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>

Author:

pvtroshin

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Field Summary

Fields

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

Fields inherited from class compbio.engine.client.SkeletalExecutable

cbuilder, ERROR, errorFile, INPUT, inputFile, OUTPUT, outputFile, ph

Constructor Summary

Constructors

Constructor and Description
Mafft()

Method Summary

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)

Methods inherited from class compbio.engine.client.SkeletalExecutable

equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, isErrorSet, isInputSet, isOutputSet, loadRunConfiguration, setError, setOutput, setParameter, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration

Field Detail

log

private static org.apache.log4j.Logger log

autoOption

private static java.lang.String autoOption

MATRIX_PAR_NAME

private final java.lang.String MATRIX_PAR_NAME

See Also:

Constant Field Values

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

Mafft

public Mafft()

Method Detail

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

getType

public java.lang.Class<Mafft> getType()

Specified by:

getType in class SkeletalExecutable<Mafft>

Returns:

subclasses must return their type