htsjdk.samtools

Interface SAMFileSpan

All Superinterfaces:

java.lang.Cloneable

public interface SAMFileSpan
extends java.lang.Cloneable

A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.

Method Summary

Methods

Modifier and Type	Method and Description
SAMFileSpan	getContentsFollowing() Gets a pointer over the data immediately following this span.
boolean	isEmpty() Does this file span point to any data, or is it completely empty?
SAMFileSpan	removeContentsBefore(SAMFileSpan fileSpan) Remove all pointers in this file span before the given file span starts.

Method Detail

getContentsFollowing

SAMFileSpan getContentsFollowing()

Gets a pointer over the data immediately following this span.

Returns:

The a pointer to data immediately following this span.

removeContentsBefore

SAMFileSpan removeContentsBefore(SAMFileSpan fileSpan)

Remove all pointers in this file span before the given file span starts.

Parameters:

fileSpan - The filespan before which to eliminate.

Returns:

The portion of the chunk list after the given chunk.

isEmpty

boolean isEmpty()

Does this file span point to any data, or is it completely empty?

Returns:

True if the file span is empty, false otherwise.