Package org.snpeff.geneOntology
Class GoTerm
- java.lang.Object
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- org.snpeff.geneOntology.GoTerm
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Comparable<GoTerm>
,java.lang.Iterable<java.lang.String>
public class GoTerm extends java.lang.Object implements java.lang.Comparable<GoTerm>, java.lang.Iterable<java.lang.String>, java.io.Serializable
An instance of a GO term (a node in the DAG)- Author:
- Pablo Cingolani
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addChild(GoTerm childGoTerm)
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'void
addInterestingSymbolId(java.lang.String symbolId)
Add one gene to interestingGenesSetvoid
addSymbolId(java.lang.String symbolId)
Add one gene to genesSetvoid
addSymbolsFromChilds(GoTerm goTerm)
Add all symbols from childs to goTermint
compareTo(GoTerm goTerm)
java.lang.String
getAcc()
java.util.HashSet<GoTerm>
getChilds()
java.lang.String
getDescription()
GoTerm
getFirstChild()
Return first child in the listGoTerm
getFirstParent()
Return first parent in the listGoTerms
getGoTerms()
java.util.HashSet<java.lang.String>
getInterestingSymbolIdSet()
int
getInterestingSymbolIdsSize()
Number of 'interesting' symbolsint
getLevel()
Calculate node's levelint
getMaxRank()
java.lang.String
getNameSpace()
java.util.HashSet<GoTerm>
getParents()
int
getRankedSymbols()
java.util.Set<java.lang.String>
getSymbolIdSet()
Number of symbols in this node (total = interesting + not-interesting)int
getTotalCount()
Number of symbols in this node (total = interesting + not-interesting)void
intersection(GoTerm goTerm)
Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').boolean
isLeave()
Is this GOTerm a leave?java.util.Iterator<java.lang.String>
iterator()
GoTerm
rootNode()
Get the root nodevoid
setAcc(java.lang.String go)
void
setChilds(java.util.HashSet<GoTerm> childs)
void
setGenesSet(java.util.HashSet<java.lang.String> genesSet)
void
setGoTerms(GoTerms goTerms)
void
setInterestingSymbolIdSet(java.util.HashSet<java.lang.String> interestingSymbolIdSet)
void
setLevel(int level)
void
setMaxRank(int maxRank)
void
setMinus(GoTerm goTerm)
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').void
setNameSpace(java.lang.String goTermType)
void
setParents(java.util.HashSet<GoTerm> parents)
void
setRankedSymbols(int rankedSymbols)
void
setRankSum(int rankSum)
void
setSescription(java.lang.String description)
void
setSymbolIdSet(java.util.HashSet<java.lang.String> symbolIdSet)
java.lang.String
toString()
java.lang.String
toStringAll()
java.lang.String
toStringAll(boolean showSymbols)
void
union(GoTerm goTerm)
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').
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Method Detail
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addChild
public void addChild(GoTerm childGoTerm)
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'- Parameters:
goTermAcc
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addInterestingSymbolId
public void addInterestingSymbolId(java.lang.String symbolId)
Add one gene to interestingGenesSet- Parameters:
symbolId
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addSymbolId
public void addSymbolId(java.lang.String symbolId)
Add one gene to genesSet- Parameters:
symbolId
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addSymbolsFromChilds
public void addSymbolsFromChilds(GoTerm goTerm)
Add all symbols from childs to goTerm
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compareTo
public int compareTo(GoTerm goTerm)
- Specified by:
compareTo
in interfacejava.lang.Comparable<GoTerm>
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getAcc
public java.lang.String getAcc()
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getChilds
public java.util.HashSet<GoTerm> getChilds()
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getDescription
public java.lang.String getDescription()
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getFirstChild
public GoTerm getFirstChild()
Return first child in the list- Returns:
- First child (or null if there are no children)
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getFirstParent
public GoTerm getFirstParent()
Return first parent in the list- Returns:
- First parent (or null if there are no parents)
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getGoTerms
public GoTerms getGoTerms()
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getInterestingSymbolIdSet
public java.util.HashSet<java.lang.String> getInterestingSymbolIdSet()
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getInterestingSymbolIdsSize
public int getInterestingSymbolIdsSize()
Number of 'interesting' symbols- Returns:
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getLevel
public int getLevel()
Calculate node's level- Returns:
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getMaxRank
public int getMaxRank()
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getNameSpace
public java.lang.String getNameSpace()
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getParents
public java.util.HashSet<GoTerm> getParents()
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getRankedSymbols
public int getRankedSymbols()
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getSymbolIdSet
public java.util.Set<java.lang.String> getSymbolIdSet()
Number of symbols in this node (total = interesting + not-interesting)- Returns:
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getTotalCount
public int getTotalCount()
Number of symbols in this node (total = interesting + not-interesting)- Returns:
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intersection
public void intersection(GoTerm goTerm)
Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').- Parameters:
goTerm
- : GOTerm to intercept
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isLeave
public boolean isLeave()
Is this GOTerm a leave?- Returns:
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iterator
public java.util.Iterator<java.lang.String> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<java.lang.String>
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rootNode
public GoTerm rootNode()
Get the root node- Returns:
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setAcc
public void setAcc(java.lang.String go)
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setChilds
public void setChilds(java.util.HashSet<GoTerm> childs)
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setGenesSet
public void setGenesSet(java.util.HashSet<java.lang.String> genesSet)
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setGoTerms
public void setGoTerms(GoTerms goTerms)
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setInterestingSymbolIdSet
public void setInterestingSymbolIdSet(java.util.HashSet<java.lang.String> interestingSymbolIdSet)
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setLevel
public void setLevel(int level)
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setMaxRank
public void setMaxRank(int maxRank)
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setMinus
public void setMinus(GoTerm goTerm)
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').- Parameters:
goTerm
- : GOTerm to use for 'set minus' operation
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setNameSpace
public void setNameSpace(java.lang.String goTermType)
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setParents
public void setParents(java.util.HashSet<GoTerm> parents)
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setRankedSymbols
public void setRankedSymbols(int rankedSymbols)
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setRankSum
public void setRankSum(int rankSum)
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setSescription
public void setSescription(java.lang.String description)
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setSymbolIdSet
public void setSymbolIdSet(java.util.HashSet<java.lang.String> symbolIdSet)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringAll
public java.lang.String toStringAll()
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toStringAll
public java.lang.String toStringAll(boolean showSymbols)
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union
public void union(GoTerm goTerm)
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').- Parameters:
goTerm
- : GOTerm to use for union
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