Nothing
###############################################################################
#
# biopax2Classes.R: This file contains the class definitons, getters, setters
# for the BioPax level 2 representation in R. This
# representation is based on S3-classes, so there is no real
# type-checking, inheritance, etc possible.
# For more information on BioPax please visit biopax.org.
# author: Frank Kramer <dev@frankkramer.de>
#
# This is released under GPL-2.
#
# Documentation was created using roxygen
#
###############################################################################
#' Class inheritance relationships in Biopax Level 2.
#'
#' A data.frame listing all direct superclasses for every Biopax Level 2 class.
#' The variables are as follows:
#'
#' \itemize{
#' \item class. Name of the class
#' \item superclass. Name of the superclass
#' }
#'
#' @docType data
#' @keywords datasets
#' @name CLASS_INHERITANCE_BP2
#' @title CLASS_INHERITANCE_BP2
#' @usage CLASS_INHERITANCE_BP2
#' @format A data frame with 46 rows and 2 columns
#' @export
CLASS_INHERITANCE_BP2 = data.frame(
matrix(ncol=2,byrow=T, dimnames=list(list(),list("class","superclass")),data= c(
"entity", "",
"pathway", "entity",
"interaction", "entity",
"physicalInteraction", "interaction",
"control", "physicalInteraction",
"catalysis", "control",
"modulation", "control",
"conversion", "physicalInteraction",
"complexAssembly", "conversion",
"biochemicalReaction", "conversion",
"transport", "conversion",
"transportWithBiochemicalReaction", "biochemicalReaction",
"transportWithBiochemicalReaction", "transport",
"physicalEntity", "entity",
"dna", "physicalEntity",
"rna", "physicalEntity",
"protein", "physicalEntity",
"smallMolecule", "physicalEntity",
"complex", "physicalEntity",
"utilityClass", "",
"chemicalStructure", "utilityClass",
"deltaGprimeO", "utilityClass",
"kPrime", "utilityClass",
"confidence", "utilityClass",
"evidence", "utilityClass",
"experimentalForm", "utilityClass",
"pathwayStep", "utilityClass",
"sequenceFeature", "utilityClass",
"sequenceLocation", "utilityClass",
"sequenceInterval", "sequenceLocation",
"sequenceSite", "sequenceLocation",
"physicalEntityParticipant", "utilityClass",
"sequenceParticipant", "physicalEntityParticipant",
"dnaParticipant", "physicalEntityParticipant",
"rnaParticipant", "physicalEntityParticipant",
"proteinParticipant", "physicalEntityParticipant",
"smallMoleculeParticipant", "physicalEntityParticipant",
"complexParticipant", "physicalEntityParticipant",
"externalReferenceUtilityClass", "utilityClass",
"dataSource", "externalReferenceUtilityClass",
"bioSource", "externalReferenceUtilityClass",
"openControlledVocabulary", "externalReferenceUtilityClass",
"xref", "externalReferenceUtilityClass",
"unificationXref", "xref",
"relationshipXref", "xref",
"publicationXref", "xref"
)), stringsAsFactors = FALSE
)
#' Class properties in Biopax Level 2.
#'
#' A data.frame listing all direct properties for every Biopax Level 2 class.
#' Together with CLASS_INHERITANCE_BP2 this allows to list all properties, including the inherited ones, of every class.
#'
#' The variables are as follows:
#'
#' \itemize{
#' \item class. Name of the class
#' \item property. Name of the superclass
#' \item property_type.Type of the property, value or reference
#' \item cardinality. Maximum allowed cardinality of a property. Many properties may only be singular.
#' }
#'
#' @docType data
#' @keywords datasets
#' @name CLASS_PROPERTIES_BP2
#' @title CLASS_PROPERTIES_BP2
#' @usage CLASS_PROPERTIES_BP2
#' @format A data frame with 106 rows and 4 columns
#' @export
CLASS_PROPERTIES_BP2 = data.frame(
matrix(ncol=4,byrow=T, dimnames=list(list(),list("class","property","property_type","cardinality")),data= c(
"entity", "NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"entity", "SHORT-NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"entity", "SYNONYMS", "http://www.w3.org/2001/XMLSchema#string", "*",
"entity", "COMMENT", "http://www.w3.org/2001/XMLSchema#string", "*",
"entity", "AVAILABILITY", "http://www.w3.org/2001/XMLSchema#string", "*",
"entity", "DATA-SOURCE", "dataSource", "*",
"entity", "XREF", "xref", "*",
"pathway", "ORGANISM", "bioSource", "1",
"pathway", "EVIDENCE", "evidence", "*",
"pathway", "PATHWAY-COMPONENTS", "interaction", "*",
