org.biojava.nbio.structure.align.client

Class FarmJobParameters

java.lang.Object

org.biojava.nbio.structure.align.client.FarmJobParameters

public class FarmJobParameters
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BATCH_SIZE
static int	DEFAULT_JOB_TIME
static int	DEFAULT_NR_ALIGNMENTS
static int	DEFAULT_NR_THREADS
static String	DEFAULT_PDB_PATH
static String	DEFAULT_SERVER_URL

Constructor Summary

Constructors

Constructor and Description
FarmJobParameters()

Method Summary

Methods

Modifier and Type	Method and Description
String	getCacheFilePath()
int	getNrAlignments()
String	getPdbFilePath()
String	getServer()
int	getStepSize() how many pairs should be requested for alignment from server?
int	getThreads()
int	getTime()
String	getUsername()
boolean	isRunBackground() Flag if a job that only runs one parallell job should be run in its own thread or in the main thread.
boolean	isUpdateRemediatedFiles()
boolean	isVerbose() Flag if the job should be run in verbose mode.
void	setCacheFilePath(String cacheFilePath)
void	setNrAlignments(int nrAlignments)
void	setPdbFilePath(String pdbFilePath)
void	setRunBackground(boolean runBackground)
void	setServer(String server)
void	setStepSize(int stepSize)
void	setThreads(int threads)
void	setTime(int time)
void	setUpdateRemediatedFiles(boolean updateRemediatedFiles)
void	setUsername(String username)
void	setVerbose(boolean verbose)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_JOB_TIME

public static final int DEFAULT_JOB_TIME

See Also:

Constant Field Values

DEFAULT_NR_ALIGNMENTS

public static final int DEFAULT_NR_ALIGNMENTS

See Also:

Constant Field Values

DEFAULT_NR_THREADS

public static final int DEFAULT_NR_THREADS

See Also:

Constant Field Values

DEFAULT_SERVER_URL

public static final String DEFAULT_SERVER_URL

DEFAULT_PDB_PATH

public static final String DEFAULT_PDB_PATH

See Also:

Constant Field Values

DEFAULT_BATCH_SIZE

public static final int DEFAULT_BATCH_SIZE

See Also:

Constant Field Values

Constructor Detail

FarmJobParameters

public FarmJobParameters()

Method Detail

getPdbFilePath

public String getPdbFilePath()

setPdbFilePath

public void setPdbFilePath(String pdbFilePath)

getCacheFilePath

public String getCacheFilePath()

setCacheFilePath

public void setCacheFilePath(String cacheFilePath)

getNrAlignments

public int getNrAlignments()

setNrAlignments

public void setNrAlignments(int nrAlignments)

getTime

public int getTime()

setTime

public void setTime(int time)

getThreads

public int getThreads()

setThreads

public void setThreads(int threads)

getServer

public String getServer()

setServer

public void setServer(String server)

getUsername

public String getUsername()

setUsername

public void setUsername(String username)

isRunBackground

public boolean isRunBackground()

Flag if a job that only runs one parallell job should be run in its own thread or in the main thread. For User interface related apps should be set to true. Default: false;

Returns:

flag

setRunBackground

public void setRunBackground(boolean runBackground)

getStepSize

public int getStepSize()

how many pairs should be requested for alignment from server?

Returns:

stepsize

setStepSize

public void setStepSize(int stepSize)

isVerbose

public boolean isVerbose()

Flag if the job should be run in verbose mode. Default: false

Returns:

flag if the job should be run in verbose mode

setVerbose

public void setVerbose(boolean verbose)

isUpdateRemediatedFiles

public boolean isUpdateRemediatedFiles()

setUpdateRemediatedFiles

public void setUpdateRemediatedFiles(boolean updateRemediatedFiles)

toString

public String toString()

Overrides:

toString in class Object