compbio.runner.conservation

Class AACon

java.lang.Object

compbio.engine.client.SkeletalExecutable<AACon>

compbio.runner.conservation.AACon

All Implemented Interfaces:

Executable<AACon>

public class AACon
extends SkeletalExecutable<AACon>

Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out

Author:

pvtroshin

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	KEY_VALUE_SEPARATOR
private static org.apache.log4j.Logger	log
private int	ncoreNumber Number of cores to use, defaults to 1 for local execution or the value of "jronn.cluster.cpunum" property for cluster execution
private java.lang.String	ncorePrm
static java.lang.String	STAT_FILE

Fields inherited from class compbio.engine.client.SkeletalExecutable

cbuilder, ERROR, errorFile, INPUT, inputFile, OUTPUT, outputFile, ph

Constructor Summary

Constructors

Constructor and Description
AACon()

Method Summary

Modifier and Type	Method and Description
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
private static java.lang.String	getLibPath()
(package private) int	getNCore()
CommandBuilder<AACon>	getParameters(Executable.ExecProvider provider)
ScoreManager	getResults(java.lang.String workDirectory)
static java.lang.String	getStatFile()
java.lang.Class<AACon>	getType()
AACon	setInput(java.lang.String inFile)
void	setNCore(int ncoreNumber)
AACon	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, isErrorSet, isInputSet, isOutputSet, loadRunConfiguration, setError, setParameter, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

log

private static org.apache.log4j.Logger log

ncoreNumber

private int ncoreNumber

Number of cores to use, defaults to 1 for local execution or the value of "jronn.cluster.cpunum" property for cluster execution

ncorePrm

private final java.lang.String ncorePrm

See Also:

Constant Field Values

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

STAT_FILE

public static final java.lang.String STAT_FILE

See Also:

Constant Field Values

Constructor Detail

AACon

public AACon()

Method Detail

getResults

public ScoreManager getResults(java.lang.String workDirectory)
                        throws ResultNotAvailableException

Throws:

ResultNotAvailableException

getLibPath

private static java.lang.String getLibPath()

getCreatedFiles

public java.util.List<java.lang.String> getCreatedFiles()

Description copied from class: SkeletalExecutable

This method cannot really tell whether the files has actually been created or not. It must be overridden as required.

Specified by:

getCreatedFiles in interface Executable<AACon>

Overrides:

getCreatedFiles in class SkeletalExecutable<AACon>

See Also:

Executable.getCreatedFiles()

setInput

public AACon setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<AACon>

setOutput

public AACon setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<AACon>

getType

public java.lang.Class<AACon> getType()

Specified by:

getType in class SkeletalExecutable<AACon>

Returns:

subclasses must return their type

getStatFile

public static java.lang.String getStatFile()

setNCore

public void setNCore(int ncoreNumber)

getNCore

int getNCore()

getParameters

public CommandBuilder<AACon> getParameters(Executable.ExecProvider provider)

Specified by:

getParameters in interface Executable<AACon>

Overrides:

getParameters in class SkeletalExecutable<AACon>