htsjdk.samtools.util.htsget

Class HtsgetRequest

java.lang.Object

htsjdk.samtools.util.htsget.HtsgetRequest

Direct Known Subclasses:

HtsgetPOSTRequest

public class HtsgetRequest
extends java.lang.Object

Builder for an htsget GET request that allows opening a connection using the request after validating that it is properly formed.

This class currently supports version 1.2.0 of the spec as defined in https://samtools.github.io/hts-specs/htsget.html

Field Summary

Fields

Modifier and Type	Field and Description
protected static java.lang.String	ACCEPT_TYPE
protected HtsgetClass	dataClass
protected java.util.EnumSet<HtsgetRequestField>	fields
protected HtsgetFormat	format
protected Locatable	interval
protected java.util.Set<java.lang.String>	notags
protected static java.lang.String	PROTOCOL_VERSION
protected java.util.Set<java.lang.String>	tags
static Interval	UNMAPPED_UNPLACED_INTERVAL

Constructor Summary

Constructors

Constructor and Description
HtsgetRequest(java.net.URI endpoint) Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server

Method Summary

Modifier and Type	Method and Description
void	addField(HtsgetRequestField field)
void	addFields(java.util.Collection<HtsgetRequestField> fields)
void	addNotag(java.lang.String notag)
void	addNotags(java.util.Collection<java.lang.String> notags)
void	addTag(java.lang.String tag)
void	addTags(java.util.Collection<java.lang.String> tags)
protected java.net.HttpURLConnection	getConnection()
HtsgetClass	getDataClass()
java.net.URI	getEndpoint()
java.util.Set<HtsgetRequestField>	getFields()
HtsgetFormat	getFormat()
Locatable	getInterval()
java.util.Set<java.lang.String>	getNoTags()
HtsgetResponse	getResponse() Attempt to make htsget request and return response if there are no errors
java.util.Set<java.lang.String>	getTags()
void	setDataClass(HtsgetClass dataClass)
void	setFormat(HtsgetFormat format)
void	setInterval(Locatable interval)
java.net.URI	toURI() Convert request to a URI which can be used to make http request for data blocks
void	validateRequest() Validates that the user query obeys htsget spec
HtsgetRequest	withDataClass(HtsgetClass dataClass)
HtsgetRequest	withField(HtsgetRequestField field)
HtsgetRequest	withFields(java.util.Collection<HtsgetRequestField> fields)
HtsgetRequest	withFormat(HtsgetFormat format)
HtsgetRequest	withInterval(Locatable interval)
HtsgetRequest	withNotag(java.lang.String notag)
HtsgetRequest	withNotags(java.util.Collection<java.lang.String> notags)
HtsgetRequest	withTag(java.lang.String tag)
HtsgetRequest	withTags(java.util.Collection<java.lang.String> tags)

Methods inherited from class java.lang.Object

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

Field Detail

UNMAPPED_UNPLACED_INTERVAL

public static final Interval UNMAPPED_UNPLACED_INTERVAL

PROTOCOL_VERSION

protected static final java.lang.String PROTOCOL_VERSION

See Also:

Constant Field Values

ACCEPT_TYPE

protected static final java.lang.String ACCEPT_TYPE

See Also:

Constant Field Values

format

protected HtsgetFormat format

dataClass

protected HtsgetClass dataClass

interval

protected Locatable interval

fields

protected final java.util.EnumSet<HtsgetRequestField> fields

tags

protected final java.util.Set<java.lang.String> tags

notags

protected final java.util.Set<java.lang.String> notags

Constructor Detail

HtsgetRequest

public HtsgetRequest(java.net.URI endpoint)

Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server

Parameters:

endpoint - the full URI including both server path and the ID of the htsget resource, without the filtering parameters defined in the htsget spec such as start or referenceName

Method Detail

getEndpoint

public java.net.URI getEndpoint()

getFormat

public HtsgetFormat getFormat()

getDataClass

public HtsgetClass getDataClass()

getInterval

public Locatable getInterval()

getFields

public java.util.Set<HtsgetRequestField> getFields()

getTags

public java.util.Set<java.lang.String> getTags()

getNoTags

public java.util.Set<java.lang.String> getNoTags()

setFormat

public void setFormat(HtsgetFormat format)

setDataClass

public void setDataClass(HtsgetClass dataClass)

setInterval

public void setInterval(Locatable interval)

addField

public void addField(HtsgetRequestField field)

addFields

public void addFields(java.util.Collection<HtsgetRequestField> fields)

addTag

public void addTag(java.lang.String tag)

addTags

public void addTags(java.util.Collection<java.lang.String> tags)

addNotag

public void addNotag(java.lang.String notag)

addNotags

public void addNotags(java.util.Collection<java.lang.String> notags)

withFormat

public HtsgetRequest withFormat(HtsgetFormat format)

withDataClass

public HtsgetRequest withDataClass(HtsgetClass dataClass)

withInterval

public HtsgetRequest withInterval(Locatable interval)

withField

public HtsgetRequest withField(HtsgetRequestField field)

withFields

public HtsgetRequest withFields(java.util.Collection<HtsgetRequestField> fields)

withTag

public HtsgetRequest withTag(java.lang.String tag)

withTags

public HtsgetRequest withTags(java.util.Collection<java.lang.String> tags)

withNotag

public HtsgetRequest withNotag(java.lang.String notag)

withNotags

public HtsgetRequest withNotags(java.util.Collection<java.lang.String> notags)

validateRequest

public void validateRequest()

Validates that the user query obeys htsget spec

toURI

public java.net.URI toURI()

Convert request to a URI which can be used to make http request for data blocks

getConnection

protected java.net.HttpURLConnection getConnection()

getResponse

public HtsgetResponse getResponse()

Attempt to make htsget request and return response if there are no errors

Returns:

the response from the htsget server if request is successful as an HtsgetResponse object