public class Mafft extends SkeletalExecutable<Mafft> implements PipedExecutable<Mafft>
Executable.ExecProvider
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
autoOption |
static java.lang.String |
KEY_VALUE_SEPARATOR |
private static org.apache.log4j.Logger |
log |
private java.lang.String |
MATRIX_PAR_NAME |
cbuilder, ERROR, errorFile, INPUT, inputFile, OUTPUT, outputFile, ph
Constructor and Description |
---|
Mafft() |
Modifier and Type | Method and Description |
---|---|
Mafft |
addParameters(java.util.List<java.lang.String> parameters)
Mafft input must always be the last parameter!
|
Alignment |
getResults(java.lang.String workDirectory) |
java.lang.Class<Mafft> |
getType() |
Mafft |
setInput(java.lang.String inFile) |
equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, isErrorSet, isInputSet, isOutputSet, loadRunConfiguration, setError, setOutput, setParameter, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
private static org.apache.log4j.Logger log
private static java.lang.String autoOption
private final java.lang.String MATRIX_PAR_NAME
public static final java.lang.String KEY_VALUE_SEPARATOR
public Alignment getResults(java.lang.String workDirectory) throws ResultNotAvailableException
getResults
in interface Executable<Mafft>
ResultNotAvailableException
public Mafft setInput(java.lang.String inFile)
setInput
in class SkeletalExecutable<Mafft>
public Mafft addParameters(java.util.List<java.lang.String> parameters)
addParameters
in interface Executable<Mafft>
addParameters
in class SkeletalExecutable<Mafft>
public java.lang.Class<Mafft> getType()
getType
in class SkeletalExecutable<Mafft>