Package org.snpeff.interval.tree
Interface Itree
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- All Superinterfaces:
java.lang.Iterable<Marker>
- All Known Implementing Classes:
IntervalTree
,IntervalTreeArray
,IntervalTreeOri
public interface Itree extends java.lang.Iterable<Marker>
Interval tree interface
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
add(Marker interval)
Add an interval object to the interval tree's listvoid
add(Markers markers)
Add all intervals to interval tree's listvoid
build()
Build the interval tree to reflect the list of intervals.Markers
getIntervals()
boolean
isEmpty()
boolean
isInSync()
Is the tree 'in sync'? If false, the tree must be 'build()' before the next queryvoid
load(java.lang.String fileName, Genome genome)
Load intervals from fileMarkers
query(Interval interval)
Perform an interval query, returning the intervals that intersect with 'interval'int
size()
Size: number of entries in this treeMarkers
stab(int point)
Perform a stabbing query, returning the interval objects
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Method Detail
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add
void add(Marker interval)
Add an interval object to the interval tree's list
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add
void add(Markers markers)
Add all intervals to interval tree's list
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build
void build()
Build the interval tree to reflect the list of intervals. Must not run if this is currently in sync
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getIntervals
Markers getIntervals()
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isEmpty
boolean isEmpty()
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isInSync
boolean isInSync()
Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
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load
void load(java.lang.String fileName, Genome genome)
Load intervals from file
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query
Markers query(Interval interval)
Perform an interval query, returning the intervals that intersect with 'interval'- Returns:
- All intervals that intersect 'interval'
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size
int size()
Size: number of entries in this tree
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stab
Markers stab(int point)
Perform a stabbing query, returning the interval objects- Returns:
- All intervals intersecting 'point'
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