compbio.runner.disorder

Class Disembl

java.lang.Object

compbio.engine.client.SkeletalExecutable<Disembl>

compbio.runner.disorder.Disembl

All Implemented Interfaces:

Executable<Disembl>, PipedExecutable<Disembl>

public class Disembl
extends SkeletalExecutable<Disembl>
implements PipedExecutable<Disembl>

DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' This version of DisEMBL is 1.4 (latest available for download in Feb 2011) capable of outputting raw values The values of the parameters are hard coded in DisEMBL.py script. smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4 fold_rem465=1.2 Changing these values are not recommended by developers, apart from smoothing window. However, 5 orders of magnitude changes in this parameter does not change the output so allowing this change also seems pointless. Finally, the binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to these values, so changing them can lead to problems. This is not a standard DisEMBL! The script has been modified!

Nested Class Summary

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

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
double	COILS_EXPECTATION_THRESHOLD For the region to be considered disordered the values must exceed these
private static org.apache.log4j.Logger	log
double	LOOPS_EXPECTATION_THRESHOLD
double	REM_EXPECTATION_THRESHOLD

Fields inherited from class compbio.engine.client.SkeletalExecutable

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

Constructor Summary

Constructors

Constructor and Description
Disembl()

Method Summary

Modifier and Type	Method and Description
ScoreManager	getResults(java.lang.String workDirectory)
java.lang.Class<Disembl>	getType()
Disembl	setInput(java.lang.String inFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface compbio.engine.client.Executable

addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration

Field Detail

log

private static org.apache.log4j.Logger log

COILS_EXPECTATION_THRESHOLD

public final double COILS_EXPECTATION_THRESHOLD

For the region to be considered disordered the values must exceed these

See Also:

Constant Field Values

REM_EXPECTATION_THRESHOLD

public final double REM_EXPECTATION_THRESHOLD

See Also:

Constant Field Values

LOOPS_EXPECTATION_THRESHOLD

public final double LOOPS_EXPECTATION_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

Disembl

public Disembl()

Method Detail

getResults

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

Specified by:

getResults in interface Executable<Disembl>

Throws:

ResultNotAvailableException

setInput

public Disembl setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<Disembl>

getType

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

Specified by:

getType in class SkeletalExecutable<Disembl>

Returns:

subclasses must return their type