compbio.runner.disorder

Class IUPred

java.lang.Object

compbio.engine.client.SkeletalExecutable<IUPred>

compbio.runner.disorder.IUPred

All Implemented Interfaces:

Executable<IUPred>

public class IUPred
extends SkeletalExecutable<IUPred>

iupred sequenceFile Maximum sequence length is 40000 chars. Single string length max is a 1000 chars!

Nested Class Summary

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

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	GLOB_OUTPUT
private static org.apache.log4j.Logger	log
private static java.lang.String	LONG_OUTPUT
private static java.lang.String	SHORT_OUTPUT

Fields inherited from class compbio.engine.client.SkeletalExecutable

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

Constructor Summary

Constructors

Constructor and Description
IUPred()

Method Summary

Modifier and Type	Method and Description
(package private) void	combineScores(java.util.Map<java.lang.String,java.util.Set<Score>> combined, java.util.Map<java.lang.String,Score> scores)
java.lang.String	getOutput()
ScoreManager	getResults(java.lang.String workDirectory)
java.lang.Class<IUPred>	getType()
(package private) java.lang.UnsupportedOperationException	newUnsupportedOutputException()
IUPred	setInput(java.lang.String inFile)
IUPred	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getParameters, 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

GLOB_OUTPUT

private static final java.lang.String GLOB_OUTPUT

See Also:

Constant Field Values

SHORT_OUTPUT

private static final java.lang.String SHORT_OUTPUT

See Also:

Constant Field Values

LONG_OUTPUT

private static final java.lang.String LONG_OUTPUT

See Also:

Constant Field Values

Constructor Detail

IUPred

public IUPred()

Method Detail

getResults

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

Throws:

ResultNotAvailableException

combineScores

void combineScores(java.util.Map<java.lang.String,java.util.Set<Score>> combined,
                   java.util.Map<java.lang.String,Score> scores)

setInput

public IUPred setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<IUPred>

setOutput

public IUPred setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<IUPred>

newUnsupportedOutputException

java.lang.UnsupportedOperationException newUnsupportedOutputException()

getOutput

public java.lang.String getOutput()

Specified by:

getOutput in interface Executable<IUPred>

Overrides:

getOutput in class SkeletalExecutable<IUPred>

getType

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

Specified by:

getType in class SkeletalExecutable<IUPred>

Returns:

subclasses must return their type