org.oncoblocks.centromere.core.dataimport

Class BasicImportOptions

java.lang.Object

org.oncoblocks.centromere.core.dataimport.BasicImportOptions

All Implemented Interfaces:

ImportOptions

public class BasicImportOptions
extends Object
implements ImportOptions

Captures basic parameters required for a data import pipeline.

Author:

woemler

Field Summary

Fields inherited from interface org.oncoblocks.centromere.core.dataimport.ImportOptions

SKIP_EXISTING_FILES, SKIP_INVALID_DATA_SETS, SKIP_INVALID_GENES, SKIP_INVALID_METADATA, SKIP_INVALID_RECORDS, SKIP_INVALID_SAMPLES, TEMP_DIRECTORY_PATH

Constructor Summary

Constructors

Constructor and Description
BasicImportOptions()
BasicImportOptions(ImportOptions importOptions)
BasicImportOptions(Map<String,String> options)

Method Summary

Modifier and Type	Method and Description
boolean	getBoolean(String name)
String	getOption(String name) Returns the string value of the given option, if it exists.
Map<String,String>	getOptions() Returns all of the key-value option pairs in the object.
String	getTempDirectoryPath()
boolean	hasOption(String name) Tests whether the option is present in the object's key-value map.
boolean	isSkipExistingFiles()
boolean	isSkipInvalidDataSets()
boolean	isSkipInvalidGenes()
boolean	isSkipInvalidMetadata()
boolean	isSkipInvalidRecords()
boolean	isSkipInvalidSamples()
void	setOption(String name, String value)
void	setOptions(Map<String,String> options)
void	setSkipExistingFiles(boolean skipExistingFiles)
void	setSkipInvalidDataSets(boolean skipInvalidDataSets)
void	setSkipInvalidGenes(boolean skipInvalidGenes)
void	setSkipInvalidMetadata(boolean skipInvalidMetadata)
void	setSkipInvalidRecords(boolean skipInvalidRecords)
void	setSkipInvalidSamples(boolean skipInvalidSamples)
void	setTempDirectoryPath(String tempDirectoryPath)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicImportOptions

public BasicImportOptions()

BasicImportOptions

public BasicImportOptions(Map<String,String> options)

BasicImportOptions

public BasicImportOptions(ImportOptions importOptions)

Method Detail

getOptions

public Map<String,String> getOptions()

Description copied from interface: ImportOptions

Returns all of the key-value option pairs in the object.

Specified by:

getOptions in interface ImportOptions

Returns:

Map of string options.

getOption

public String getOption(String name)

Description copied from interface: ImportOptions

Returns the string value of the given option, if it exists.

Specified by:

getOption in interface ImportOptions

Parameters:

name - Key name of the option.

Returns:

String value of the option.

getBoolean

public boolean getBoolean(String name)

setOption

public void setOption(String name,
                      String value)

setOptions

public void setOptions(Map<String,String> options)

hasOption

public boolean hasOption(String name)

Description copied from interface: ImportOptions

Tests whether the option is present in the object's key-value map.

Specified by:

hasOption in interface ImportOptions

Parameters:

name - Key name of the option.

Returns:

true if the option exists, false otherwise.

isSkipInvalidSamples

public boolean isSkipInvalidSamples()

isSkipInvalidDataSets

public boolean isSkipInvalidDataSets()

isSkipInvalidGenes

public boolean isSkipInvalidGenes()

isSkipInvalidMetadata

public boolean isSkipInvalidMetadata()

isSkipInvalidRecords

public boolean isSkipInvalidRecords()

setSkipInvalidSamples

public void setSkipInvalidSamples(boolean skipInvalidSamples)

setSkipInvalidDataSets

public void setSkipInvalidDataSets(boolean skipInvalidDataSets)

setSkipInvalidGenes

public void setSkipInvalidGenes(boolean skipInvalidGenes)

setSkipInvalidMetadata

public void setSkipInvalidMetadata(boolean skipInvalidMetadata)

setSkipInvalidRecords

public void setSkipInvalidRecords(boolean skipInvalidRecords)

setTempDirectoryPath

public void setTempDirectoryPath(String tempDirectoryPath)

isSkipExistingFiles

public boolean isSkipExistingFiles()

setSkipExistingFiles

public void setSkipExistingFiles(boolean skipExistingFiles)

getTempDirectoryPath

public String getTempDirectoryPath()

toString

public String toString()

Overrides:

toString in class Object