org.intermine.bio.postprocess
Class FlyBaseUniProtRefsTask

java.lang.Object
  org.apache.tools.ant.ProjectComponent
      org.apache.tools.ant.Task
          org.intermine.bio.postprocess.FlyBaseUniProtRefsTask

public class FlyBaseUniProtRefsTask
extends org.apache.tools.ant.Task

Task to read a file mapping cds identifiers to UniProt accession numbers and create a protein reference in the CDSs.

Field Summary

protected java.io.File	linkFile
protected java.lang.String	objectStoreWriter
protected ObjectStore	os
protected ObjectStoreWriter	osw

Fields inherited from class org.apache.tools.ant.Task

description, location, target, taskName, taskType, wrapper

Fields inherited from class org.apache.tools.ant.ProjectComponent

project

Constructor Summary

FlyBaseUniProtRefsTask()

Method Summary

void	execute() Use the linkFile attribute (which is a file containing FlyBase Translation <-> UniProt accession numbers) to link Translation objects to Protein objects in the ObjectStoreWriter.
void	setLinkFile(java.io.File linkFile) Set the linkFile attribute.
void	setObjectStoreWriter(java.lang.String objectStoreWriter) Sets the value of objectStoreWriter

Methods inherited from class org.apache.tools.ant.Task

getDescription, getLocation, getOwningTarget, getRuntimeConfigurableWrapper, getTaskName, getTaskType, getWrapper, handleErrorFlush, handleErrorOutput, handleFlush, handleInput, handleOutput, init, isInvalid, log, log, maybeConfigure, perform, reconfigure, setDescription, setLocation, setOwningTarget, setRuntimeConfigurableWrapper, setTaskName, setTaskType

Methods inherited from class org.apache.tools.ant.ProjectComponent

getProject, setProject

Methods inherited from class java.lang.Object

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

Field Detail

osw

protected ObjectStoreWriter osw

os

protected ObjectStore os

objectStoreWriter

protected java.lang.String objectStoreWriter

linkFile

protected java.io.File linkFile

Constructor Detail

FlyBaseUniProtRefsTask

public FlyBaseUniProtRefsTask()

Method Detail

setObjectStoreWriter

public void setObjectStoreWriter(java.lang.String objectStoreWriter)

Sets the value of objectStoreWriter

Parameters:

objectStoreWriter - an objectStoreWriter alias for operations that require one

setLinkFile

public void setLinkFile(java.io.File linkFile)

Set the linkFile attribute.

Parameters:

linkFile - the File to read in execute()

execute

public void execute()
             throws org.apache.tools.ant.BuildException

Use the linkFile attribute (which is a file containing FlyBase Translation <-> UniProt accession numbers) to link Translation objects to Protein objects in the ObjectStoreWriter. Sets the protein reference in the CDS objects.

Overrides:

execute in class org.apache.tools.ant.Task

Throws:

org.apache.tools.ant.BuildException - if there is a problem while executing