public interface Index
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.
|
List<Block> getBlocks(String chr, int start, int end)
chr
- the chromosomestart
- the start positionend
- the end positionIllegalArgumentException
- of chr isn't part of this indexboolean isCurrentVersion()
List<String> getSequenceNames()
boolean containsChromosome(String chr)
chr
- the chromosome (or contig) namevoid write(LittleEndianOutputStream stream) throws IOException
stream
- the stream to write the index to. Caller must close after invocation.IOException
- if the index is unable to write to the specified locationvoid write(File idxFile) throws IOException
idxFile
- Where to write the index.IOException
- if the index is unable to write to the specified filevoid writeBasedOnFeatureFile(File featureFile) throws IOException
featureFile
- IOException
Map<String,String> getProperties()
boolean equalsIgnoreProperties(Object obj)
obj
-