A B C D F G I L O P R S T V W

A

AbstractSolrLoader - Class in owltools.solrj
Root class for loading ontologies or ontology-related data into a Solr instance using web services and the solrj library
AbstractSolrLoader(SolrServer) - Constructor for class owltools.solrj.AbstractSolrLoader
 
AbstractSolrLoader(String) - Constructor for class owltools.solrj.AbstractSolrLoader
 
add(FlexLine) - Method in class owltools.flex.FlexDocument
Add a line to the document.
add(SolrInputDocument) - Method in class owltools.solrj.AbstractSolrLoader
 
add(String) - Method in class owltools.yaml.golrconfig.ConfigManager
Work with a flexible document definition from a configuration file.
addAll(Collection<SolrInputDocument>) - Method in class owltools.solrj.AbstractSolrLoader
 
addAllAndCommit() - Method in class owltools.solrj.AbstractSolrLoader
 
addAssociatedGeneProduct(String, String) - Method in class owltools.panther.PANTHERTree
Add an associated id/label for a term in this tree.
associatedIdentifierSet() - Method in class owltools.panther.PANTHERTree
Return a set of all identifiers associated with this family.

B

boost_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
boost_weights - Variable in class owltools.yaml.golrconfig.GOlrField
 

C

cardinality - Variable in class owltools.yaml.golrconfig.GOlrField
 
collect(FlexDocument) - Method in class owltools.solrj.FlexSolrDocumentLoader
Take args and add it index (no commits) Main wrapping for adding ontology documents to GOlr.
collect(OWLObject, OWLGraphWrapper) - Method in class owltools.solrj.OntologyGeneralSolrDocumentLoader
 
collect(OWLObject, OWLGraphWrapper) - Method in class owltools.solrj.OntologySolrLoader
Deprecated.  
config - Variable in class owltools.flex.FlexCollection
 
ConfigManager - Class in owltools.yaml.golrconfig
 
ConfigManager() - Constructor for class owltools.yaml.golrconfig.ConfigManager
Constructor.

D

description - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
description - Variable in class owltools.yaml.golrconfig.GOlrField
 
display_name - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
display_name - Variable in class owltools.yaml.golrconfig.GOlrField
 
docs - Variable in class owltools.flex.FlexCollection
 
document_category - Variable in class owltools.yaml.golrconfig.GOlrConfig
 

F

field - Variable in class owltools.flex.FlexLine
 
field() - Method in class owltools.flex.FlexLine
Return the field name.
fields - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
fileCount - Variable in class owltools.panther.PANTHERForest
 
filter_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
filter_weights - Variable in class owltools.yaml.golrconfig.GOlrField
 
FlexCollection - Class in owltools.flex
Pull defined sources into a middle state for output, loading into Solr, etc.
FlexCollection(OWLGraphWrapper) - Constructor for class owltools.flex.FlexCollection
More fun init.
FlexCollection(ConfigManager, OWLGraphWrapper) - Constructor for class owltools.flex.FlexCollection
More fun init.
FlexDocument - Class in owltools.flex
Pull defined sources into a middle state for output, loading into Solr, etc.
FlexDocument() - Constructor for class owltools.flex.FlexDocument
Init.
FlexLine - Class in owltools.flex
Workalike for a singleton line in a Solr document.
FlexLine(String, String) - Constructor for class owltools.flex.FlexLine
Singleton init.
FlexLine(String, ArrayList<String>) - Constructor for class owltools.flex.FlexLine
List init.
FlexSolrDocumentLoader - Class in owltools.solrj
A slightly generic class for loading a Solr index compatible with the constraints defined by a BBOP-JS Solr index.
FlexSolrDocumentLoader(String, FlexCollection) - Constructor for class owltools.solrj.FlexSolrDocumentLoader
 

