compbio.runner
Class _SkeletalCommandBuilder

java.lang.Object
  compbio.runner._SkeletalCommandBuilder

All Implemented Interfaces:

Executable<_SkeletalCommandBuilder>

Direct Known Subclasses:

BlastAll, Mcl, OB, PSIBlast, Ronn, RPSBlast

Deprecated.

@Deprecated
public abstract class _SkeletalCommandBuilder
extends Object
implements Executable<_SkeletalCommandBuilder>

Nested Class Summary

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

Executable.ExecProvider

Constructor Summary

_SkeletalCommandBuilder()
Deprecated.

Method Summary

_SkeletalCommandBuilder	addParameter(String parameter) Deprecated.
_SkeletalCommandBuilder	addParameters(List<String> parameters) Deprecated. Adds parameter to the list of parameters for a native executable
_SkeletalCommandBuilder	addParameters(String[] parameters) Deprecated.
String	getClusterJobSettings() Deprecated.
String	getEmail() Deprecated.
String	getError() Deprecated.
Limit<_SkeletalCommandBuilder>	getLimit(String presetName) Deprecated.
LimitsManager<_SkeletalCommandBuilder>	getLimits() Deprecated.
String	getName() Deprecated.
String	getOutput() Deprecated.
CommandBuilder<_SkeletalCommandBuilder>	getParameters(Executable.ExecProvider provider) Deprecated.
<V> V	getResults(String directory) Deprecated.
Executable<?>	loadRunConfiguration(RunConfiguration rconfig) Deprecated.
_SkeletalCommandBuilder	setEmail(String email) Deprecated.
_SkeletalCommandBuilder	setName(String name) Deprecated.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

getCreatedFiles, getInput

Constructor Detail

_SkeletalCommandBuilder

public _SkeletalCommandBuilder()

Deprecated.

Method Detail

setEmail

public _SkeletalCommandBuilder setEmail(String email)

Deprecated.

setName

public _SkeletalCommandBuilder setName(String name)

Deprecated.

getName

public String getName()

Deprecated.

getEmail

public String getEmail()

Deprecated.

addParameters

public _SkeletalCommandBuilder addParameters(String[] parameters)

Deprecated.

addParameters

public _SkeletalCommandBuilder addParameters(List<String> parameters)

Deprecated.

Description copied from interface: Executable

Adds parameter to the list of parameters for a native executable

Specified by:

addParameters in interface Executable<_SkeletalCommandBuilder>

Returns:

this Executable

getParameters

public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)

Deprecated.

Specified by:

getParameters in interface Executable<_SkeletalCommandBuilder>

addParameter

public _SkeletalCommandBuilder addParameter(String parameter)

Deprecated.

getResults

public <V> V getResults(String directory)

Deprecated.

Specified by:

getResults in interface Executable<_SkeletalCommandBuilder>

loadRunConfiguration

public Executable<?> loadRunConfiguration(RunConfiguration rconfig)

Deprecated.

Specified by:

loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>

getOutput

public String getOutput()

Deprecated.

Specified by:

getOutput in interface Executable<_SkeletalCommandBuilder>

getError

public String getError()

Deprecated.

Specified by:

getError in interface Executable<_SkeletalCommandBuilder>

getLimit

public Limit<_SkeletalCommandBuilder> getLimit(String presetName)

Deprecated.

Specified by:

getLimit in interface Executable<_SkeletalCommandBuilder>

getLimits

public LimitsManager<_SkeletalCommandBuilder> getLimits()

Deprecated.

Specified by:

getLimits in interface Executable<_SkeletalCommandBuilder>

getClusterJobSettings

public String getClusterJobSettings()

Deprecated.

Specified by:

getClusterJobSettings in interface Executable<_SkeletalCommandBuilder>