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