htsjdk.tribble

Interface FeatureReader<T extends Feature>

Type Parameters:

T - a feature type

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Implementing Classes:

AbstractFeatureReader, TabixFeatureReader, TribbleIndexedFeatureReader

public interface FeatureReader<T extends Feature>
extends java.io.Closeable

the basic interface that feature sources need to match

Method Summary

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

Method Detail

query

CloseableTribbleIterator<T> query(java.lang.String chr,
                                  int start,
                                  int end)
                           throws java.io.IOException

Query the reader for a particular interval corresponding to a contig and a 1-based closed

Parameters:

chr - the contig to be queried

start - the start of the interval (1-based) to be queried

end - the last base in the interval to be queried

Returns:

an iterator containing the features that at in the interval.

Throws:

java.io.IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.

query

default CloseableTribbleIterator<T> query(Locatable locus)
                                   throws java.io.IOException

Query the reader for a particular interval corresponding to a contig and a 1-based closed

Parameters:

locus - The locus to be queried

Returns:

an iterator containing the features that at in the interval.

Throws:

java.io.IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.

iterator

CloseableTribbleIterator<T> iterator()
                              throws java.io.IOException

Provides access to all the features in the reader

Returns:

an iterator to all the features in the reader

Throws:

java.io.IOException - If there's a problem reading.

close

void close()
    throws java.io.IOException

Closes the reader

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Throws:

java.io.IOException

getSequenceNames

java.util.List<java.lang.String> getSequenceNames()

Provides the list of sequenceNames if known. Otherwise will return an empty list.

Returns:

the list of sequenceNames if known. Otherwise will return an empty list.

getHeader

java.lang.Object getHeader()

Provide access to the header of the reader

Returns:

the header of the reader. May be null.

isQueryable

default boolean isQueryable()

Returns:

true if the reader has an index, which means that it can be queried. Must be implemented to return true if the implementation supports query(Locatable)