Index

A B C F G I N O P R S T U V
All Classes and Interfaces|All Packages|Constant Field Values

A

autoName(Provenance) - Static method in class org.biopax.paxtools.normalizer.Normalizer

Auto-generates standard and other names for the datasource from either its URI or one of the names (preferably - standard name)

B

BIOREGISTRY_IO - Static variable in class org.biopax.paxtools.normalizer.Resolver

BIOREGISTRY_JSON_URL - Static variable in class org.biopax.paxtools.normalizer.Resolver

C

checkRegExp(String, String) - Static method in class org.biopax.paxtools.normalizer.Resolver

Checks if the identifier given follows the regular expression of its data type (also provided).

chemDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

Set to prefer collecting chemical IDs of such Xrefs where the small molecules db starts with or equals given string, ignoring case.

ConfigurableIDFetcher - Class in org.biopax.paxtools.normalizer

Tries to get preferred type IDs of an entity reference.

ConfigurableIDFetcher() - Constructor for class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

Constructor.

convertToLevel3(String) - Static method in class org.biopax.paxtools.normalizer.Normalizer

Converts BioPAX L1 or L2 RDF/XML string data to BioPAX L3 string.

F

fetchID(BioPAXElement) - Method in class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

G

getBanana() - Method in class org.biopax.paxtools.normalizer.Namespace

getBanana_peel() - Method in class org.biopax.paxtools.normalizer.Namespace

getChemDbStartsWithOrEquals() - Method in class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

getCURIE(String, String) - Static method in class org.biopax.paxtools.normalizer.Resolver

Builds a normalized CURIE (Compact URI/ID) of the biochemical entity from the collection name/synonym and bio id.

getDescription() - Method in class org.biopax.paxtools.normalizer.Normalizer

Description of the model to normalize.

getNamespace(String) - Static method in class org.biopax.paxtools.normalizer.Resolver

Gets Namespace by its Name, Prefix, URI (URN/URL), known synonym or misspelling.

getNamespace(String, boolean) - Static method in class org.biopax.paxtools.normalizer.Resolver

Gets Namespace by its Name, Prefix, URN/URL, or (optionally) spelling variant or synonym

getNamespaces() - Static method in class org.biopax.paxtools.normalizer.Resolver

Gets the unmodifiable map of the bio identifier types registry records.

getSeqDbStartsWithOrEquals() - Method in class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

getSpellmap() - Static method in class org.biopax.paxtools.normalizer.Resolver

Gets the unmodifiable map - mapping a sanitized id-type name/variant/synonym (non-alphanumeric chars are removed) to the corresponding namespace prefix.

getSynonymap() - Static method in class org.biopax.paxtools.normalizer.Resolver

Gets the unmodifiable map - mapping an identifier type synonym to the corresponding namespace prefix.

getURI(String, String) - Static method in class org.biopax.paxtools.normalizer.Resolver

Builds a URI of the bioentity (e.g., "http://bioregistry.io/go:0045202") from the collection name/synonym and bio id.

getXmlBase() - Method in class org.biopax.paxtools.normalizer.Normalizer

I

isFixDisplayName() - Method in class org.biopax.paxtools.normalizer.Normalizer

isKnownNameOrVariant(String) - Static method in class org.biopax.paxtools.normalizer.Resolver

N

Namespace - Class in org.biopax.paxtools.normalizer

Namespace() - Constructor for class org.biopax.paxtools.normalizer.Namespace

normalize(Model) - Method in class org.biopax.paxtools.normalizer.Normalizer

BioPAX normalization (modifies the original Model)

normalize(Model, boolean) - Method in class org.biopax.paxtools.normalizer.Normalizer

BioPAX normalization (modifies the original Model)

Normalizer - Class in org.biopax.paxtools.normalizer

BioPAX (Level 3) Normalizer, an advanced BioPAX utility to help pathway data integrating and linking.

Normalizer() - Constructor for class org.biopax.paxtools.normalizer.Normalizer

Constructor

normalizeXrefs(Model, boolean) - Method in class org.biopax.paxtools.normalizer.Normalizer

Normalizes xrefs to ease normalizing or merging other BioPAX objects later on, and also because some original xref URIs should in fact be used for different BioPAX types (for CV or ProteinReference instead); so, this will also replace URIs of xrefs having bad 'db' or 'id'.

O

org.biopax.paxtools.normalizer - package org.biopax.paxtools.normalizer

P

PROPERTY_NORMALIZER_URI_STRATEGY - Static variable in class org.biopax.paxtools.normalizer.Normalizer

R

Resolver - Class in org.biopax.paxtools.normalizer

Singleton bio identifier resolver utility.

Resolver() - Constructor for class org.biopax.paxtools.normalizer.Resolver

S

seqDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.normalizer.ConfigurableIDFetcher

Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case.

setDescription(String) - Method in class org.biopax.paxtools.normalizer.Normalizer

setFixDisplayName(boolean) - Method in class org.biopax.paxtools.normalizer.Normalizer

setSpellmap(Map<String, String>) - Static method in class org.biopax.paxtools.normalizer.Resolver

Customize the mapping from a bio identifier type name/variant/synonym (non-alphanumeric chars should be removed) to the corresponding record/namespace prefix.

setSynonymap(Map<String, String>) - Static method in class org.biopax.paxtools.normalizer.Resolver

Customize the mapping from a bio identifier type synonym to the corresponding namespace prefix.

setXmlBase(String) - Method in class org.biopax.paxtools.normalizer.Normalizer

T

typeCodes - Static variable in class org.biopax.paxtools.normalizer.Normalizer

U

uri(String, String, String, Class<? extends BioPAXElement>) - Static method in class org.biopax.paxtools.normalizer.Normalizer

Generates a new BioPAX element URI using given URI namespace (xml:base), BioPAX class, and two different identifiers (at least one is required).

uri(String, String, String, Class<? extends BioPAXElement>, boolean) - Static method in class org.biopax.paxtools.normalizer.Normalizer

Generates a new BioPAX element URI using given URI namespace (xml:base), BioPAX class, and two different identifiers (at least one is required).

useNameWhenNoDbMatch(boolean) - Method in class org.biopax.paxtools.normalizer.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 were no xrefs at all).

V

VALUE_NORMALIZER_URI_STRATEGY_MD5 - Static variable in class org.biopax.paxtools.normalizer.Normalizer

VALUE_NORMALIZER_URI_STRATEGY_SIMPLE - Static variable in class org.biopax.paxtools.normalizer.Normalizer

A B C F G I N O P R S T U V
All Classes and Interfaces|All Packages|Constant Field Values