compbio.runner.msa

Class ClustalW

java.lang.Object

compbio.engine.client.SkeletalExecutable<ClustalW>

compbio.runner.msa.ClustalW

All Implemented Interfaces:

Executable<ClustalW>

public class ClustalW
extends SkeletalExecutable<ClustalW>

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	EXEC_STAT_FILE
static java.lang.String	KEY_VALUE_SEPARATOR
private static org.apache.log4j.Logger	log
private static java.lang.String	TREE_FILE_EXT

Fields inherited from class compbio.engine.client.SkeletalExecutable

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

Constructor Summary

Constructors

Constructor and Description
ClustalW()

Method Summary

Modifier and Type	Method and Description
private java.lang.String	convertInputNameToTreeName() Clustal output tree with same name as input file but .dnd extension e.g.
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
Alignment	getResults(java.lang.String workDirectory)
static java.lang.String	getStatFile()
java.lang.Class<ClustalW>	getType()
ClustalW	setInput(java.lang.String inFile)
ClustalW	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

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

Methods inherited from class java.lang.Object

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

Field Detail

log

private static org.apache.log4j.Logger log

EXEC_STAT_FILE

private static final java.lang.String EXEC_STAT_FILE

See Also:

Constant Field Values

TREE_FILE_EXT

private static final java.lang.String TREE_FILE_EXT

See Also:

Constant Field Values

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

ClustalW

public ClustalW()

Method Detail

setOutput

public ClustalW setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<ClustalW>

setInput

public ClustalW setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<ClustalW>

getResults

public Alignment getResults(java.lang.String workDirectory)
                     throws ResultNotAvailableException

Throws:

ResultNotAvailableException

getCreatedFiles

public java.util.List<java.lang.String> getCreatedFiles()

Description copied from class: SkeletalExecutable

This method cannot really tell whether the files has actually been created or not. It must be overridden as required.

Specified by:

getCreatedFiles in interface Executable<ClustalW>

Overrides:

getCreatedFiles in class SkeletalExecutable<ClustalW>

See Also:

Executable.getCreatedFiles()

convertInputNameToTreeName

private java.lang.String convertInputNameToTreeName()

Clustal output tree with same name as input file but .dnd extension e.g. this methods do similar conversion TO122.fasta -> TO122.dnd or TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any limits on the name length

Returns:

getStatFile

public static java.lang.String getStatFile()

getType

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

Specified by:

getType in class SkeletalExecutable<ClustalW>

Returns:

subclasses must return their type