htsjdk.beta.plugin.interval

Class HtsQueryInterval

java.lang.Object

htsjdk.beta.plugin.interval.HtsQueryInterval

All Implemented Interfaces:

HtsInterval

public class HtsQueryInterval
extends java.lang.Object
implements HtsInterval

An concrete query interval implementation of HtsInterval used for random access queries on file formats represented by HtsDecoders that support random access.

Constructor Summary

Constructors

Constructor and Description
HtsQueryInterval(QueryInterval queryInterval, SAMSequenceDictionary dictionary) Convenience method for creating a query interval from an old-style QueryInterval.
HtsQueryInterval(java.lang.String queryName, long start, long end) Create an HtsQueryInterval from query components

Method Summary

Modifier and Type	Method and Description
long	getEnd() Get the inclusive end coordinate for this interval.
java.lang.String	getQueryName() Get the name part of this interval query.
long	getStart() Get the 1-based inclusive start coordinate for this interval.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HtsQueryInterval

public HtsQueryInterval(java.lang.String queryName,
                        long start,
                        long end)

Create an HtsQueryInterval from query components

Parameters:

queryName - the string query nae

start - the integer start position

end - the end position

HtsQueryInterval

public HtsQueryInterval(QueryInterval queryInterval,
                        SAMSequenceDictionary dictionary)

Convenience method for creating a query interval from an old-style QueryInterval.

Parameters:

queryInterval - the query interval to convert

dictionary - the sequence dictionary to use to do the conversion

Method Detail

getQueryName

public java.lang.String getQueryName()

Description copied from interface: HtsInterval

Get the name part of this interval query.

Specified by:

getQueryName in interface HtsInterval

Returns:

the name part of this interval query

getStart

public long getStart()

Description copied from interface: HtsInterval

Get the 1-based inclusive start coordinate for this interval.

Specified by:

getStart in interface HtsInterval

Returns:

the 1-based inclusive start coordinate for this interval

getEnd

public long getEnd()

Description copied from interface: HtsInterval

Get the inclusive end coordinate for this interval.

Specified by:

getEnd in interface HtsInterval

Returns:

the inclusive end coordinate for this interval