compbio.runner.msa
Class Mafft
java.lang.Object
compbio.engine.client.SkeletalExecutable<Mafft>
compbio.runner.msa.Mafft
- All Implemented Interfaces:
- Executable<Mafft>, PipedExecutable<Mafft>
public class Mafft
- extends SkeletalExecutable<Mafft>
- implements PipedExecutable<Mafft>
Constructor Summary |
Mafft()
|
Methods inherited from class compbio.engine.client.SkeletalExecutable |
equals, getClusterSettings, getCreatedFiles, getError, getInput, 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
Mafft
public Mafft()
getResults
public Alignment getResults(java.lang.String workDirectory)
throws ResultNotAvailableException
- Specified by:
getResults
in interface Executable<Mafft>
- Throws:
ResultNotAvailableException
setInput
public Mafft setInput(java.lang.String inFile)
- Overrides:
setInput
in class SkeletalExecutable<Mafft>
addParameters
public Mafft addParameters(java.util.List<java.lang.String> parameters)
- Mafft input must always be the last parameter!
- Specified by:
addParameters
in interface Executable<Mafft>
- Overrides:
addParameters
in class SkeletalExecutable<Mafft>
- Returns:
- this Executable
getLimit
public Limit<Mafft> getLimit(java.lang.String presetName)
- Specified by:
getLimit
in interface Executable<Mafft>
getLimits
public LimitsManager<Mafft> getLimits()
- Specified by:
getLimits
in interface Executable<Mafft>
getType
public java.lang.Class<? extends Executable<?>> getType()
- Specified by:
getType
in class SkeletalExecutable<Mafft>