public class IntervalTreeIndex extends AbstractIndex
IntervalTree| Modifier and Type | Class and Description |
|---|---|
static class |
IntervalTreeIndex.ChrIndex |
AbstractIndex.BlockStats, AbstractIndex.IndexType| Modifier and Type | Field and Description |
|---|---|
static int |
INDEX_TYPE |
chrIndices, flags, indexedFileMD5, indexedFileSize, indexedFileTS, indexedPath, logger, MAGIC_NUMBER, version, VERSION| Constructor and Description |
|---|
IntervalTreeIndex(java.io.InputStream inputStream)
Load from file.
|
IntervalTreeIndex(java.nio.file.Path featureFile)
Prepare to build an index.
|
IntervalTreeIndex(java.lang.String featureFile)
Prepare to build an index.
|
| Modifier and Type | Method and Description |
|---|---|
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, getIndexedPath, getProperties, getSequenceNames, getVersion, hasFileSize, hasMD5, hasTimestamp, isCurrentVersion, printIndexInfo, read, setMD5, statsSummary, validateIndexHeader, write, write, writeBasedOnFeaturePathclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitwrite, writeBasedOnFeatureFilepublic 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.IOExceptionpublic IntervalTreeIndex(java.nio.file.Path featureFile)
featureFile - File which we are indexingpublic IntervalTreeIndex(java.lang.String featureFile)
featureFile - File which we are indexingpublic java.lang.Class getChrIndexClass()
AbstractIndexgetChrIndexClass in class AbstractIndexprotected int getType()
AbstractIndexgetType in class AbstractIndexpublic void insert(java.lang.String chr,
Interval interval)
chr - Chromosomeinterval - protected void setChrIndex(java.util.List<IntervalTreeIndex.ChrIndex> indicies)
public void printTree()