Package org.snpeff.geneOntology
Class GoTerm
java.lang.Object
org.snpeff.geneOntology.GoTerm
- All Implemented Interfaces:
Serializable
,Comparable<GoTerm>
,Iterable<String>
An instance of a GO term (a node in the DAG)
- Author:
- Pablo Cingolani
- See Also:
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'void
addInterestingSymbolId
(String symbolId) Add one gene to interestingGenesSetvoid
addSymbolId
(String symbolId) Add one gene to genesSetvoid
addSymbolsFromChilds
(GoTerm goTerm) Add all symbols from childs to goTermint
getAcc()
Return first child in the listReturn first parent in the listint
Number of 'interesting' symbolsint
getLevel()
Calculate node's levelint
int
Number of symbols in this node (total = interesting + not-interesting)int
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?iterator()
rootNode()
Get the root nodevoid
void
void
setGenesSet
(HashSet<String> genesSet) void
setGoTerms
(GoTerms goTerms) void
setInterestingSymbolIdSet
(HashSet<String> interestingSymbolIdSet) void
setLevel
(int level) void
setMaxRank
(int maxRank) void
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').void
setNameSpace
(String goTermType) void
setParents
(HashSet<GoTerm> parents) void
setRankedSymbols
(int rankedSymbols) void
setRankSum
(int rankSum) void
setSescription
(String description) void
setSymbolIdSet
(HashSet<String> symbolIdSet) toString()
toStringAll
(boolean showSymbols) void
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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debug
public static boolean debug
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Constructor Details
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GoTerm
Create a new GOTerm by joining all GOTerms in the list- Parameters:
goTermList
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GoTerm
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Method Details
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addChild
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'- Parameters:
goTermAcc
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addInterestingSymbolId
Add one gene to interestingGenesSet- Parameters:
symbolId
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addSymbolId
Add one gene to genesSet- Parameters:
symbolId
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addSymbolsFromChilds
Add all symbols from childs to goTerm -
compareTo
- Specified by:
compareTo
in interfaceComparable<GoTerm>
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getAcc
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getChilds
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getDescription
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getFirstChild
Return first child in the list- Returns:
- First child (or null if there are no children)
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getFirstParent
Return first parent in the list- Returns:
- First parent (or null if there are no parents)
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getGoTerms
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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() -
getNameSpace
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getParents
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getRankedSymbols
public int getRankedSymbols() -
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
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
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rootNode
Get the root node- Returns:
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setAcc
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setChilds
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setGenesSet
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setGoTerms
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setInterestingSymbolIdSet
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setLevel
public void setLevel(int level) -
setMaxRank
public void setMaxRank(int maxRank) -
setMinus
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
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setParents
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setRankedSymbols
public void setRankedSymbols(int rankedSymbols) -
setRankSum
public void setRankSum(int rankSum) -
setSescription
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setSymbolIdSet
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toString
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toStringAll
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toStringAll
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union
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').- Parameters:
goTerm
- : GOTerm to use for union
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