G

GafSolrDocumentLoader - Class in owltools.solrj
A very specific class for the specific use case of loading in a GAF-like document into a Solr index.
GafSolrDocumentLoader(String) - Constructor for class owltools.solrj.GafSolrDocumentLoader
 
getAncestorAnnotations(String) - Method in class owltools.panther.PANTHERTree
Return all annotations to ancestor nodes.
getAncestors(String) - Method in class owltools.panther.PANTHERTree
Return the ancestors of this node as an ID set.
getAssociatedGeneProductIDs() - Method in class owltools.panther.PANTHERTree
Return the associated gene/product ids for this tree.
getAssociatedGeneProductJSONMap() - Method in class owltools.panther.PANTHERTree
Return the mapping of associated gene/product ids to labels for this tree.
getAssociatedGeneProductLabels() - Method in class owltools.panther.PANTHERTree
Return the associated gene/product labels for this tree.
getAssociatedTrees(String) - Method in class owltools.panther.PANTHERForest
Return the number of unique bioentity identifiers found in the set.
getDescendantAnnotations(String) - Method in class owltools.panther.PANTHERTree
Return all annotations to descendant nodes.
getDescendants(String) - Method in class owltools.panther.PANTHERTree
Return the descendants of this node as an ID set.
getExtString(OWLObject, ArrayList<String>) - Method in class owltools.flex.FlexCollection
Get properly formatted output from the OWLGraphWrapper.
getExtStringList(OWLObject, ArrayList<String>) - Method in class owltools.flex.FlexCollection
Get properly formatted output from the OWLGraphWrapper.
getFieldComments(String) - Method in class owltools.yaml.golrconfig.ConfigManager
Return the comments associated with the GOlrCoreField id; empty list if there weren't any.
getFields() - Method in class owltools.yaml.golrconfig.ConfigManager
Get all the fields.
getGafDocument() - Method in class owltools.solrj.GafSolrDocumentLoader
 
getGraph() - Method in class owltools.solrj.AbstractSolrLoader
 
getNHXString() - Method in class owltools.panther.PANTHERTree
Return the raw Newick-type input string.
getNumberOfFilesInSet() - Method in class owltools.panther.PANTHERForest
Return the number of files read into the set.
getNumberOfIdentifiersInSet() - Method in class owltools.panther.PANTHERForest
Return the number of unique identifiers found in the set.
getOWLShuntGraph() - Method in class owltools.panther.PANTHERTree
Return the complete OWL shunt graph representation of the phylogenic tree.
getPANTHERID() - Method in class owltools.panther.PANTHERTree
Return the tree public (PANTHER) identifier.
getTreeByID(String) - Method in class owltools.panther.PANTHERForest
Return the tree for the tree unique identifier, If nothing was found, return null.
getTreeID() - Method in class owltools.panther.PANTHERTree
Return the tree internal identifier.
getTreeIDSet() - Method in class owltools.panther.PANTHERForest
Return the unique tree identifiers found in the forest.
getTreeLabel() - Method in class owltools.panther.PANTHERTree
Return the tree label.
GOlrConfig - Class in owltools.yaml.golrconfig
 
GOlrConfig() - Constructor for class owltools.yaml.golrconfig.GOlrConfig
 
GOlrDynamicField - Class in owltools.yaml.golrconfig
Deprecated. 
GOlrDynamicField() - Constructor for class owltools.yaml.golrconfig.GOlrDynamicField
Deprecated.  
GOlrField - Class in owltools.yaml.golrconfig
 
GOlrField() - Constructor for class owltools.yaml.golrconfig.GOlrField
 
GOlrFixedField - Class in owltools.yaml.golrconfig
Deprecated. 
GOlrFixedField() - Constructor for class owltools.yaml.golrconfig.GOlrFixedField
Deprecated.  
graph - Variable in class owltools.flex.FlexCollection
 
graph - Variable in class owltools.solrj.AbstractSolrLoader
 

I

id - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
id - Variable in class owltools.yaml.golrconfig.GOlrField
 
incrementalAddAndCommit() - Method in class owltools.solrj.AbstractSolrLoader
 
indexed - Variable in class owltools.yaml.golrconfig.GOlrField
 
isMulti() - Method in class owltools.flex.FlexLine
Return whether or not the line has a single value or multiple values.
isSingle() - Method in class owltools.flex.FlexLine
Return whether or not the line has a single value or multiple values.
iterator() - Method in class owltools.flex.FlexCollection
 
iterator() - Method in class owltools.flex.FlexDocument
 
iterator() - Method in class owltools.flex.FlexLine
 

L

lines - Variable in class owltools.flex.FlexDocument
 
load() - Method in class owltools.solrj.AbstractSolrLoader
 
load() - Method in class owltools.solrj.FlexSolrDocumentLoader
 
load() - Method in class owltools.solrj.GafSolrDocumentLoader
 
load() - Method in class owltools.solrj.OntologyGeneralSolrDocumentLoader
 
load() - Method in class owltools.solrj.OntologySolrLoader
Deprecated.  
load() - Method in class owltools.solrj.OptimizeSolrDocumentLoader
 
load() - Method in class owltools.solrj.PANTHERGeneralSolrDocumentLoader
 
load() - Method in class owltools.solrj.PANTHERSolrDocumentLoader
 

O

OntologyGeneralSolrDocumentLoader - Class in owltools.solrj
A highly hard-wired class to specifically load the ontology graph into a set of hard-wired fields for the AmiGO 2/GOlr general-config.yaml schema.
OntologyGeneralSolrDocumentLoader(String, OWLGraphWrapper) - Constructor for class owltools.solrj.OntologyGeneralSolrDocumentLoader
 
