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!
Methods inherited from class compbio.engine.client.SkeletalExecutable |
addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString |
Methods inherited from class java.lang.Object |
getClass, notify, notifyAll, wait, wait, wait |
KEY_VALUE_SEPARATOR
public static final java.lang.String KEY_VALUE_SEPARATOR
- See Also:
- Constant Field Values
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
Disembl
public Disembl()
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