"pathway", "PATHWAY-COMPONENTS", "pathway", "*",
"pathway", "PATHWAY-COMPONENTS", "pathwayStep", "*",
"interaction", "PARTICIPANTS", "entity", "*",
"interaction", "PARTICIPANTS", "physicalEntityParticipant", "*",
"interaction", "EVIDENCE", "evidence", "*",
"physicalInteraction", "INTERACTION-TYPE", "openControlledVocabulary", "*",
"control", "CONTROL-TYPE", "http://www.w3.org/2001/XMLSchema#string", "1",
"control", "CONTROLLER", "entity", "*",
"control", "CONTROLLER", "physicalEntityParticipant", "*",
"control", "CONTROLLED", "entity", "*",
"control", "CONTROLLED", "physicalEntityParticipant", "*",
"control", "CONTROLLED", "pathway", "*",
"control", "CONTROLLED", "interaction", "*",
"catalysis", "DIRECTION", "http://www.w3.org/2001/XMLSchema#string", "1",
"catalysis", "COFACTOR", "entity", "*",
"catalysis", "COFACTOR", "physicalEntityParticipant", "*",
"conversion", "SPONTANEUS", "http://www.w3.org/2001/XMLSchema#string", "1",
"conversion", "LEFT", "entity", "*",
"conversion", "LEFT", "physicalEntityParticipant", "*",
"conversion", "RIGHT", "entity", "*",
"conversion", "RIGHT", "physicalEntityParticipant", "*",
"biochemicalReaction", "DELTA-H", "http://www.w3.org/2001/XMLSchema#double", "*",
"biochemicalReaction", "DELTA-S", "http://www.w3.org/2001/XMLSchema#double", "*",
"biochemicalReaction", "EC-NUMBER", "http://www.w3.org/2001/XMLSchema#string", "*",
"biochemicalReaction", "DELTA-G", "deltaGprimeO", "*",
"biochemicalReaction", "KEQ", "kPrime", "*",
"dna", "SEQUENCE", "http://www.w3.org/2001/XMLSchema#string", "1",
"dna", "ORGANISM", "bioSource", "1",
"rna", "SEQUENCE", "http://www.w3.org/2001/XMLSchema#string", "1",
"rna", "ORGANISM", "bioSource", "1",
"protein", "SEQUENCE", "http://www.w3.org/2001/XMLSchema#string", "1",
"protein", "ORGANISM", "bioSource", "1",
"complex", "COMPONENTS", "physicalEntityParticipant", "*",
"complex", "ORGANISM", "bioSource", "1",
"smallMolecule", "MOLECULAR-WEIGHT", "http://www.w3.org/2001/XMLSchema#double", "1",
"smallMolecule", "CHEMICAL-FORMULA", "http://www.w3.org/2001/XMLSchema#string", "1",
"smallMolecule", "STRUCTURE", "chemicalStructure", "*",
"utilityClass", "COMMENT", "http://www.w3.org/2001/XMLSchema#string", "*",
"chemicalStructure", "STRUCTURE-DATA", "http://www.w3.org/2001/XMLSchema#string", "1",
"chemicalStructure", "STRUCTURE-FORMAT", "http://www.w3.org/2001/XMLSchema#string", "1",
"confidence", "XREF", "publicationXref", "*",
"confidence", "CONFIDENCE-VALUE", "http://www.w3.org/2001/XMLSchema#string", "1",
"deltaGprimeO", "DELTA-G-PRIME-O", "http://www.w3.org/2001/XMLSchema#float", "1",
"deltaGprimeO", "IONIC-STRENGTH", "http://www.w3.org/2001/XMLSchema#float", "1",
"deltaGprimeO", "PH", "http://www.w3.org/2001/XMLSchema#float", "1",
"deltaGprimeO", "PMG", "http://www.w3.org/2001/XMLSchema#float", "1",
"deltaGprimeO", "TEMPERATURE", "http://www.w3.org/2001/XMLSchema#float", "1",
"kPrime", "IONIC-STRENGTH", "http://www.w3.org/2001/XMLSchema#float", "1",
"kPrime", "PH", "http://www.w3.org/2001/XMLSchema#float", "1",
"kPrime", "PMG", "http://www.w3.org/2001/XMLSchema#float", "1",
"kPrime", "TEMPERATURE", "http://www.w3.org/2001/XMLSchema#float", "1",
"evidence", "XREF", "xref", "*",
"evidence", "CONFIDENCE", "confidence", "*",
"evidence", "EVIDENCE-CODE", "openControlledVocabulary", "*",
"evidence", "EXPERIMENTAL-FORM", "experimentalForm", "*",
"experimentalForm", "EXPERIMENTAL-FORM-TYPE", "openControlledVocabulary", "*",
"experimentalForm", "PARTICIPANT", "physicalEntityParticipant", "*",
"pathwayStep", "NEXT-STEP", "pathwayStep", "*",
"pathwayStep", "PATHWAY-COMPONENTS", "interaction", "*",
"pathwayStep", "PATHWAY-COMPONENTS", "pathway", "*",
"pathwayStep", "PATHWAY-COMPONENTS", "pathwayStep", "*",
"pathwayStep", "STEP-INTERACTIONS", "interaction", "*",
"pathwayStep", "STEP-INTERACTIONS", "pathway", "*",
"sequenceFeature", "NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"sequenceFeature", "SHORT-NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"sequenceFeature", "SYNONYMS", "http://www.w3.org/2001/XMLSchema#string", "*",
"sequenceFeature", "XREF", "xref", "*",
"sequenceFeature", "FEATURE-TYPE", "openControlledVocabulary", "1",
"sequenceFeature", "FEATURE-LOCATION", "sequenceLocation", "*",
"sequenceFeature", "SEQUENCE-FEATURE-LIST", "sequenceFeature", "*",
