CommandBuilder (Cannoli_2.11: Core 0.2.0 API)

java.lang.Object
- org.bdgenomics.cannoli.builder.CommandBuilder

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

DockerBuilder, LocalBuilder, SingularityBuilder
```
public abstract class CommandBuilder
extends Object
implements Serializable
```
Abstract command builder.

See Also:

Serialized Form

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`CommandBuilder()` Create a new command builder.
`protected`	`CommandBuilder(String executable)` Create a new command builder with the specified executable.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`CommandBuilder`	`add(Iterable<String> arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder`	`add(String... arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder`	`addArgument(String argument)` Add an argument to the list of command arguments for this command builder.
`CommandBuilder`	`addArguments(Iterable<String> arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder`	`addArguments(String... arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder`	`addEnvironment(Map<String,String> environment)` Add environment variables to the map of environment variables for this command builder.
`CommandBuilder`	`addEnvironment(String variable, String value)` Add an environment variable to the map of environment variables for this command builder.
`CommandBuilder`	`addFile(String file)` Add a file to the list of files to make available locally for this command builder.
`CommandBuilder`	`addFiles(Iterable<String> files)` Add files to the list of files to make available locally for this command builder.
`CommandBuilder`	`addFiles(String... files)` Add zero or more files to the list of files to make available locally for this command builder.
`CommandBuilder`	`addMount(String mount)` Add the specified mount point to the map of mount points for this command builder.
`CommandBuilder`	`addMount(String source, String target)` Add the specified mount point to the map of mount points for this command builder.
`CommandBuilder`	`addMounts(Map<String,String> mounts)` Add the specified mount points to the map of mount points for this command builder.
`abstract List<String>`	`build()` Build and return the command for this command builder as a list of strings.
`List<String>`	`getArguments()` Return an immutable list of command arguments for this command builder.
`Map<String,String>`	`getEnvironment()` Return an immutable map of environment variables for this command builder.
`String`	`getExecutable()` Return the executable for this command builder.
`List<String>`	`getFiles()` Return an immutable list of files to make available locally for this command builder.
`Integer`	`getFlankSize()` Return the number of bases to flank each command invocation by for this builder.
`String`	`getImage()` Return the image for this command builder.
`Map<String,String>`	`getMounts()` Return the map of mount points for this command builder.
`Optional<Integer>`	`getOptFlankSize()` Return the number of bases to flank each command invocation by for this builder, as an optional.
`Optional<Long>`	`getOptTimeout()` Return how long to let a single partition run for, in seconds, for this builder, as an optional.
`boolean`	`getSudo()` Return true to run via sudo for this command builder.
`Long`	`getTimeout()` Return how long to let a single partition run for, in seconds, for this builder.
`boolean`	`isSudo()` Return true to run via sudo for this command builder.
`CommandBuilder`	`reset()` Reset this command builder.
`CommandBuilder`	`setExecutable(String executable)` Set the executable for this command builder.
`CommandBuilder`	`setFlankSize(Integer flankSize)` Set the number of bases to flank each command invocation by for this builder.
`CommandBuilder`	`setImage(String image)` Set the image for this command builder.
`CommandBuilder`	`setSudo(boolean sudo)` Set to true to run via sudo for this command builder.
`CommandBuilder`	`setTimeout(Long timeout)` Set how long to let a single partition run for, in seconds, for this builder.
`CommandBuilder`	`setTimeout(long duration, TimeUnit timeUnit)` Set how long to let a single partition run for, in the specified time unit, for this builder.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CommandBuilder
```
protected CommandBuilder()
```
    Create a new command builder.
  - CommandBuilder
```
protected CommandBuilder(String executable)
```
    Create a new command builder with the specified executable.
    
    Parameters:
    
    executable - executable, must not be null
- Method Detail
  - setExecutable
```
public final CommandBuilder setExecutable(String executable)
```
    Set the executable for this command builder.
    
    Parameters:
    
    executable - executable, must not be null
    
    Returns:
    
    this command builder
  - setFlankSize
```
public final CommandBuilder setFlankSize(@Nullable
                                         Integer flankSize)
```
    Set the number of bases to flank each command invocation by for this builder.
    
    Parameters:
    
    flankSize - number of bases to flank each command invocation by
    
    Returns:
    
    this command builder
  - setImage
```
public final CommandBuilder setImage(String image)
```
    Set the image for this command builder.
    
    Parameters:
    
    image - image, must not be null
    
    Returns:
    
    this command builder
  - setSudo
```
public final CommandBuilder setSudo(boolean sudo)
```
    Set to true to run via sudo for this command builder.
    
    Parameters:
    
    sudo - true to run via sudo
    
    Returns:
    
    this command builder
  - setTimeout
```
public final CommandBuilder setTimeout(@Nullable
                                       Long timeout)
```
    Set how long to let a single partition run for, in seconds, for this builder.
    
