compbio.engine.client

Class SkeletalExecutable<T>

java.lang.Object

compbio.engine.client.SkeletalExecutable<T>

All Implemented Interfaces:

Executable<T>

Direct Known Subclasses:

AACon, ClustalO, ClustalW, Disembl, GlobPlot, GLprobs, IUPred, Jronn, Mafft, MSAprobs, Muscle, Probcons, RNAalifold, Tcoffee

public abstract class SkeletalExecutable<T>
extends java.lang.Object
implements Executable<T>

Nested Class Summary

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

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
protected CommandBuilder<T>	cbuilder This has to allow duplicate parameters as different options may have the same value e.g.
static java.lang.String	ERROR
protected java.lang.String	errorFile
static java.lang.String	INPUT
protected java.lang.String	inputFile
private boolean	isErrorSet
private boolean	isInputSet
private boolean	isOutputSet
private LimitsManager<T>	limits
private static org.apache.log4j.Logger	log
static java.lang.String	OUTPUT
protected java.lang.String	outputFile
protected static compbio.util.PropertyHelper	ph

Constructor Summary

Constructors

Constructor and Description
SkeletalExecutable()
SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)

Method Summary

Modifier and Type	Method and Description
Executable<T>	addParameters(java.util.List<java.lang.String> parameters) Adds parameter to the list of parameters for a native executable
boolean	equals(java.lang.Object obj)
static int	getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)
java.lang.String	getClusterJobSettings()
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
java.lang.String	getError()
java.lang.String	getInput()
Limit<T>	getLimit(java.lang.String presetName)
LimitsManager<T>	getLimits()
java.lang.String	getOutput()
CommandBuilder<T>	getParameters(Executable.ExecProvider provider)
abstract java.lang.Class<T>	getType()
int	hashCode()
protected boolean	isErrorSet()
protected boolean	isInputSet()
protected boolean	isOutputSet()
Executable<?>	loadRunConfiguration(RunConfiguration rconfig)
(package private) void	paramValueUpdater() This is a generic method of changing values of the parameters with properties This method iterates via commands for an executable finding matches from the Executable.properties file and replacing values in CommandBuilder with a combination of value from CommandBuilder to merge path from properties
SkeletalExecutable<T>	setError(java.lang.String errFile)
SkeletalExecutable<T>	setInput(java.lang.String inFile)
SkeletalExecutable<T>	setOutput(java.lang.String outFile)
Executable<T>	setParameter(java.lang.String parameter)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface compbio.engine.client.Executable

getResults

Field Detail

ph

protected static final compbio.util.PropertyHelper ph

log

private static org.apache.log4j.Logger log

limits

private LimitsManager<T> limits

INPUT

public static final java.lang.String INPUT

See Also:

Constant Field Values

OUTPUT

public static final java.lang.String OUTPUT

See Also:

Constant Field Values

ERROR

public static final java.lang.String ERROR

See Also:

Constant Field Values

inputFile

protected java.lang.String inputFile

outputFile

protected java.lang.String outputFile

errorFile

protected java.lang.String errorFile

isInputSet

private boolean isInputSet

isOutputSet

private boolean isOutputSet

isErrorSet

private boolean isErrorSet

cbuilder

protected CommandBuilder<T> cbuilder

This has to allow duplicate parameters as different options may have the same value e.g. Muscle -weight1 clustalw -weight2 clustalw

Constructor Detail

SkeletalExecutable

public SkeletalExecutable()

SkeletalExecutable

public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)

Method Detail

setInput

public SkeletalExecutable<T> setInput(java.lang.String inFile)

setOutput

public SkeletalExecutable<T> setOutput(java.lang.String outFile)

setError

public SkeletalExecutable<T> setError(java.lang.String errFile)

getParameters

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

Specified by:

getParameters in interface Executable<T>

addParameters

public Executable<T> addParameters(java.util.List<java.lang.String> parameters)

Description copied from interface: Executable

Adds parameter to the list of parameters for a native executable

Specified by:

addParameters in interface Executable<T>

Returns:

this Executable

setParameter

public Executable<T> setParameter(java.lang.String parameter)

paramValueUpdater

void paramValueUpdater()

This is a generic method of changing values of the parameters with properties This method iterates via commands for an executable finding matches from the Executable.properties file and replacing values in CommandBuilder with a combination of value from CommandBuilder to merge path from properties

getCreatedFiles

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

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<T>

See Also:

Executable.getCreatedFiles()

getInput

public java.lang.String getInput()

Specified by:

getInput in interface Executable<T>

isInputSet

protected boolean isInputSet()

isOutputSet

protected boolean isOutputSet()

isErrorSet

protected boolean isErrorSet()

getOutput

public java.lang.String getOutput()

Specified by:

getOutput in interface Executable<T>

getError

public java.lang.String getError()

Specified by:

getError in interface Executable<T>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

loadRunConfiguration

public Executable<?> loadRunConfiguration(RunConfiguration rconfig)

Specified by:

loadRunConfiguration in interface Executable<T>

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

getClusterJobSettings

public java.lang.String getClusterJobSettings()

Specified by:

getClusterJobSettings in interface Executable<T>

getClusterCpuNum

public static int getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)

Returns:

number of cpus to use on the cluster or 0 if the value is undefined

getLimit

public Limit<T> getLimit(java.lang.String presetName)

Specified by:

getLimit in interface Executable<T>

getLimits

public LimitsManager<T> getLimits()

Specified by:

getLimits in interface Executable<T>

getType

public abstract java.lang.Class<T> getType()

Returns:

subclasses must return their type