"sequenceInterval", "SEQUENCE-INTERVAL-BEGIN", "sequenceSite", "1",
"sequenceInterval", "SEQUENCE-INTERVAL-END", "sequenceSite", "1",
"sequenceSite", "POSITION-STATUS", "http://www.w3.org/2001/XMLSchema#string", "1",
"sequenceSite", "SEQUENCE-POSITION", "http://www.w3.org/2001/XMLSchema#integer", "1",
"physicalEntityParticipant", "STOICHIOMETRIC-COEFFICIENT","http://www.w3.org/2001/XMLSchema#double", "1",
"physicalEntityParticipant", "CELLULAR-LOCATION", "openControlledVocabulary", "1",
"physicalEntityParticipant", "PHYSICAL-ENTITY", "physicalEntity", "1",
"sequenceParticipant", "SEQUENCE-FEATURE-LIST", "sequenceFeature", "*",
"bioSource", "NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"bioSource", "CELLTYPE", "openControlledVocabulary", "1",
"bioSource", "TISSUE", "openControlledVocabulary", "1",
"bioSource", "TAXON-XREF", "unificationXref", "1",
"dataSource", "NAME", "http://www.w3.org/2001/XMLSchema#string", "1",
"dataSource", "XREF", "xref", "*",
"openControlledVocabulary", "XREF", "unificationXref", "*",
"openControlledVocabulary", "TERM", "http://www.w3.org/2001/XMLSchema#string", "*",
"xref", "DB", "http://www.w3.org/2001/XMLSchema#string", "1",
"xref", "DB-VERSION", "http://www.w3.org/2001/XMLSchema#string", "1",
"xref", "ID", "http://www.w3.org/2001/XMLSchema#string", "1",
"xref", "ID-VERSION", "http://www.w3.org/2001/XMLSchema#string", "1",
"relationshipXref", "RELATIONSHIP-TYPE", "http://www.w3.org/2001/XMLSchema#string", "1",
"publicationXref", "AUTHORS", "http://www.w3.org/2001/XMLSchema#string", "*",
"publicationXref", "TITLE", "http://www.w3.org/2001/XMLSchema#string", "*",
"publicationXref", "YEAR", "http://www.w3.org/2001/XMLSchema#string", "*",
"publicationXref", "URL", "http://www.w3.org/2001/XMLSchema#string", "*",
"publicationXref", "SOURCE", "http://www.w3.org/2001/XMLSchema#string", "*"
)), stringsAsFactors = FALSE
)
#' Class inheritance relationships in Biopax Level 3.
#'
#' A data.frame listing all direct superclasses for every Biopax Level 3 class.
#' The variables are as follows:
#'
#' \itemize{
#' \item class. Name of the class
#' \item superclass. Name of the superclass
#' }
#'
#' NOT UPDATED TO BP3 yet!
#'
#' @docType data
#' @keywords datasets
#' @name CLASS_INHERITANCE_BP3
#' @title CLASS_INHERITANCE_BP3
#' @usage CLASS_INHERITANCE_BP3
#' @format A data frame with 46 rows and 2 columns
#' @export
CLASS_INHERITANCE_BP3 = data.frame(
matrix(ncol=2,byrow=T, dimnames=list(list(),list("class","superclass")),data= c(
"Entity", "",
"Pathway", "Entity",
"Interaction", "Entity",
"PhysicalInteraction", "Interaction",
"Control", "PhysicalInteraction",
"Catalysis", "Control",
"Modulation", "Control",
"Conversion", "PhysicalInteraction",
"ComplexAssembly", "Conversion",
"BiochemicalReaction", "Conversion",
"Transport", "Conversion",
"TransportWithBiochemicalReaction", "BiochemicalReaction",
"TransportWithBiochemicalReaction", "Transport",
"PhysicalEntity", "Entity",
"Dna", "PhysicalEntity",
"Rna", "PhysicalEntity",
"Protein", "PhysicalEntity",
"SmallMolecule", "PhysicalEntity",
"Complex", "PhysicalEntity",
"UtilityClass", "",
"ChemicalStructure", "UtilityClass",
"DeltaG", "UtilityClass",
"kPrime", "UtilityClass",
"Evidence", "UtilityClass",
"ExperimentalForm", "UtilityClass",
"PathwayStep", "UtilityClass",
"EntityFeature", "UtilityClass",
"EntityRference", "UtilityClass",
"SequenceLocation", "UtilityClass",
"SequenceInterval", "SequenceLocation",
"SequenceSite", "SequenceLocation",
"PhysicalEntityParticipant", "UtilityClass",
"SequenceParticipant", "PhysicalEntityParticipant",
"DnaParticipant", "PhysicalEntityParticipant",
"RnaParticipant", "PhysicalEntityParticipant",
"ProteinParticipant", "PhysicalEntityParticipant",
"SmallMoleculeParticipant", "PhysicalEntityParticipant",
"ComplexParticipant", "PhysicalEntityParticipant",
"ExternalReferenceUtilityClass", "UtilityClass",
"BioSource", "ExternalReferenceUtilityClass",
"OpenControlledVocabulary", "ExternalReferenceUtilityClass",
"Xref", "ExternalReferenceUtilityClass",
"UnificationXref", "Xref",
"RelationshipXref", "Xref",
"PublicationXref", "Xref"
)), stringsAsFactors = FALSE
)
#' Class properties in Biopax Level 3.
#'
#' A data.frame listing all direct properties for every Biopax Level 3 class.
