compbio.runner.msa
Class ClustalW
java.lang.Object
compbio.engine.client.SkeletalExecutable<ClustalW>
compbio.runner.msa.ClustalW
- All Implemented Interfaces:
- Executable<ClustalW>
public class ClustalW
- extends SkeletalExecutable<ClustalW>
Methods inherited from class compbio.engine.client.SkeletalExecutable |
addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, 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
ClustalW
public ClustalW()
setOutput
public ClustalW setOutput(java.lang.String outFile)
- Overrides:
setOutput
in class SkeletalExecutable<ClustalW>
setInput
public ClustalW setInput(java.lang.String inFile)
- Overrides:
setInput
in class SkeletalExecutable<ClustalW>
getResults
public Alignment getResults(java.lang.String workDirectory)
throws ResultNotAvailableException
- Throws:
ResultNotAvailableException
getCreatedFiles
public java.util.List<java.lang.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<ClustalW>
- Overrides:
getCreatedFiles
in class SkeletalExecutable<ClustalW>
- See Also:
Executable.getCreatedFiles()
getStatFile
public static java.lang.String getStatFile()
getType
public java.lang.Class<ClustalW> getType()
- Specified by:
getType
in class SkeletalExecutable<ClustalW>
- Returns:
- subclasses must return their type