java.lang.Object

htsjdk.samtools.util.htsget.HtsgetRequest

htsjdk.samtools.util.htsget.HtsgetPOSTRequest

public class HtsgetPOSTRequest extends HtsgetRequest

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

This class is experimental and subject to change as the POST api evolves.

See https://github.com/samtools/hts-specs/pull/285 for the API specification.

Field Summary

Fields inherited from class htsjdk.samtools.util.htsget.HtsgetRequest
ACCEPT_TYPE, dataClass, fields, format, interval, notags, PROTOCOL_VERSION, tags, UNMAPPED_UNPLACED_INTERVAL
Constructor Summary

Constructors

Constructor

Description

HtsgetPOSTRequest(HtsgetRequest req)

HtsgetPOSTRequest(URI endpoint)

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

Modifier and Type

Method

Description

void

addInterval(Locatable interval)

void

addIntervals(Collection<Locatable> intervals)

protected HttpURLConnection

getConnection()

mjson.Json

queryBody()

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

HtsgetPOSTRequest

withDataClass(HtsgetClass dataClass)

HtsgetPOSTRequest

withField(HtsgetRequestField field)

HtsgetPOSTRequest

withFields(Collection<HtsgetRequestField> fields)

HtsgetPOSTRequest

withFormat(HtsgetFormat format)

HtsgetPOSTRequest

withInterval(Locatable interval)

HtsgetPOSTRequest

withIntervals(Collection<Locatable> intervals)

HtsgetPOSTRequest

withNotag(String notag)

HtsgetPOSTRequest

withNotags(Collection<String> notags)

HtsgetPOSTRequest

withTag(String tag)

HtsgetPOSTRequest

withTags(Collection<String> tags)

Methods inherited from class htsjdk.samtools.util.htsget.HtsgetRequest
addField, addFields, addNotag, addNotags, addTag, addTags, getDataClass, getEndpoint, getFields, getFormat, getInterval, getNoTags, getResponse, getTags, setDataClass, setFormat

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- HtsgetPOSTRequest
  
  public HtsgetPOSTRequest(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
- HtsgetPOSTRequest
  
  public HtsgetPOSTRequest(HtsgetRequest req)
Method Details
- setInterval
  
  public void setInterval(Locatable interval)
  
  Overrides:
  
  setInterval in class HtsgetRequest
- addInterval
  
  public void addInterval(Locatable interval)
- addIntervals
  
  public void addIntervals(Collection<Locatable> intervals)
- withFormat
  
  public HtsgetPOSTRequest withFormat(HtsgetFormat format)
  
  Overrides:
  
  withFormat in class HtsgetRequest
- withDataClass
  
  public HtsgetPOSTRequest withDataClass(HtsgetClass dataClass)
  
  Overrides:
  
  withDataClass in class HtsgetRequest
- withInterval
  
  public HtsgetPOSTRequest withInterval(Locatable interval)
  
  Overrides:
  
  withInterval in class HtsgetRequest
- withIntervals
  
  public HtsgetPOSTRequest withIntervals(Collection<Locatable> intervals)
- withField
  
  public HtsgetPOSTRequest withField(HtsgetRequestField field)
  
  Overrides:
  
  withField in class HtsgetRequest
- withFields
  
  public HtsgetPOSTRequest withFields(Collection<HtsgetRequestField> fields)
  
  Overrides:
  
  withFields in class HtsgetRequest
- withTag
  
  public HtsgetPOSTRequest withTag(String tag)
  
  Overrides:
  
  withTag in class HtsgetRequest
- withTags
  
  public HtsgetPOSTRequest withTags(Collection<String> tags)
  
  Overrides:
  
  withTags in class HtsgetRequest
- withNotag
  
  public HtsgetPOSTRequest withNotag(String notag)
  
  Overrides:
  
  withNotag in class HtsgetRequest
- withNotags
  
  public HtsgetPOSTRequest withNotags(Collection<String> notags)
  
  Overrides:
  
  withNotags in class HtsgetRequest
- validateRequest
  
  public void validateRequest()
  
  Description copied from class: HtsgetRequest
  
  Validates that the user query obeys htsget spec
  
  Overrides:
  
  validateRequest in class HtsgetRequest
- toURI
  
  public URI toURI()
  
  Description copied from class: HtsgetRequest
  
  Convert request to a URI which can be used to make http request for data blocks
  
  Overrides:
  
  toURI in class HtsgetRequest
- queryBody
  
  public mjson.Json queryBody()
- getConnection
  
  protected HttpURLConnection getConnection()
  
  Overrides:
  
  getConnection in class HtsgetRequest

Class HtsgetPOSTRequest

Field Summary

Fields inherited from class htsjdk.samtools.util.htsget.HtsgetRequest

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.util.htsget.HtsgetRequest

Methods inherited from class java.lang.Object

Constructor Details

HtsgetPOSTRequest

HtsgetPOSTRequest

Method Details

setInterval

addInterval

addIntervals

withFormat

withDataClass

withInterval

withIntervals

withField

withFields

withTag

withTags

withNotag

withNotags

validateRequest

toURI

queryBody

getConnection