#' Together with CLASS_INHERITANCE_BP3 this allows to list all properties, including the inherited ones, of every class.
#'
#' The variables are as follows:
#'
#' \itemize{
#' \item class. Name of the class
#' \item property. Name of the superclass
#' \item property_type.Type of the property, value or reference
#' \item cardinality. Maximum allowed cardinality of a property. Many properties may only be singular.
#' }
#'
#' @docType data
#' @keywords datasets
#' @name CLASS_PROPERTIES_BP3
#' @title CLASS_PROPERTIES_BP3
#' @usage CLASS_PROPERTIES_BP3
#' @format A data frame with 106 rows and 4 columns
#' @export
CLASS_PROPERTIES_BP3 = data.frame(
matrix(ncol=4,byrow=T, dimnames=list(list(),list("class","property","property_type","cardinality")),data= c(
"Entity", "name", "http://www.w3.org/2001/XMLSchema#string", "*",
"Entity", "displayName", "http://www.w3.org/2001/XMLSchema#string", "*",
"Entity", "standardName", "http://www.w3.org/2001/XMLSchema#string", "*",
"Entity", "comment", "http://www.w3.org/2001/XMLSchema#string", "*",
"Entity", "availability", "http://www.w3.org/2001/XMLSchema#string", "*",
"Entity", "dataSource", "Provenance", "*",
"Entity", "xref", "Xref", "*",
"Pathway", "organism", "BioSource", "*",
"Pathway", "evidence", "Evidence", "*",
"Pathway", "pathwayComponent", "Interaction", "*",
"Pathway", "pathwayComponent", "Pathway", "*",
"Pathway", "pathwayComponent", "PathwayStep", "*",
"Interaction", "participant", "Entity", "*",
"Interaction", "participant", "physicalEntityParticipant", "*",
"Interaction", "evidence", "Evidence", "*",
"Interaction", "interactionType", "OpenControlledVocabulary", "*",
"Control", "controlType", "http://www.w3.org/2001/XMLSchema#string", "*",
"Control", "controller", "entity", "*",
"Control", "controlled", "entity", "*",
"Control", "controlled", "Pathway", "*",
"Control", "controlled", "Interaction", "*",
"Catalysis", "direction", "http://www.w3.org/2001/XMLSchema#string", "*",
"Catalysis", "cofactor", "entity", "*",
"Conversion", "spontaneus", "http://www.w3.org/2001/XMLSchema#string", "*",
"Conversion", "left", "entity", "*",
"Conversion", "left", "physicalEntityParticipant", "*",
"Conversion", "right", "entity", "*",
"Conversion", "right", "physicalEntityParticipant", "*",
"BiochemicalReaction", "DELTA-H", "http://www.w3.org/2001/XMLSchema#double", "*",
"BiochemicalReaction", "DELTA-S", "http://www.w3.org/2001/XMLSchema#double", "*",
"BiochemicalReaction", "EC-NUMBER", "http://www.w3.org/2001/XMLSchema#string", "*",
"BiochemicalReaction", "DELTA-G", "deltaGprimeO", "*",
"BiochemicalReaction", "KEQ", "kPrime", "*",
"Dna", "sequence", "http://www.w3.org/2001/XMLSchema#string", "*",
"Dna", "organism", "bioSource", "*",
"Rna", "sequence", "http://www.w3.org/2001/XMLSchema#string", "*",
"Rna", "organism", "bioSource", "*",
"Protein", "sequence", "http://www.w3.org/2001/XMLSchema#string", "*",
"Protein", "organism", "bioSource", "*",
"Complex", "component", "physicalEntityParticipant", "*",
"Complex", "organism", "bioSource", "*",
"SmallMolecule", "molecularWeight", "http://www.w3.org/2001/XMLSchema#double", "*",
"SmallMolecule", "chemicalFormula", "http://www.w3.org/2001/XMLSchema#string", "*",
"SmallMolecule", "structure", "chemicalStructure", "*",
"UtilityClass", "comment", "http://www.w3.org/2001/XMLSchema#string", "*",
"ChemicalStructure", "structureData", "http://www.w3.org/2001/XMLSchema#string", "*",
"ChemicalStructure", "structureFormat", "http://www.w3.org/2001/XMLSchema#string", "*",
"DeltaG", "DELTA-G-PRIME-O", "http://www.w3.org/2001/XMLSchema#float", "*",
"DeltaG", "IONIC-STRENGTH", "http://www.w3.org/2001/XMLSchema#float", "*",
"DeltaG", "PH", "http://www.w3.org/2001/XMLSchema#float", "*",
"DeltaG", "PMG", "http://www.w3.org/2001/XMLSchema#float", "*",
"DeltaG", "temperature", "http://www.w3.org/2001/XMLSchema#float", "*",
"kPrime", "IONIC-STRENGTH", "http://www.w3.org/2001/XMLSchema#float", "*",
"kPrime", "PH", "http://www.w3.org/2001/XMLSchema#float", "*",
"kPrime", "PMG", "http://www.w3.org/2001/XMLSchema#float", "*",
"kPrime", "temperature", "http://www.w3.org/2001/XMLSchema#float", "*",
"Evidence", "xref", "Xref", "*",
"Evidence", "confidence", "Confidence", "*",
"Evidence", "evidenceCode", "OpenControlledVocabulary", "*",
"Evidence", "experimentalForm", "ExperimentalForm", "*",
