com.pacbio.secondary.vis.svc.server

Class HDFService

java.lang.Object

com.pacbio.secondary.vis.svc.server.HDFService

public class HDFService
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected static boolean	forceGC

Constructor Summary

Constructors

Constructor and Description
HDFService() default constructor

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	getAnnotatedInsertions(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop, int mode) Returns annotated reads with insertions from cmp.h5 results file serialized inside gzip archive.
byte[]	getAnnotatedResults(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop, int mode) Returns annotated reads and stats from cmp.h5 file serialized inside gzip archive
byte[]	getConsensusSequence(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop) get consensus sequence from cmp.h5 file as byte array.
java.lang.String[]	getContigNames(java.lang.String url) Returns the names of all contigs in cmp.h5
java.lang.String	getFileHeader(java.lang.String url) Returns header and summary info about cmp.h5
byte[]	getIPDConsensus(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop) get IPDRatio sequence from cmp.h5 file as two-dimensional short array.
java.lang.String	getServiceExperienceIndex()
java.lang.String	getServiceInfo() returns info about server and this service

Methods inherited from class java.lang.Object

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

Field Detail

forceGC

protected static final boolean forceGC

See Also:

Constant Field Values

Constructor Detail

HDFService

public HDFService()

default constructor

Method Detail

getServiceInfo

public java.lang.String getServiceInfo()

returns info about server and this service

Returns:

getServiceExperienceIndex

public java.lang.String getServiceExperienceIndex()

Returns:

getFileHeader

public java.lang.String getFileHeader(java.lang.String url)

Returns header and summary info about cmp.h5

Parameters:

url -

Returns:

getContigNames

public java.lang.String[] getContigNames(java.lang.String url)

Returns the names of all contigs in cmp.h5

Parameters:

url -

Returns:

getAnnotatedResults

public byte[] getAnnotatedResults(java.lang.String url,
                         java.lang.String contig_id,
                         int client_contig_index,
                         long start,
                         long stop,
                         int mode)

Returns annotated reads and stats from cmp.h5 file serialized inside gzip archive

Parameters:

url -

contig_id -

client_contig_index -

start -

stop -

mode -

Returns:

getAnnotatedInsertions

public byte[] getAnnotatedInsertions(java.lang.String url,
                            java.lang.String contig_id,
                            int client_contig_index,
                            long start,
                            long stop,
                            int mode)

Returns annotated reads with insertions from cmp.h5 results file serialized inside gzip archive.

getConsensusSequence

public byte[] getConsensusSequence(java.lang.String url,
                          java.lang.String contig_id,
                          int client_contig_index,
                          long start,
                          long stop)

get consensus sequence from cmp.h5 file as byte array. contig index and coordinates are 1 based... requested start and end are inclusive returned start and end may be different from requested

Parameters:

url -

contig_index -

contig_name -

start -

end -

Returns:

getIPDConsensus

public byte[] getIPDConsensus(java.lang.String url,
                     java.lang.String contig_id,
                     int client_contig_index,
                     long start,
                     long stop)

get IPDRatio sequence from cmp.h5 file as two-dimensional short array. contig index and coordinates are 1 based... requested start and end are inclusive returned start and end may be different from requested

Parameters:

url -

contig_index -

contig_name -

start -

end -

Returns: