org.coolmap.core.util.bioparser.simpleobo

Class SimpleOBOTree

java.lang.Object

org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

public class SimpleOBOTree
extends java.lang.Object

records the relationship between GO terms

Constructor Summary

Constructors

Constructor and Description
SimpleOBOTree()

Method Summary

Modifier and Type	Method and Description
void	addEntry(SimpleOBOEntry entry)
void	addTreeBranch(java.lang.String parent, java.lang.String child)
java.util.Set<SimpleOBOEntry>	getAllEntries()
java.util.Set<java.lang.String>	getAllNodeIDs()
java.util.Set<java.lang.String>	getChildNodes(java.lang.String parentNodeID) return all nodeIDs that are children of the given parentNodeID
SimpleOBOEntry	getEntry(java.lang.String id)
java.util.Set<java.lang.String>	getParentNodeIDs() return all nodeIDs that have children
com.google.common.collect.HashMultimap<java.lang.String,java.lang.String>	getTree() returns the go tree - not a copy, for efficiency and economy concerns
static SimpleOBOTree	parse(java.lang.String name, java.io.InputStream in)
void	printBranches()
void	printEntries()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleOBOTree

public SimpleOBOTree()

Method Detail

addEntry

public void addEntry(SimpleOBOEntry entry)

getTree

public com.google.common.collect.HashMultimap<java.lang.String,java.lang.String> getTree()

returns the go tree - not a copy, for efficiency and economy concerns

Returns:

addTreeBranch

public void addTreeBranch(java.lang.String parent,
                          java.lang.String child)

parse

public static SimpleOBOTree parse(java.lang.String name,
                                  java.io.InputStream in)
                           throws java.io.IOException

Throws:

java.io.IOException

printEntries

public void printEntries()

printBranches

public void printBranches()

getParentNodeIDs

public java.util.Set<java.lang.String> getParentNodeIDs()

return all nodeIDs that have children

Returns:

getChildNodes

public java.util.Set<java.lang.String> getChildNodes(java.lang.String parentNodeID)

return all nodeIDs that are children of the given parentNodeID

Parameters:

parentNodeID -

Returns:

getEntry

public SimpleOBOEntry getEntry(java.lang.String id)

getAllNodeIDs

public java.util.Set<java.lang.String> getAllNodeIDs()

getAllEntries

public java.util.Set<SimpleOBOEntry> getAllEntries()