"ExperimentalForm", "experimentalForm", "OpenControlledVocabulary", "*",
"ExperimentalForm", "participant", "physicalEntityParticipant", "*",
"PathwayStep", "nextStep", "PathwayStep", "*",
"PathwayStep", "pathwayComponent", "Interaction", "*",
"PathwayStep", "pathwayComponent", "Pathway", "*",
"PathwayStep", "pathwayComponent", "PathwayStep", "*",
"PathwayStep", "stepProcess", "Interaction", "*",
"PathwayStep", "stepProcess", "Pathway", "*",
"EntityFeature", "name", "http://www.w3.org/2001/XMLSchema#string", "*",
"EntityFeature", "SYNONYMS", "http://www.w3.org/2001/XMLSchema#string", "*",
"EntityFeature", "xref", "Xref", "*",
"EntityFeature", "FEATURE-TYPE", "OpenControlledVocabulary", "*",
"EntityFeature", "FEATURE-LOCATION", "SequenceLocation", "*",
"EntityFeature", "SEQUENCE-FEATURE-LIST", "SequenceFeature", "*",
"SequenceInterval", "SEQUENCE-INTERVAL-BEGIN", "sequenceSite", "*",
"SequenceInterval", "SEQUENCE-INTERVAL-END", "sequenceSite", "*",
"SequenceSite", "POSITION-STATUS", "http://www.w3.org/2001/XMLSchema#string", "*",
"SequenceSite", "SEQUENCE-POSITION", "http://www.w3.org/2001/XMLSchema#integer", "*",
"BioSource", "name", "http://www.w3.org/2001/XMLSchema#string", "*",
"BioSource", "CELLTYPE", "OpenControlledVocabulary", "*",
"BioSource", "TISSUE", "OpenControlledVocabulary", "*",
"BioSource", "TAXON-XREF", "UnificationXref", "*",
"DataSource", "name", "http://www.w3.org/2001/XMLSchema#string", "*",
"DataSource", "xref", "Xref", "*",
"OpenControlledVocabulary", "xref", "UnificationXref", "*",
"OpenControlledVocabulary", "TERM", "http://www.w3.org/2001/XMLSchema#string", "*",
"Xref", "DB", "http://www.w3.org/2001/XMLSchema#string", "*",
"Xref", "DB-VERSION", "http://www.w3.org/2001/XMLSchema#string", "*",
"Xref", "ID", "http://www.w3.org/2001/XMLSchema#string", "*",
"Xref", "ID-VERSION", "http://www.w3.org/2001/XMLSchema#string", "*",
"RelationshipXref", "RELATIONSHIP-TYPE", "http://www.w3.org/2001/XMLSchema#string", "*",
"PublicationXref", "AUTHORS", "http://www.w3.org/2001/XMLSchema#string", "*",
"PublicationXref", "TITLE", "http://www.w3.org/2001/XMLSchema#string", "*",
"PublicationXref", "YEAR", "http://www.w3.org/2001/XMLSchema#string", "*",
"PublicationXref", "URL", "http://www.w3.org/2001/XMLSchema#string", "*",
"PublicationXref", "SOURCE", "http://www.w3.org/2001/XMLSchema#string", "*"
)), stringsAsFactors = FALSE
)
#' This function returns the subclasses of the supplied biopax class.
#'
#' This function returns the subclasses of the supplied biopax class.
#'
#' @param classname A string containing a class name
#' @param biopaxlevel Numeric. Specifies the Biopax Level to use.
#' @return Returns character vector containing the subclasses of the supplied class
#' @author Frank Kramer
#' @export
#' @examples
#' getSubClasses("control")
getSubClasses <- function(classname, biopaxlevel=3) {
classname = stripns(classname)
ret = list()
for(x in 1:10) {
if(biopaxlevel==2) {
ret = CLASS_INHERITANCE_BP2$class[CLASS_INHERITANCE_BP2$superclass %in% c(classname,ret)]
}
if(biopaxlevel==3) {
ret = CLASS_INHERITANCE_BP3$class[CLASS_INHERITANCE_BP3$superclass %in% c(classname,ret)]
}
}
ret
}
#' This function returns the superclasses of the supplied biopax class.
#'
#' This function returns the superclasses of the supplied biopax class.
#'
#' @param classname A string containing a class name
#' @param biopaxlevel Numeric. Specifies the Biopax Level to use.
#' @return Returns character vector containing the superclasses of the supplied class
#' @author Frank Kramer
#' @export
#' @examples
#' getSuperClasses("control")
getSuperClasses <- function(classname, biopaxlevel=3) {
classname = stripns(classname)
ret = list()
for(x in 1:10) {
if(biopaxlevel==2) {
ret = CLASS_INHERITANCE_BP2$superclass[CLASS_INHERITANCE_BP2$class %in% c(classname,ret)]
}
if(biopaxlevel==3) {
ret = CLASS_INHERITANCE_BP3$superclass[CLASS_INHERITANCE_BP3$class %in% c(classname,ret)]
}
}
ret[ret != ""]
}
#' This function returns the properties of the supplied biopax class.
#'
#' This function returns the properties of the supplied biopax class. It always considers inhertance.
#' Every class inhertis the properties of its super classes. A table listing all available properties and their cardinalities (for Biopax Level 2).
