com.pacbio.secondary.vis.svc.hdf.client

Class HDFServiceWrapper

java.lang.Object

com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper

public class HDFServiceWrapper
extends java.lang.Object

Author:

mmilletti

Constructor Summary

Constructors

Constructor and Description
HDFServiceWrapper(java.lang.String url, VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	doAsyncGetAnnotatedResults(java.lang.String url, int client_contig_index, long start, long stop, int mode, java.lang.Object clientData) Gets high resolution, fully annotated reads
boolean	doASyncGetConsensusSequence(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, java.lang.Object clientData) Gets consensus sequence from cmp.h5
boolean	doASyncGetIPDConsensus(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, java.lang.Object clientData) Gets IPD consensus from cmp.h5
javax.activation.DataHandler	doSyncGetAnnotatedInsertions(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop, int mode)
javax.activation.DataHandler	doSyncGetAnnotatedResults(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long stop, int mode)
javax.activation.DataHandler	doSyncGetConsensusSequence(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end) Gets consensus sequence from cmp.h5
java.lang.String	doSyncGetFileHeader(java.lang.String url)
javax.activation.DataHandler	doSyncGetIPDConsensus(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end) Gets IPD consensus sequence from cmp.h5
java.lang.String	doSyncGetServiceExperienceIndex()
java.lang.String	doSyncGetServiceInfo()
static void	main(java.lang.String[] args) Test only...
protected static void	testFile(HDFServiceWrapper test2, java.lang.String unsorted_file_url, java.lang.String ctg_id, int ctg_idx, long start, long end, int mode)

Methods inherited from class java.lang.Object

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

Constructor Detail

HDFServiceWrapper

public HDFServiceWrapper(java.lang.String url,
                 VioletApp app)

Method Detail

doAsyncGetAnnotatedResults

public boolean doAsyncGetAnnotatedResults(java.lang.String url,
                                 int client_contig_index,
                                 long start,
                                 long stop,
                                 int mode,
                                 java.lang.Object clientData)

Gets high resolution, fully annotated reads

Parameters:

url -

clientData -

client_contig_index -

start -

stop -

Returns:

doASyncGetConsensusSequence

public boolean doASyncGetConsensusSequence(java.lang.String url,
                                  java.lang.String contig_id,
                                  int client_contig_index,
                                  long start,
                                  long end,
                                  java.lang.Object clientData)

Gets consensus sequence from cmp.h5

Parameters:

url -

contig_id -

contig_name -

start -

end -

clientData -

Returns:

doASyncGetIPDConsensus

public boolean doASyncGetIPDConsensus(java.lang.String url,
                             java.lang.String contig_id,
                             int client_contig_index,
                             long start,
                             long end,
                             java.lang.Object clientData)

Gets IPD consensus from cmp.h5

Parameters:

url -

contig_id -

contig_name -

start -

end -

clientData -

Returns:

doSyncGetAnnotatedResults

public javax.activation.DataHandler doSyncGetAnnotatedResults(java.lang.String url,
                                                     java.lang.String contig_id,
                                                     int client_contig_index,
                                                     long start,
                                                     long stop,
                                                     int mode)

Parameters:

url -

contig_id -

client_contig_index -

start -

stop -

mode -

Returns:

doSyncGetAnnotatedInsertions

public javax.activation.DataHandler doSyncGetAnnotatedInsertions(java.lang.String url,
                                                        java.lang.String contig_id,
                                                        int client_contig_index,
                                                        long start,
                                                        long stop,
                                                        int mode)

Parameters:

url -

contig_id -

client_contig_index -

start -

stop -

mode -

Returns:

doSyncGetConsensusSequence

public javax.activation.DataHandler doSyncGetConsensusSequence(java.lang.String url,
                                                      java.lang.String contig_id,
                                                      int client_contig_index,
                                                      long start,
                                                      long end)

Gets consensus sequence from cmp.h5

Parameters:

url -

contig_id -

contig_name -

start -

end -

clientData -

Returns:

doSyncGetIPDConsensus

public javax.activation.DataHandler doSyncGetIPDConsensus(java.lang.String url,
                                                 java.lang.String contig_id,
                                                 int client_contig_index,
                                                 long start,
                                                 long end)

Gets IPD consensus sequence from cmp.h5

Parameters:

url -

contig_id -

contig_name -

start -

end -

clientData -

Returns:

doSyncGetServiceInfo

public java.lang.String doSyncGetServiceInfo()

Returns:

doSyncGetFileHeader

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

Returns:

doSyncGetServiceExperienceIndex

public java.lang.String doSyncGetServiceExperienceIndex()

Returns:

main

public static void main(java.lang.String[] args)

Test only...

Parameters:

args -

testFile

protected static void testFile(HDFServiceWrapper test2,
            java.lang.String unsorted_file_url,
            java.lang.String ctg_id,
            int ctg_idx,
            long start,
            long end,
            int mode)