Fields
Modifier and Type	Field	Description
`protected LinkedHashMap<String,ChrIndex>`	`chrIndices`	the map of our chromosome bins
`protected int`	`flags`
`protected String`	`indexedFileMD5`
`protected long`	`indexedFileSize`
`protected long`	`indexedFileTS`
`protected Path`	`indexedPath`
`protected Log`	`logger`
`static int`	`MAGIC_NUMBER`
`protected int`	`version`
`static int`	`VERSION`

Constructors
Constructor	Description
`AbstractIndex()`	create an abstract index, with defaults for the version value, and empty properties and chromosome lists
`AbstractIndex(AbstractIndex parent)`
`AbstractIndex(File featureFile)`
`AbstractIndex(String featureFile)`	create an index file from the target feature file
`AbstractIndex(Path featurePath)`

All Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`addProperties(Map<String,String> properties)`
`void`	`addProperty(String key, String value)`
`boolean`	`containsChromosome(String chr)`
`boolean`	`equalsIgnoreProperties(Object obj)`	Returns true if this and obj are 'effectively' equivalent indices.
`void`	`finalizeIndex()`
`List<Block>`	`getBlocks(String chr)`
`List<Block>`	`getBlocks(String chr, int start, int end)`	Query the index.
`protected AbstractIndex.BlockStats`	`getBlockStats(boolean logDetails)`
`abstract Class`	`getChrIndexClass()`	returns the class for the index type
`int`	`getFlags()`
`File`	`getIndexedFile()`	Deprecated. on 03/2017.
`String`	`getIndexedFileMD5()`
`long`	`getIndexedFileSize()`
`long`	`getIndexedFileTS()`
`Path`	`getIndexedPath()`
`Map<String,String>`	`getProperties()`	return a mapping of name to property value
`List<String>`	`getSequenceNames()`
`protected abstract int`	`getType()`	get the index type
`int`	`getVersion()`
`boolean`	`hasFileSize()`
`boolean`	`hasMD5()`
`boolean`	`hasTimestamp()`
`boolean`	`isCurrentVersion()`	check the current version against the version we read in
`protected void`	`printIndexInfo()`
`void`	`read(LittleEndianInputStream dis)`
`void`	`setMD5(String md5)`
`protected String`	`statsSummary()`
`protected void`	`validateIndexHeader(int indexType, LittleEndianInputStream dis)`

Modifier and Type	Class	Description
`protected static class`	`AbstractIndex.BlockStats`
`static class`	`AbstractIndex.IndexType`

Class AbstractIndex