#'
#' @param classname A string containing a class name
#' @param biopaxlevel Numeric. Specifies the Biopax Level to use.
#' @return Returns a data.frame containing the properties and cardinalities of the supplied class
#' @author Frank Kramer
#' @export
#' @examples
#' getClassProperties("control")
getClassProperties <- function(classname, biopaxlevel=3) {
classname = stripns(classname)
if(biopaxlevel==2) {
classes = c(classname,getSuperClasses(classname,biopaxlevel))
return(CLASS_PROPERTIES_BP2[CLASS_PROPERTIES_BP2$class %in% classes,])
}
if(biopaxlevel==3) {
classes = c(classname,getSuperClasses(classname,biopaxlevel))
return(CLASS_PROPERTIES_BP3[CLASS_PROPERTIES_BP3$class %in% classes,])
}
return(NULL)
}
#
########### BIOPAX LEVEL 2 CORE CLASS DEFINITIONS
#
########### ENTITY
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @returnType
##' @return
##' @author fkramer
##' @export
#newEntity <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability)
# class(ret) <- c("biopax2_Entity",class(ret))
# ret
#}
#
########### PATHWAY
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param organism
##' @param evidence
##' @param pathwaycomponents
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPathway <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), organism=list(), evidence=list(), pathwaycomponents=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,organism=organism,evidence=evidence,pathwaycomponents=pathwaycomponents)
# class(ret) <- c("biopax2_Pathway","biopax2_Entity",class(ret))
# ret
#}
#
########### PHYSICAL ENTITY
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPhysicalEntity <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability)
# class(ret) <- c("biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param sequence
##' @param organism
##' @returnType
##' @return
##' @author fkramer
##' @export
#newDNA <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), sequence=list(), organism=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability, sequence=sequence, organism=organism)
# class(ret) <- c("biopax2_DNA","biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param sequence
##' @param organism
##' @returnType
##' @return
##' @author fkramer
##' @export
#newRNA <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), sequence=list(), organism=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability, sequence=sequence, organism=organism)
# class(ret) <- c("biopax2_RNA","biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param sequence
##' @param organism
##' @returnType
##' @return
##' @author fkramer
##' @export
#newProtein <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), sequence=list(), organism=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability, sequence=sequence, organism=organism)
# class(ret) <- c("biopax2_Protein","biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param components
##' @param organism
##' @returnType
##' @return
##' @author fkramer
##' @export
#newComplex <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), components=list(), organism=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability, components=components, organism=organism)
# class(ret) <- c("biopax2_Complex","biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param structure
##' @param chemicalformula
##' @param molecularweight
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSmallMolecule <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), structure=list(), chemicalformula=list(), molecularweight=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,structure=structure,chemicalformula=chemicalformula,
# molecularweight=molecularweight)
# class(ret) <- c("biopax2_SmallMolecule","biopax2_PhysicalEntity","biopax2_Entity",class(ret))
# ret
#}
#
########### INTERACTION
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @returnType
##' @return
##' @author fkramer
##' @export
#newInteraction <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence)
# class(ret) <- c("biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPhysicalInteraction <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype)
# class(ret) <- c("biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param controltype
##' @param controller
##' @param controlled
##' @returnType
##' @return
##' @author fkramer
##' @export
#newControl <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# controltype=list(), controller=list(), controlled=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,controltype=controltype,controller=controller,controlled=controlled)
# class(ret) <- c("biopax2_Control","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param controltype
##' @param controller
##' @param controlled
##' @param direction
##' @param cofactor
##' @returnType
##' @return
##' @author fkramer
##' @export
#newCatalysis <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# controltype=list(), controller=list(), controlled=list(), direction=list(), cofactor=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,controltype=controltype,controller=controller,controlled=controlled,
# direction=direction,cofactor=cofactor)
# class(ret) <- c("biopax2_Catalysis","biopax2_Control","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param controltype
##' @param controller
##' @param controlled
##' @param direction
##' @param cofactor
##' @returnType
##' @return
##' @author fkramer
##' @export
#newModulation <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# controltype=list(), controller=list(), controlled=list(), direction=list(), cofactor=list() ){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,controltype=controltype,controller=controller,controlled=controlled)
# class(ret) <- c("biopax2_Modulation","biopax2_Control","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param spontaneous
##' @param left
##' @param right
##' @returnType
##' @return
##' @author fkramer
##' @export
#newConversion <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# spontaneous=list(), left=list(), right=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,spontaneous=spontaneous,left=left,right=right)
# class(ret) <- c("biopax2_Conversion","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param spontaneous
##' @param left
##' @param right
##' @returnType
##' @return
##' @author fkramer
##' @export
#newComplexAssembly <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# spontaneous=list(), left=list(), right=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,spontaneous=spontaneous,left=left,right=right)
# class(ret) <- c("biopax2_ComplexAssembly","biopax2_Conversion","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param spontaneous
##' @param left
##' @param right
##' @returnType
##' @return
##' @author fkramer
##' @export
#newTransport <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# spontaneous=list(), left=list(), right=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,spontaneous=spontaneous,left=left,right=right)
# class(ret) <- c("biopax2_Transport","biopax2_Conversion","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param spontaneous
##' @param left
##' @param right
##' @param deltag
##' @param deltah
##' @param deltas
##' @param keq
##' @param ecnumber
##' @returnType
##' @return
##' @author fkramer
##' @export
#newBiochemicalReaction <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# spontaneous=list(), left=list(), right=list(), deltag=list(), deltah=list(), deltas=list(), keq=list(),
# ecnumber=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,spontaneous=spontaneous,left=left,right=right,
# deltag=deltag,deltah=deltah,deltas=deltas,keq=keq,ecnumber=ecnumber)
# class(ret) <- c("biopax2_BiochemicalReaction","biopax2_Conversion","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param name
##' @param shortname
##' @param synonyms
##' @param comment
##' @param datasource
##' @param xref
##' @param availability
##' @param participants
##' @param evidence
##' @param interactiontype
##' @param spontaneous
##' @param left
##' @param right
##' @param deltag
##' @param deltah
##' @param deltas
##' @param keq
##' @param ecnumber
##' @returnType
##' @return
##' @author fkramer
##' @export
#newTransportWithBiochemicalReaction <- function( instance_id, name, shortname=list(), synonyms=list(), comment=list(), datasource=list(),
# xref=list(), availability=list(), participants=list(), evidence=list(), interactiontype=list(),
# spontaneous=list(), left=list(), right=list(), deltag=list(), deltah=list(), deltas=list(), keq=list(),
# ecnumber=list()){
# ret = list(name=name, instance_id=instance_id,shortname=shortname,synonyms=synonyms,comment=comment,datasource=datasource,
# xref=xref,availability=availability,participants=participants,evidence=evidence,
# interactiontype=interactiontype,spontaneous=spontaneous,left=left,right=right,
# deltag=deltag,deltah=deltah,deltas=deltas,keq=keq,ecnumber=ecnumber)
# class(ret) <- c("biopax2_TransportWithBiochemicalReaction","biopax2_BiochemicalReaction","biopax2_Transport","biopax2_Conversion","biopax2_PhysicalInteraction","biopax2_Interaction","biopax2_Entity",class(ret))
# ret
#}
#
############## END OF CORE CLASS DEFINITIONS
############## UTILITY CLASS DEFINITIONS
##utilityClass:
##chemicalStructure,confidence, evidence, externalReferenceUtilityClass, pathwayStep,
##physicalEntityParticipant, sequenceFeature, and sequenceLocation
#
########### ENTITY
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @returnType
##' @return
##' @author fkramer
##' @export
#newUtilityClass <- function( instance_id, comment=list() ){
# ret = list(instance_id=instance_id,comment=comment)
# class(ret) <- c("biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param structureformat
##' @param structuredata
##' @returnType
##' @return
##' @author fkramer
##' @export
#newChemicalStructure <- function( instance_id, comment=list(), structureformat=list(), structuredata=list() ){
# ret = list(instance_id=instance_id,comment=comment,structureformat=structureformat, structuredata=structuredata)
# class(ret) <- c("biopax2_ChemicalStructure","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param confidencevalue
##' @param xref
##' @returnType
##' @return
##' @author fkramer
##' @export
#newConfidence <- function( instance_id, comment=list(), confidencevalue=list(), xref=list() ){
# ret = list(instance_id=instance_id,comment=comment,confidencevalue=confidencevalue,xref=xref)
# class(ret) <- c("biopax2_Confidence","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param xref
##' @param experimentalform
##' @param evidencecode
##' @param confidence
##' @returnType
##' @return
##' @author fkramer
##' @export
#newEvidence <- function( instance_id, comment=list(), xref=list(), experimentalform=list(), evidencecode=list(), confidence=list() ){
# ret = list(instance_id=instance_id,comment=comment, xref=xref, experimentalform=experimentalform, evidencecode=evidencecode, confidence=confidence)
# class(ret) <- c("biopax2_Evidence","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param experimentalformtype
##' @param participant
##' @returnType
##' @return
##' @author fkramer
##' @export
#newExperimentalForm <- function( instance_id, comment=list(), experimentalformtype=list(), participant=list() ){
# ret = list(instance_id=instance_id,comment=comment, experimentalformtype=experimentalformtype, participant=participant)
# class(ret) <- c("biopax2_ExperimentalForm","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param stepinteractions
##' @param nextstep
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPathwayStep <- function( instance_id, comment=list(), stepinteractions=list(), nextstep=list() ){
# ret = list(instance_id=instance_id,comment=comment, stepinteractions=stepinteractions, nextstep=nextstep)
# class(ret) <- c("biopax2_PathwayStep","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param name
##' @param featuretype
##' @param shortname
##' @param synonyms
##' @param xref
##' @param featurelocation
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSequenceFeature <- function( instance_id, comment=list(), name=list(), featuretype=list(), shortname=list(),
# synonyms=list(), xref=list(), featurelocation=list() ){
# ret = list(instance_id=instance_id,comment=comment, name=name, featuretype=featuretype, shortname=shortname,
# synonyms=synonyms, xref=xref, featurelocation=featurelocation )
# class(ret) <- c("biopax2_SequenceFeature","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSequenceLocation <- function( instance_id, comment=list() ){
# ret = list(instance_id=instance_id,comment=comment)
# class(ret) <- c("biopax2_SequenceLocation","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param sequenceintervalbegin
##' @param sequenceintervalend
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSequenceInterval <- function( instance_id, comment=list(), sequenceintervalbegin=list(), sequenceintervalend=list() ){
# ret = list(instance_id=instance_id,comment=comment,sequenceintervalbegin=sequenceintervalbegin,sequenceintervalend=sequenceintervalend)
# class(ret) <- c("biopax2_SequenceInterval","biopax2_SequenceLocation","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param positionstatus
##' @param sequenceposition
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSequenceSite <- function( instance_id, comment=list(), positionstatus=list(), sequenceposition=list() ){
# ret = list(instance_id=instance_id,comment=comment, positionstatus=positionstatus, sequenceposition=sequenceposition)
# class(ret) <- c("biopax2_SequenceSite","biopax2_SequenceLocation","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPhysicalEntityParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @param sequencefeaturelist
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSequenceParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list(), sequencefeaturelist=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity, sequencefeaturelist=sequencefeaturelist)
# class(ret) <- c("biopax2_SequenceParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newDNAParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_DNAParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newRNAParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_RNAParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newProteinEntityParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_ProteinParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newSmallMoleculeParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_SmallMoleculeParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param cellularlocation
##' @param stoichiometriccoefficient
##' @param physicalentity
##' @returnType
##' @return
##' @author fkramer
##' @export
#newComplexParticipant <- function( instance_id, comment=list(), cellularlocation=list(), stoichiometriccoefficient=list(), physicalentity=list() ){
# ret = list(instance_id=instance_id,comment=comment, cellularlocation=cellularlocation, stoichiometriccoefficient=stoichiometriccoefficient, physicalentity=physicalentity)
# class(ret) <- c("biopax2_ComplexParticipant","biopax2_PhysicalEntityParticipant","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @returnType
##' @return
##' @author fkramer
##' @export
#newExternalReferenceUtilityClass <- function( instance_id, comment=list() ){
# ret = list(instance_id=instance_id,comment=comment)
# class(ret) <- c("biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param name
##' @param xref
##' @returnType
##' @return
##' @author fkramer
##' @export
#newDataSource <- function( instance_id, comment=list(), name=list(), xref=list() ){
# ret = list(instance_id=instance_id,comment=comment, name=name, xref=xref)
# class(ret) <- c("biopax2_DataSource","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param name
##' @param taxonxref
##' @param tissue
##' @param celltype
##' @returnType
##' @return
##' @author fkramer
##' @export
#newBioSource <- function( instance_id, comment=list(), name=list(), taxonxref=list(), tissue=list(), celltype=list() ){
# ret = list(instance_id=instance_id,comment=comment, name=name, taxonxref=taxonxref, tissue=tissue, celltype=celltype)
# class(ret) <- c("biopax2_BioSource","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param term
##' @param xref
##' @returnType
##' @return
##' @author fkramer
##' @export
#newOpenControlledVocabulary <- function( instance_id, comment=list(), term=list(), xref=list() ){
# ret = list(instance_id=instance_id,comment=comment, term=term, xref=xref)
# class(ret) <- c("biopax2_OpenControlledVocabulary","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param db
##' @param dbversion
##' @param id
##' @param idversion
##' @returnType
##' @return
##' @author fkramer
##' @export
#newXref <- function( instance_id, comment=list(), db=list(), dbversion=list(), id=list(), idversion=list() ){
# ret = list(instance_id=instance_id,comment=comment, db=db, dbversion=dbversion, id=id, idversion=idversion)
# class(ret) <- c("biopax2_Xref","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param db
##' @param dbversion
##' @param id
##' @param idversion
##' @returnType
##' @return
##' @author fkramer
##' @export
#newUnificationXref <- function( instance_id, comment=list(), db=list(), dbversion=list(), id=list(), idversion=list() ){
# ret = list(instance_id=instance_id,comment=comment, db=db, dbversion=dbversion, id=id, idversion=idversion)
# class(ret) <- c("biopax2_UnificationXref","biopax2_Xref","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param db
##' @param dbversion
##' @param id
##' @param idversion
##' @param relationshiptype
##' @returnType
##' @return
##' @author fkramer
##' @export
#newRelationshipXref <- function( instance_id, comment=list(), db=list(), dbversion=list(), id=list(), idversion=list(), relationshiptype=list() ){
# ret = list(instance_id=instance_id,comment=comment, db=db, dbversion=dbversion, id=id, idversion=idversion, relationshiptype=relationshiptype)
# class(ret) <- c("biopax2_RelationshipXref","biopax2_Xref","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
##'
##' @param instance_id ID of the instance. Should be a a string, should be unique.
##' @param comment
##' @param db
##' @param dbversion
##' @param id
##' @param idversion
##' @param title
##' @param year
##' @param authors
##' @param url
##' @param source
##' @returnType
##' @return
##' @author fkramer
##' @export
#newPublicationXref <- function( instance_id, comment=list(), db=list(), dbversion=list(), id=list(), idversion=list(), title=list(), year=list(), authors=list(), url=list(), source=list() ){
# ret = list(instance_id=instance_id,comment=comment, db=db, dbversion=dbversion, id=id, idversion=idversion, title=title, year=year, authors=authors, url=url, source=source)
# class(ret) <- c("biopax2_PublicationXref","biopax2_Xref","biopax2_ExternalReferenceUtilityClass","biopax2_UtilityClass",class(ret))
# ret
#}
#
############## END OF CLASS DEFINITIONS
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.