Package htsjdk.samtools.util.htsget

Class HtsgetRequest

java.lang.Object

htsjdk.samtools.util.htsget.HtsgetRequest

Direct Known Subclasses:

HtsgetPOSTRequest

public class HtsgetRequest
extends 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	Description
protected static final String	ACCEPT_TYPE
protected HtsgetClass	dataClass
protected final EnumSet<HtsgetRequestField>	fields
protected HtsgetFormat	format
protected Locatable	interval
protected final Set<String>	notags
protected static final String	PROTOCOL_VERSION
protected final Set<String>	tags
static final Interval	UNMAPPED_UNPLACED_INTERVAL

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	addField(HtsgetRequestField field)
void	addFields(Collection<HtsgetRequestField> fields)
void	addNotag(String notag)
void	addNotags(Collection<String> notags)
void	addTag(String tag)
void	addTags(Collection<String> tags)
protected HttpURLConnection	getConnection()
HtsgetClass	getDataClass()
URI	getEndpoint()
Set<HtsgetRequestField>	getFields()
HtsgetFormat	getFormat()
Locatable	getInterval()
Set<String>	getNoTags()
HtsgetResponse	getResponse()	Attempt to make htsget request and return response if there are no errors
Set<String>	getTags()
void	setDataClass(HtsgetClass dataClass)
void	setFormat(HtsgetFormat format)
void	setInterval(Locatable interval)
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(Collection<HtsgetRequestField> fields)
HtsgetRequest	withFormat(HtsgetFormat format)
HtsgetRequest	withInterval(Locatable interval)
HtsgetRequest	withNotag(String notag)
HtsgetRequest	withNotags(Collection<String> notags)
HtsgetRequest	withTag(String tag)
HtsgetRequest	withTags(Collection<String> tags)

Methods inherited from class java.lang.Object

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

Field Details

UNMAPPED_UNPLACED_INTERVAL

public static final Interval UNMAPPED_UNPLACED_INTERVAL

PROTOCOL_VERSION

protected static final String PROTOCOL_VERSION

See Also:

• Constant Field Values

ACCEPT_TYPE

protected static final String ACCEPT_TYPE

See Also:

• Constant Field Values

format

protected HtsgetFormat format

dataClass

protected HtsgetClass dataClass

interval

protected Locatable interval

fields

protected final EnumSet<HtsgetRequestField> fields

tags

protected final Set<String> tags

notags

protected final Set<String> notags

Constructor Details

HtsgetRequest

public HtsgetRequest(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 Details

getEndpoint

public URI getEndpoint()

getFormat

public HtsgetFormat getFormat()

getDataClass

public HtsgetClass getDataClass()

getInterval

public Locatable getInterval()

getFields

public Set<HtsgetRequestField> getFields()

getTags

public Set<String> getTags()

getNoTags

public Set<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(Collection<HtsgetRequestField> fields)

addTag

public void addTag(String tag)

addTags

public void addTags(Collection<String> tags)

addNotag

public void addNotag(String notag)

addNotags

public void addNotags(Collection<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(Collection<HtsgetRequestField> fields)

withTag

public HtsgetRequest withTag(String tag)

withTags

public HtsgetRequest withTags(Collection<String> tags)

withNotag

public HtsgetRequest withNotag(String notag)

withNotags

public HtsgetRequest withNotags(Collection<String> notags)

validateRequest

public void validateRequest()

Validates that the user query obeys htsget spec

toURI

public URI toURI()

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

getConnection

protected 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