor with parameters, with mediators.

SimpleInteractionConverter - Class in org.biopax.paxtools.io.sif

Deprecated.

use the pattern (new Paxtools' module) api instead

SimpleInteractionConverter(InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Constructor with the mining rules to use.

SimpleInteractionConverter(Map, InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Constructor with mining rules and options.

SimpleInteractionConverter(Map, Set<String>, InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Constructor with mining rules, options, and black list.

Simplify - Class in org.biopax.paxtools.io.sif.level3

Simplify() - Constructor for class org.biopax.paxtools.io.sif.level3.Simplify

T

toString() - Method in class org.biopax.paxtools.io.sif.level3.Group

toString() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange

toString() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction

Returns "source type target".

V

valueOf(String) - Static method in enum org.biopax.paxtools.io.sif.BinaryInteractionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biopax.paxtools.io.sif.BinaryInteractionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType

Returns an array containing the constants of this enum type, in the order they are declared.

W

writeInteractionsInSIF(Model, OutputStream) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

Infers simple interactions from the model using SimpleInteractionConverter.inferInteractions(org.biopax.paxtools.model.Model) and wrties them to an output stream.

writeInteractionsInSIFNX(Model, OutputStream, OutputStream, List<String>, List<String>, boolean) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter

Deprecated.

This method outputs inferred interactions in SIF annotation extended format (Sifnx).

writeStateNetworkAnalysis(OutputStream) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

This method writes out the results of the stateNetworkAnalysis for each detected state change.

A B C E G H I M O P R S T V W