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

static String	KEY_VALUE_SEPARATOR
static String	STAT_FILE

Fields inherited from class compbio.engine.client.SkeletalExecutable

ERROR, INPUT, OUTPUT

Constructor Summary

AACon()

Method Summary

List<String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
CommandBuilder<AACon>	getParameters(Executable.ExecProvider provider)
ScoreManager	getResults(String workDirectory)
static String	getStatFile()
Class<AACon>	getType()
AACon	setInput(String inFile)
void	setNCore(int ncoreNumber)
AACon	setOutput(String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

KEY_VALUE_SEPARATOR

public static final String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

STAT_FILE

public static final String STAT_FILE

See Also:

Constant Field Values

Constructor Detail

AACon

public AACon()

Method Detail

getResults

public ScoreManager getResults(String workDirectory)
                        throws ResultNotAvailableException

Throws:

ResultNotAvailableException

getCreatedFiles

public List<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(String inFile)

Overrides:

setInput in class SkeletalExecutable<AACon>

setOutput

public AACon setOutput(String outFile)

Overrides:

setOutput in class SkeletalExecutable<AACon>

getType

public Class<AACon> getType()

Specified by:

getType in class SkeletalExecutable<AACon>

Returns:

subclasses must return their type

getStatFile

public static String getStatFile()

setNCore

public void setNCore(int ncoreNumber)

getParameters

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

Specified by:

getParameters in interface Executable<AACon>

Overrides:

getParameters in class SkeletalExecutable<AACon>