Package htsjdk.tribble.index.interval
Class IntervalTreeIndex
- java.lang.Object
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- htsjdk.tribble.index.AbstractIndex
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- htsjdk.tribble.index.interval.IntervalTreeIndex
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- All Implemented Interfaces:
Index
,MutableIndex
public class IntervalTreeIndex extends AbstractIndex
Index based on an interval tree- See Also:
IntervalTree
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
IntervalTreeIndex.ChrIndex
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Nested classes/interfaces inherited from class htsjdk.tribble.index.AbstractIndex
AbstractIndex.BlockStats, AbstractIndex.IndexType
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Field Summary
Fields Modifier and Type Field Description static int
INDEX_TYPE
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Fields inherited from class htsjdk.tribble.index.AbstractIndex
chrIndices, flags, indexedFileMD5, indexedFileSize, indexedFileTS, indexedPath, logger, MAGIC_NUMBER, version, VERSION
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Constructor Summary
Constructors Constructor Description IntervalTreeIndex(InputStream inputStream)
Load from file.IntervalTreeIndex(String featureFile)
Prepare to build an index.IntervalTreeIndex(Path featureFile)
Prepare to build an index.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Class
getChrIndexClass()
returns the class for the index typeprotected int
getType()
get the index typevoid
insert(String chr, Interval interval)
Add a new interval to this indexvoid
printTree()
protected void
setChrIndex(List<IntervalTreeIndex.ChrIndex> indicies)
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Methods inherited from class htsjdk.tribble.index.AbstractIndex
addProperties, addProperty, containsChromosome, equalsIgnoreProperties, finalizeIndex, getBlocks, getBlocks, getBlockStats, getFlags, getIndexedFile, getIndexedFileMD5, getIndexedFileSize, getIndexedFileTS, getIndexedPath, getProperties, getSequenceNames, getVersion, hasFileSize, hasMD5, hasTimestamp, isCurrentVersion, printIndexInfo, read, setMD5, statsSummary, validateIndexHeader, write, write, writeBasedOnFeaturePath
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface htsjdk.tribble.index.Index
write, writeBasedOnFeatureFile
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Constructor Detail
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IntervalTreeIndex
public IntervalTreeIndex(InputStream inputStream) throws IOException
Load from file.- Parameters:
inputStream
- This method assumes that the input stream is already buffered as appropriate. Caller should close after this object is constructed.- Throws:
IOException
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IntervalTreeIndex
public IntervalTreeIndex(Path featureFile)
Prepare to build an index.- Parameters:
featureFile
- File which we are indexing
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IntervalTreeIndex
public IntervalTreeIndex(String featureFile)
Prepare to build an index.- Parameters:
featureFile
- File which we are indexing
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Method Detail
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getChrIndexClass
public Class getChrIndexClass()
Description copied from class:AbstractIndex
returns the class for the index type- Specified by:
getChrIndexClass
in classAbstractIndex
- Returns:
- a Class, from which a new instance can be created
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getType
protected int getType()
Description copied from class:AbstractIndex
get the index type- Specified by:
getType
in classAbstractIndex
- Returns:
- The index type
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insert
public void insert(String chr, Interval interval)
Add a new interval to this index- Parameters:
chr
- Chromosomeinterval
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setChrIndex
protected void setChrIndex(List<IntervalTreeIndex.ChrIndex> indicies)
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printTree
public void printTree()
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