Package org.anchoranalysis.plugin.io.bean.task

Class CombineCSV

Object

AnchorBean<Task<FileInput,CSVWriter>>

Task<FileInput,CSVWriter>

CombineCSV

public class CombineCSV
extends Task<FileInput,CSVWriter>

Combines multiple CSV files into a single CSV file.

No check occurs that the same number of rows/columns exist in the files being combined.

The following outputs are produced:

Output Name	Default?	Description
"combined"	yes	A CSV combining the input CSV files.
inherited from Task

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
CombineCSV()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(CSVWriter writer, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
CSVWriter	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doJobOnInput(InputBound<FileInput,CSVWriter> parameters)	Performs the task on a particular input.
String	getSeperator()
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
boolean	isAddName()
boolean	isFirstLineHeaders()
boolean	isTransposed()
void	setAddName(boolean addName)
void	setFirstLineHeaders(boolean firstLineHeaders)
void	setSeperator(String seperator)
void	setTransposed(boolean transposed)

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

executeJob, isInputCompatibleWith

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

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

Constructor Details

CombineCSV

public CombineCSV()

Method Details

beforeAnyJobIsExecuted

public CSVWriter beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<FileInput> inputs,
 ParametersExperiment parameters)
                                 throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<FileInput,CSVWriter>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<FileInput,CSVWriter>

Returns:

true iff the execution is expected to be very quick, false otherwise.

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: Task

Highest class(es) that will function as a valid input.

This is usually the class of T (or sometimes the absolute base class InputFromManager).

Specified by:

inputTypesExpected in class Task<FileInput,CSVWriter>

Returns:

the input-types that a task expects.

doJobOnInput

public void doJobOnInput(InputBound<FileInput,CSVWriter> parameters)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<FileInput,CSVWriter>

Parameters:

parameters - the input for the job.

Throws:

JobExecutionException - if an error occurs executing a particular job, that is not otherwise suppressed.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(CSVWriter writer,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<FileInput,CSVWriter>

Parameters:

writer - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Description copied from class: Task

If specified, default rules for determine which outputs are enabled or not.

Overrides:

defaultOutputs in class Task<FileInput,CSVWriter>

Returns:

the default rules if they exist.

getSeperator

public String getSeperator()

setSeperator

public void setSeperator(String seperator)

isFirstLineHeaders

public boolean isFirstLineHeaders()

setFirstLineHeaders

public void setFirstLineHeaders(boolean firstLineHeaders)

isTransposed

public boolean isTransposed()

setTransposed

public void setTransposed(boolean transposed)

isAddName

public boolean isAddName()

setAddName

public void setAddName(boolean addName)