compbio.runner.msa
Class Muscle
java.lang.Object
compbio.engine.client.SkeletalExecutable<Muscle>
compbio.runner.msa.Muscle
- All Implemented Interfaces:
- Executable<Muscle>
public class Muscle
- extends SkeletalExecutable<Muscle>
Constructor Summary |
Muscle()
Default options are
-clwstrict - write output in clustal format |
Methods inherited from class compbio.engine.client.SkeletalExecutable |
addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString |
KEY_VALUE_SEPARATOR
public static final String KEY_VALUE_SEPARATOR
- See Also:
- Constant Field Values
Muscle
public Muscle()
- Default options are
-clwstrict - write output in clustal format
setOutput
public Muscle setOutput(String outFile)
- Overrides:
setOutput
in class SkeletalExecutable<Muscle>
setInput
public Muscle setInput(String inFile)
- Overrides:
setInput
in class SkeletalExecutable<Muscle>
getResults
public Alignment getResults(String workDirectory)
throws ResultNotAvailableException
- Throws:
ResultNotAvailableException
getCreatedFiles
public List<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<Muscle>
- Overrides:
getCreatedFiles
in class SkeletalExecutable<Muscle>
- See Also:
Executable.getCreatedFiles()
getStatFile
public static String getStatFile()
getType
public Class<Muscle> getType()
- Specified by:
getType
in class SkeletalExecutable<Muscle>
- Returns:
- subclasses must return their type