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+ClustalO
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+compbio.runner.msa
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+Class ClustalO
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+java.lang.Object
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compbio.engine.client.SkeletalExecutable<ClustalO>
+ compbio.runner.msa.ClustalO
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+- All Implemented Interfaces:
- Executable<ClustalO>
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+public class ClustalO
- extends SkeletalExecutable<ClustalO>
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+Nested Class Summary |
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+Constructor Summary |
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+ClustalO()
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+ --threads= Number of processors to use
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+ -l, --log= Log all non-essential output to this file |
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+| Methods inherited from class compbio.engine.client.SkeletalExecutable |
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+addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString |
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+KEY_VALUE_SEPARATOR
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+public static final String KEY_VALUE_SEPARATOR
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+- See Also:
- Constant Field Values
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+Constructor Detail |
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+ClustalO
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+public ClustalO()
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+- --threads= Number of processors to use
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+ -l, --log= Log all non-essential output to this file
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+setOutput
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+public ClustalO setOutput(String outFile)
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+- Overrides:
setOutput in class SkeletalExecutable<ClustalO>
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+setInput
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+public ClustalO setInput(String inFile)
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+- Overrides:
setInput in class SkeletalExecutable<ClustalO>
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+getResults
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+public Alignment getResults(String workDirectory)
+ throws ResultNotAvailableException
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+- Throws:
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ResultNotAvailableException
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+getStatFile
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+public static String getStatFile()
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+getType
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+public Class<ClustalO> getType()
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+- Specified by:
getType in class SkeletalExecutable<ClustalO>
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+- Returns:
- subclasses must return their type
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+getParameters
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+public CommandBuilder<ClustalO> getParameters(Executable.ExecProvider provider)
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+- Specified by:
getParameters in interface Executable<ClustalO>- Overrides:
getParameters in class SkeletalExecutable<ClustalO>
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+setNCore
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+public void setNCore(int ncoreNumber)
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