public class IntervalTreeIndex extends AbstractIndex
IntervalTree
Modifier and Type | Class and Description |
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static class |
IntervalTreeIndex.ChrIndex |
AbstractIndex.BlockStats, AbstractIndex.IndexType
Modifier and Type | Field and Description |
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static int |
INDEX_TYPE |
chrIndices, flags, indexedFile, indexedFileMD5, indexedFileSize, indexedFileTS, MAGIC_NUMBER, version, VERSION
Constructor and Description |
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IntervalTreeIndex(java.io.InputStream inputStream)
Load from file.
|
IntervalTreeIndex(java.lang.String featureFile)
Prepare to build an index.
|
Modifier and Type | Method and Description |
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java.lang.Class |
getChrIndexClass()
returns the class for the index type
|
protected int |
getType()
get the index type
|
void |
insert(java.lang.String chr,
Interval interval)
Add a new interval to this index
|
void |
printTree() |
protected void |
setChrIndex(java.util.List<IntervalTreeIndex.ChrIndex> indicies) |
addProperties, addProperty, containsChromosome, equalsIgnoreProperties, finalizeIndex, getBlocks, getBlocks, getBlockStats, getFlags, getIndexedFile, getIndexedFileMD5, getIndexedFileSize, getIndexedFileTS, getProperties, getSequenceNames, getVersion, hasFileSize, hasMD5, hasTimestamp, isCurrentVersion, printIndexInfo, read, setMD5, statsSummary, validateIndexHeader, write, writeBasedOnFeatureFile
public IntervalTreeIndex(java.io.InputStream inputStream) throws java.io.IOException
inputStream
- This method assumes that the input stream is already buffered as appropriate. Caller
should close after this object is constructed.java.io.IOException
public IntervalTreeIndex(java.lang.String featureFile)
featureFile
- File which we are indexingpublic java.lang.Class getChrIndexClass()
AbstractIndex
getChrIndexClass
in class AbstractIndex
protected int getType()
AbstractIndex
getType
in class AbstractIndex
public void insert(java.lang.String chr, Interval interval)
chr
- Chromosomeinterval
- protected void setChrIndex(java.util.List<IntervalTreeIndex.ChrIndex> indicies)
public void printTree()