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java.lang.Objectowltools.panther.PANTHERTree
public class PANTHERTree
Methods to simplify the work with the Newick-ish output we get from PANTHER.
Constructor Summary | |
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PANTHERTree(File pFile)
Create an instance for the given path |
Method Summary | |
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void |
addAssociatedGeneProduct(String bid,
String blabel)
Add an associated id/label for a term in this tree. |
Set<String> |
associatedIdentifierSet()
Return a set of all identifiers associated with this family. |
Set<String> |
getAncestorAnnotations(String baseGpID)
Return all annotations to ancestor nodes. |
Set<String> |
getAncestors(String nodeID)
Return the ancestors of this node as an ID set. |
List<String> |
getAssociatedGeneProductIDs()
Return the associated gene/product ids for this tree. |
String |
getAssociatedGeneProductJSONMap()
Return the mapping of associated gene/product ids to labels for this tree. |
List<String> |
getAssociatedGeneProductLabels()
Return the associated gene/product labels for this tree. |
Set<String> |
getDescendantAnnotations(String baseGpID)
Return all annotations to descendant nodes. |
Set<String> |
getDescendants(String nodeID)
Return the descendants of this node as an ID set. |
String |
getNHXString()
Return the raw Newick-type input string. |
OWLShuntGraph |
getOWLShuntGraph()
Return the complete OWL shunt graph representation of the phylogenic tree. |
String |
getPANTHERID()
Return the tree public (PANTHER) identifier. |
String |
getTreeID()
Return the tree internal identifier. |
String |
getTreeLabel()
Return the tree label. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PANTHERTree(File pFile) throws IOException
pFile
- path
IOException
Method Detail |
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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 id
public Set<String> getDescendants(String nodeID)
nodeID
- node id
public Set<String> getAncestorAnnotations(String baseGpID)
baseGpID
- gene product id
public Set<String> getDescendantAnnotations(String baseGpID)
baseGpID
- gene product id
public Set<String> associatedIdentifierSet()
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