uk.ac.ebi.intact.application.hierarchView.business.tulip.webService
Class TulipAccessImpl

java.lang.Object
  |
  +--uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl

All Implemented Interfaces:

TulipAccess

public class TulipAccessImpl

extends java.lang.Object

implements TulipAccess

Purpose :
Allows the user to send a TLP file to Tulip and get back the node's coordinate.

Author:

Samuel KERRIEN (skerrien@ebi.ac.uk)

Constructor Summary

TulipAccessImpl()

Method Summary

void	cleanErrorMessages() Clean message list
ProteinCoordinate[]	getComputedTlpContent(java.lang.String tlpContent, java.lang.String optionMask) get the computed TLP content from tulip
java.lang.String[]	getErrorMessages(boolean hasToBeCleaned) Allows the user to get messages produced byte the web service
java.util.Collection	parseOutputFile(java.lang.String anOutputFile) Parse the Tulip conputed TLP file to grab coordinates of each protein Here is the format of the section to parse : (property 0 layout "viewLayout" (default "(105.000000,966.000000,359.000000)" "()" ) (node 1 "(215.500000,7.000000,0.000000)") (node 2 "(57.500000,-288.000000,0.000000)") (node 3 "(40.500000,191.000000,0.000000)") (...) )

Methods inherited from class java.lang.Object

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

Constructor Detail

TulipAccessImpl

public TulipAccessImpl()

Method Detail

getComputedTlpContent

public ProteinCoordinate[] getComputedTlpContent(java.lang.String tlpContent,
                                                 java.lang.String optionMask)

get the computed TLP content from tulip

Specified by:

getComputedTlpContent in interface TulipAccess

Parameters:

tlpContent - tlp content to compute

optionMask - the option of the Tulip process

Returns:

the computed tlp file content or null if an error occurs.

getErrorMessages

public java.lang.String[] getErrorMessages(boolean hasToBeCleaned)

Allows the user to get messages produced byte the web service

Specified by:

getErrorMessages in interface TulipAccess

Parameters:

hasToBeCleaned - delete all messages after sended them back to the client

Returns:

an array of messages or null if no messages are stored.

cleanErrorMessages

public void cleanErrorMessages()

Clean message list

Specified by:

cleanErrorMessages in interface TulipAccess

parseOutputFile

public java.util.Collection parseOutputFile(java.lang.String anOutputFile)

Parse the Tulip conputed TLP file to grab coordinates of each protein Here is the format of the section to parse : (property 0 layout "viewLayout" (default "(105.000000,966.000000,359.000000)" "()" ) (node 1 "(215.500000,7.000000,0.000000)") (node 2 "(57.500000,-288.000000,0.000000)") (node 3 "(40.500000,191.000000,0.000000)") (...) )

Parameters:

anOutputFile - the path of the file to read

Returns:

a collection of ProteinCoordinate