Index (htsjdk 2.8.1 API)

All Known Subinterfaces:

MutableIndex

All Known Implementing Classes:

AbstractIndex, IntervalTreeIndex, LinearIndex, TabixIndex
```
public interface Index
```
Interface for all index implementations. An index file is used for efficient lookup of features from a feature file; and Index represents that index file.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`boolean`	`containsChromosome(String chr)`
`boolean`	`equalsIgnoreProperties(Object obj)` Returns true if this and obj are 'effectively' equivalent indices.
`List<Block>`	`getBlocks(String chr, int start, int end)` Query the index.
`Map<String,String>`	`getProperties()`
`List<String>`	`getSequenceNames()`
`boolean`	`isCurrentVersion()`
`void`	`write(File idxFile)` Writes the index into a file.
`void`	`write(LittleEndianOutputStream stream)` all indexes are writable to disk
`void`	`writeBasedOnFeatureFile(File featureFile)` Write an appropriately named and located Index file based on the name and location of the featureFile.

- Method Detail
  - getBlocks
```
List<Block> getBlocks(String chr,
                      int start,
                      int end)
```
    Query the index.
    
    Parameters:
    
    chr - the chromosome
    
    start - the start position
    
    end - the end position
    
    Returns:
    
    a list of blocks that contain the specified interval. Can never return null
    
    Throws:
    
    IllegalArgumentException - of chr isn't part of this index
  - isCurrentVersion
```
boolean isCurrentVersion()
```
    Returns:
    
    true if the index is up to date, false otherwise
  - getSequenceNames
```
List<String> getSequenceNames()
```
    Returns:
    
    a list of the sequence names we've seen during indexing, in order
  - containsChromosome
```
boolean containsChromosome(String chr)
```
    Parameters:
    
    chr - the chromosome (or contig) name
    
    Returns:
    
    true if we have an entry; false otherwise
  - write
```
void write(LittleEndianOutputStream stream)
    throws IOException
```
    all indexes are writable to disk
    
    Parameters:
    
    stream - the stream to write the index to. Caller must close after invocation.
    
    Throws:
    
    IOException - if the index is unable to write to the specified location
  - write
```
void write(File idxFile)
    throws IOException
```
    Writes the index into a file.
    
    Parameters:
    
    idxFile - Where to write the index.
    
    Throws:
    
    IOException - if the index is unable to write to the specified file
  - writeBasedOnFeatureFile
```
void writeBasedOnFeatureFile(File featureFile)
                      throws IOException
```
    Write an appropriately named and located Index file based on the name and location of the featureFile. If featureFile is not a normal file, the index will silently not be written.
    
    Parameters:
    
    featureFile -
    
    Throws:
    
    IOException
  - getProperties
```
Map<String,String> getProperties()
```
    Returns:
    
    get the list of properties for this index. Returns null if no properties.
  - equalsIgnoreProperties
```
boolean equalsIgnoreProperties(Object obj)
```
    Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices
    
    Parameters:
    
    obj -
    
    Returns:

Interface Index

Method Summary

Method Detail

getBlocks

isCurrentVersion

getSequenceNames

containsChromosome

write

write

writeBasedOnFeatureFile

getProperties

equalsIgnoreProperties