T - a feature typepublic interface FeatureReader<T extends Feature>
extends java.io.Closeable
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Closes the reader
|
java.lang.Object |
getHeader()
Provide access to the header of the reader
|
java.util.List<java.lang.String> |
getSequenceNames()
Provides the list of sequenceNames if known.
|
default boolean |
isQueryable() |
CloseableTribbleIterator<T> |
iterator()
Provides access to all the features in the reader
|
default CloseableTribbleIterator<T> |
query(Locatable locus)
Query the reader for a particular interval corresponding to a contig and a 1-based closed
|
CloseableTribbleIterator<T> |
query(java.lang.String chr,
int start,
int end)
Query the reader for a particular interval corresponding to a contig and a 1-based closed
|
CloseableTribbleIterator<T> query(java.lang.String chr, int start, int end) throws java.io.IOException
chr - the contig to be queriedstart - the start of the interval (1-based) to be queriedend - the last base in the interval to be queriedjava.io.IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.default CloseableTribbleIterator<T> query(Locatable locus) throws java.io.IOException
locus - The locus to be queriedjava.io.IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.CloseableTribbleIterator<T> iterator() throws java.io.IOException
java.io.IOException - If there's a problem reading.void close()
throws java.io.IOException
close in interface java.lang.AutoCloseableclose in interface java.io.Closeablejava.io.IOExceptionjava.util.List<java.lang.String> getSequenceNames()
java.lang.Object getHeader()
default boolean isQueryable()
query(Locatable)