OntologySolrLoader - Class in owltools.solrj
Deprecated. 
OntologySolrLoader(String, OWLGraphWrapper) - Constructor for class owltools.solrj.OntologySolrLoader
Deprecated.  
OptimizeSolrDocumentLoader - Class in owltools.solrj
A hard-wired optimize command for after we've done everything that we wanted to load.
OptimizeSolrDocumentLoader(String) - Constructor for class owltools.solrj.OptimizeSolrDocumentLoader
 
owltools.flex - package owltools.flex
Flex Document
owltools.panther - package owltools.panther
PANTHER Tree Tools
owltools.solrj - package owltools.solrj
OWLTools and Solr
owltools.yaml.golrconfig - package owltools.yaml.golrconfig
YAML GOlr Configuration

P

PANTHERForest - Class in owltools.panther
Methods to simplify the work with sets of PANTHER trees.
PANTHERForest(File) - Constructor for class owltools.panther.PANTHERForest
Create an instance for the given privitve array of files.
PANTHERGeneralSolrDocumentLoader - Class in owltools.solrj
A hard-wired loader for the general-config.yaml profile.
PANTHERGeneralSolrDocumentLoader(String) - Constructor for class owltools.solrj.PANTHERGeneralSolrDocumentLoader
 
PANTHERSolrDocumentLoader - Class in owltools.solrj
A hard-wired loader for the family-config.yaml profile.
PANTHERSolrDocumentLoader(String) - Constructor for class owltools.solrj.PANTHERSolrDocumentLoader
 
PANTHERTree - Class in owltools.panther
Methods to simplify the work with the Newick-ish output we get from PANTHER.
PANTHERTree(File) - Constructor for class owltools.panther.PANTHERTree
Create an instance for the given path
property - Variable in class owltools.yaml.golrconfig.GOlrField
 

R

required - Variable in class owltools.yaml.golrconfig.GOlrField
 
result_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
result_weights - Variable in class owltools.yaml.golrconfig.GOlrField
 

S

schema() - Method in class owltools.yaml.golrconfig.SolrSchemaXMLWriter
Dump the necessary Solr schema as a String.
schema_generating - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
searchable - Variable in class owltools.yaml.golrconfig.GOlrField
 
server - Variable in class owltools.solrj.AbstractSolrLoader
 
setEcoTools(EcoTools) - Method in class owltools.solrj.GafSolrDocumentLoader
 
setGafDocument(GafDocument) - Method in class owltools.solrj.GafSolrDocumentLoader
 
setGraph(OWLGraphWrapper) - Method in class owltools.solrj.AbstractSolrLoader
 
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.GafSolrDocumentLoader
 
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.PANTHERGeneralSolrDocumentLoader
 
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.PANTHERSolrDocumentLoader
 
setTaxonTools(TaxonTools) - Method in class owltools.solrj.GafSolrDocumentLoader
 
SolrSchemaXMLWriter - Class in owltools.yaml.golrconfig
 
SolrSchemaXMLWriter(ConfigManager) - Constructor for class owltools.yaml.golrconfig.SolrSchemaXMLWriter
 

T

transform - Variable in class owltools.yaml.golrconfig.GOlrDynamicField
Deprecated.  
transform - Variable in class owltools.yaml.golrconfig.GOlrField
 
type - Variable in class owltools.yaml.golrconfig.GOlrField
 

V

value - Variable in class owltools.flex.FlexLine
 
value() - Method in class owltools.flex.FlexLine
Return the first/only value.
values() - Method in class owltools.flex.FlexLine
Return all the values.

W

weight - Variable in class owltools.yaml.golrconfig.GOlrConfig
 
wring(OWLObject, ConfigManager) - Method in class owltools.flex.FlexCollection
Main wrapping for adding ontology documents to GOlr.

A B C D F G I L O P R S T V W

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