com.pacbio.secondary.vis.svc.server

Class VisService

java.lang.Object

com.pacbio.secondary.vis.svc.server.VisService

public class VisService
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
VisService()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getDefaultDirectory() used by remote filesystem view
java.lang.String[]	getDirectoryList(java.lang.String filename, boolean bListDirOnly) Returns list of files or directories in specified directory
byte[]	getFastaSequence(java.lang.String url, int contig_index, java.lang.String contig_name, long start, long end) get fasta sequence from fasta file as byte array.
byte[]	getFile(java.lang.String filename) gets file as byte array
WsFileInfo[]	getFilesInformation(java.lang.String filename, java.lang.String pattern, boolean bisDirectory) Returns info about files or directories.
byte[]	getGZippedFile(java.lang.String filename) gets file as gzipped byte array
WsJobMetadataInfo	getMetadataInfo(java.lang.String url, int opts) Returns reference info from selected metadata.rdf file
WsReferenceInfo	getReferenceInfo(java.lang.String url) Returns reference info from selected reference.info.xml file
java.lang.String	getServiceInfo() returns runtime info about server and this service
WsTrackInfo[]	getTracksListInfo(java.lang.String url) Returns tracks list info from selected template.info.xml or tracks.list.xml file(s)
boolean	putFile(java.lang.String filename, byte[] buffer) generic method to write bits to file on server

Methods inherited from class java.lang.Object

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

Constructor Detail

VisService

public VisService()

Method Detail

getServiceInfo

public java.lang.String getServiceInfo()

returns runtime info about server and this service

getFile

public byte[] getFile(java.lang.String filename)

gets file as byte array

getGZippedFile

public byte[] getGZippedFile(java.lang.String filename)

gets file as gzipped byte array

putFile

public boolean putFile(java.lang.String filename,
              byte[] buffer)

generic method to write bits to file on server

getDirectoryList

public java.lang.String[] getDirectoryList(java.lang.String filename,
                                  boolean bListDirOnly)

Returns list of files or directories in specified directory

Parameters:

filename -

bListDirOnly -

Returns:

getDefaultDirectory

public java.lang.String getDefaultDirectory()

used by remote filesystem view

Returns:

default root directory to view

getFilesInformation

public WsFileInfo[] getFilesInformation(java.lang.String filename,
                               java.lang.String pattern,
                               boolean bisDirectory)

Returns info about files or directories.

Parameters:

filename - file or directory path

bisDirectory - set to true if filename is a directory

Returns:

getMetadataInfo

public WsJobMetadataInfo getMetadataInfo(java.lang.String url,
                                int opts)

Returns reference info from selected metadata.rdf file

Parameters:

url - path to metadata

opts - parser options

getReferenceInfo

public WsReferenceInfo getReferenceInfo(java.lang.String url)

Returns reference info from selected reference.info.xml file

Parameters:

url -

getTracksListInfo

public WsTrackInfo[] getTracksListInfo(java.lang.String url)

Returns tracks list info from selected template.info.xml or tracks.list.xml file(s)

Parameters:

url -

Returns:

getFastaSequence

public byte[] getFastaSequence(java.lang.String url,
                      int contig_index,
                      java.lang.String contig_name,
                      long start,
                      long end)

get fasta sequence from fasta 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:

gzipped WsFastaSequenceInfo object