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

Class HtsgetRequest

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

UNMAPPED_UNPLACED_INTERVAL

PROTOCOL_VERSION

ACCEPT_TYPE

format

dataClass

interval

fields

tags

notags

Constructor Details

HtsgetRequest

Method Details

getEndpoint

getFormat

getDataClass

getInterval

getFields

getTags

getNoTags

setFormat

setDataClass

setInterval

addField

addFields

addTag

addTags

addNotag

addNotags

withFormat

withDataClass

withInterval

withField

withFields

withTag

withTags

withNotag

withNotags

validateRequest

toURI

getConnection

getResponse