public class PANTHERTree extends Object
Constructor and Description |
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PANTHERTree(File pFile)
Create an instance for the given path
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Modifier and Type | Method and Description |
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void |
addAssociatedGeneProduct(String bid,
String blabel)
Add an associated id/label for a term in this tree.
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Set<String> |
associatedIdentifierSet()
Return a set of all identifiers associated with this family.
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Set<String> |
getAncestorAnnotations(String baseGpID)
Return all annotations to ancestor nodes.
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Set<String> |
getAncestors(String nodeID)
Return the ancestors of this node as an ID set.
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List<String> |
getAssociatedGeneProductIDs()
Return the associated gene/product ids for this tree.
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String |
getAssociatedGeneProductJSONMap()
Return the mapping of associated gene/product ids to labels for this tree.
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List<String> |
getAssociatedGeneProductLabels()
Return the associated gene/product labels for this tree.
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Set<String> |
getDescendantAnnotations(String baseGpID)
Return all annotations to descendant nodes.
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Set<String> |
getDescendants(String nodeID)
Return the descendants of this node as an ID set.
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String |
getNHXString()
Return the raw Newick-type input string.
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OWLShuntGraph |
getOWLShuntGraph()
Return the complete OWL shunt graph representation of the phylogenic tree.
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String |
getPANTHERID()
Return the tree public (PANTHER) identifier.
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String |
getTreeID()
Return the tree internal identifier.
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String |
getTreeLabel()
Return the tree label.
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public PANTHERTree(File pFile) throws IOException
pFile
- pathIOException
public void addAssociatedGeneProduct(String bid, String blabel)
bid
- the idblabel
- the labelpublic List<String> getAssociatedGeneProductIDs()
public List<String> getAssociatedGeneProductLabels()
public String getAssociatedGeneProductJSONMap()
public String getNHXString()
public String getTreeLabel()
public String getTreeID()
public String getPANTHERID()
public OWLShuntGraph getOWLShuntGraph()
public Set<String> getAncestors(String nodeID)
nodeID
- node idpublic Set<String> getDescendants(String nodeID)
nodeID
- node idpublic Set<String> getAncestorAnnotations(String baseGpID)
baseGpID
- gene product idpublic Set<String> getDescendantAnnotations(String baseGpID)
baseGpID
- gene product idCopyright © 2010-2015. All Rights Reserved.