X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2FClustalO.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2FClustalO.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=91755713e42b8bbc11bd3fbca9edf278a5f17e14;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git
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-ClustalO
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-Class ClustalO
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-java.lang.Object
- compbio.engine.client.SkeletalExecutable<ClustalO>
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-- All Implemented Interfaces:
- Executable<ClustalO>
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-public class 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:
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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
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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)
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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:
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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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