com.pacbio.secondary.vis.svc.server.hdf

Class GenomicDataServer

java.lang.Object

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer

public class GenomicDataServer
extends GenomicDataBuilder

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

GenomicDataStructures.WsReadStructure

Field Summary

Fields inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

CHIMERIC_STANDARD_THRESHOLD, CHIMERIC_STROBE_THRESHOLD, LANE_EXTRA_DISTANCE, MAX_ORDINATE_PILEUP

Fields inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

BASE_DELETION, BASE_LEFT_INSERTION, BASE_MATCH, BASE_POS_INSERTION, BASE_RIGHT_INSERTION, BASE_SVN

Constructor Summary

Constructors

Constructor and Description
GenomicDataServer()

Method Summary

Methods

Modifier and Type	Method and Description
WsFastaSequenceInfo	getConsensusSequenceFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop)
byte[]	getGZippedResultsFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, int mode)
WsIPDConsensusInfo	getIPDConsensusFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop) get ipd ratio as int arrays

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder

assembleReads, copyResults, copyResults, gatherBasesData, gatherMetricsData, getReadsDataFromFile, getReadsDataWithInsertionsFromFile, prepareResults, removeDataAboveThreshold, updateIOTimeStats

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

assembleResultsWithoutStructures, assembleResultsWithStructures, createGraphLinesStructure, createGraphLinksStructure, createGraphNodesStructure, createGraphStructure, PileUpResultsWithoutStructure, PileUpResultsWithoutStructureForBaseMods, PileUpResultsWithStructures

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

buildStats, createFromRawRead, createFromRawReadWithInsertions, reverse, reverse, reverse, reverseRawRead, setQVValue, updateMetricsFromRawRead

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomicDataServer

public GenomicDataServer()

Method Detail

getConsensusSequenceFromFile

public WsFastaSequenceInfo getConsensusSequenceFromFile(java.lang.String url,
                                               java.lang.String contig_id,
                                               int client_contig_index,
                                               long start,
                                               long stop)

Parameters:

url -

contig_id -

client_contig_index -

start - 1-based offset

stop - 1-based offset

Returns:

getIPDConsensusFromFile

public WsIPDConsensusInfo getIPDConsensusFromFile(java.lang.String url,
                                         java.lang.String contig_id,
                                         int client_contig_index,
                                         long start,
                                         long stop)

get ipd ratio as int arrays

Parameters:

url -

contig_id -

client_contig_index -

start - 1-based offset

stop - 1-based offset

Returns:

getGZippedResultsFromFile

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

Parameters:

url -

contig_id -

client_contig_index -

start -

end -

Returns: