htsjdk.beta.plugin.interval

Class HtsIntervalUtils

java.lang.Object

htsjdk.beta.plugin.interval.HtsIntervalUtils

public class HtsIntervalUtils
extends java.lang.Object

Methods for interconverting between HtsQueryInterval and existing htsjdk types such as Locatable/QueryInterval

Constructor Summary

Constructors

Constructor and Description
HtsIntervalUtils()

Method Summary

Modifier and Type	Method and Description
static java.util.List<HtsInterval>	fromQueryIntervalArray(QueryInterval[] queryIntervals, SAMSequenceDictionary dictionary)
static int	toIntegerSafe(long coord) Convert a long coordinate to an integer, for use with interconverting between old style integer coordinates and new style long coordinates.
static Locatable	toLocatable(HtsInterval interval) Convert an HtsInterval to a Locatable
static java.util.List<Locatable>	toLocatableList(java.util.List<HtsInterval> intervals) Convert a List of HtsInterval to a list of Locatable.
static QueryInterval	toQueryInterval(HtsInterval interval, SAMSequenceDictionary dictionary) Convert an HtsInterval to a QueryInterval
static QueryInterval[]	toQueryIntervalArray(java.util.List<HtsInterval> intervals, SAMSequenceDictionary dictionary) Convert a list of HtsInterval to an array of QueryInterval

Methods inherited from class java.lang.Object

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

Constructor Detail

HtsIntervalUtils

public HtsIntervalUtils()

Method Detail

toQueryInterval

@InternalAPI
public static QueryInterval toQueryInterval(HtsInterval interval,
                                                         SAMSequenceDictionary dictionary)

Convert an HtsInterval to a QueryInterval

Parameters:

interval - HtsInterval to convert

dictionary - sequence dictionary to use to convert string query names to contig index

Returns:

a QueryInterval equivalent to interval

toLocatable

@InternalAPI
public static Locatable toLocatable(HtsInterval interval)

Convert an HtsInterval to a Locatable

Parameters:

interval - HtsInterval to convert

Returns:

a Locatable equivalent to interval

toLocatableList

@InternalAPI
public static java.util.List<Locatable> toLocatableList(java.util.List<HtsInterval> intervals)

Convert a List of HtsInterval to a list of Locatable.

Parameters:

intervals - list of HtsIntervals to convert

Returns:

a list of Locatable

toQueryIntervalArray

@InternalAPI
public static QueryInterval[] toQueryIntervalArray(java.util.List<HtsInterval> intervals,
                                                                SAMSequenceDictionary dictionary)

Convert a list of HtsInterval to an array of QueryInterval

Parameters:

intervals - list of HtsIntervals to convert

dictionary - sequence dictionary to use

Returns:

array of QueryInterval

fromQueryIntervalArray

@InternalAPI
public static java.util.List<HtsInterval> fromQueryIntervalArray(QueryInterval[] queryIntervals,
                                                                              SAMSequenceDictionary dictionary)

Parameters:

queryIntervals - list of QueryInterval to convert

dictionary - sequence dictionary to use for the conversion

Returns:

list of HtsInterval

toIntegerSafe

@InternalAPI
public static int toIntegerSafe(long coord)

Convert a long coordinate to an integer, for use with interconverting between old style integer coordinates and new style long coordinates. Throws on overflow.

Parameters:

coord - long coordinate to convert

Returns:

an integer representation of coord if the conversion is safe

Throws:

java.lang.IllegalArgumentException - if converting results in overflow