    Parameters:
    
    timeout - how long to let a single partition run for, in seconds
    
    Returns:
    
    this command builder
  - setTimeout
```
public final CommandBuilder setTimeout(long duration,
                                       TimeUnit timeUnit)
```
    Set how long to let a single partition run for, in the specified time unit, for this builder.
    
    Parameters:
    
    duration - duration
    
    timeUnit - time unit, must not be null
    
    Returns:
    
    this command builder
  - add
```
public final CommandBuilder add(String... arguments)
```
    Add one or more arguments to the list of command arguments for this command builder.
    
    Parameters:
    
    arguments - variable number of arguments to add, must not be null
    
    Returns:
    
    this command builder
  - add
```
public final CommandBuilder add(Iterable<String> arguments)
```
    Add one or more arguments to the list of command arguments for this command builder.
    
    Parameters:
    
    arguments - arguments to add, must not be null
    
    Returns:
    
    this command builder
  - addArgument
```
public final CommandBuilder addArgument(String argument)
```
    Add an argument to the list of command arguments for this command builder.
    
    Parameters:
    
    argument - argument to add, must not be null
    
    Returns:
    
    this command builder
  - addArguments
```
public final CommandBuilder addArguments(String... arguments)
```
    Add one or more arguments to the list of command arguments for this command builder.
    
    Parameters:
    
    arguments - variable number of arguments to add, must not be null
    
    Returns:
    
    this command builder
  - addArguments
```
public final CommandBuilder addArguments(Iterable<String> arguments)
```
    Add one or more arguments to the list of command arguments for this command builder.
    
    Parameters:
    
    arguments - arguments to add, must not be null
    
    Returns:
    
    this command builder
  - addEnvironment
```
public final CommandBuilder addEnvironment(String variable,
                                           String value)
```
    Add an environment variable to the map of environment variables for this command builder.
    
    Parameters:
    
    variable - environment variable to add, must not be null
    
    value - environment variable value to add, must not be null
    
    Returns:
    
    this command builder
  - addEnvironment
```
public final CommandBuilder addEnvironment(Map<String,String> environment)
```
    Add environment variables to the map of environment variables for this command builder.
    
    Parameters:
    
    environment - environment variables to add, must not be null
    
    Returns:
    
    this command builder
  - addFile
```
public final CommandBuilder addFile(String file)
```
    Add a file to the list of files to make available locally for this command builder.
    
    Parameters:
    
    file - file to add, must not be null
    
    Returns:
    
    this command builder
  - addFiles
```
public final CommandBuilder addFiles(String... files)
```
    Add zero or more files to the list of files to make available locally for this command builder.
    
    Parameters:
    
    files - variable number of files to add, must not be null
    
    Returns:
    
    this command builder
  - addFiles
```
public final CommandBuilder addFiles(Iterable<String> files)
```
    Add files to the list of files to make available locally for this command builder.
    
    Parameters:
    
    files - files to add, must not be null
    
    Returns:
    
    this command builder
  - addMount
```
public final CommandBuilder addMount(String mount)
```
    Add the specified mount point to the map of mount points for this command builder.
    
    Parameters:
    
    mount - mount point source and target, must not be null
    
    Returns:
    
    this command builder
  - addMount
```
public final CommandBuilder addMount(String source,
                                     String target)
```
    Add the specified mount point to the map of mount points for this command builder.
    
    Parameters:
    
    source - mount point source, must not be null
    
    target - mount point target, must not be null
    
    Returns:
    
    this command builder
  - addMounts
```
public final CommandBuilder addMounts(Map<String,String> mounts)
```
    Add the specified mount points to the map of mount points for this command builder.
    
    Parameters:
    
    mounts - mount points to add, must not be null
    
    Returns:
    
    this command builder
  - getExecutable
```
public final String getExecutable()
```
    Return the executable for this command builder.
    
    Returns:
    
    the executable for this command builder
  - getFlankSize
```
public final Integer getFlankSize()
```
    Return the number of bases to flank each command invocation by for this builder. May be null.
    
    Returns:
    
    the number of bases to flank each command invocation by for this builder
  - getOptFlankSize
```
public final Optional<Integer> getOptFlankSize()
```
    Return the number of bases to flank each command invocation by for this builder, as an optional.
    
    Returns:
    
    the number of bases to flank each command invocation by for this builder, as an optional
  - getImage
```
public final String getImage()
```
    Return the image for this command builder.
    
    Returns:
    
    the image for this command builder.
  - getTimeout
```
public final Long getTimeout()
```
    Return how long to let a single partition run for, in seconds, for this builder. May be null.
    
    Returns:
    
    how long to let a single partition run for, in seconds, for this builder
  - getOptTimeout
```
public final Optional<Long> getOptTimeout()
```
    Return how long to let a single partition run for, in seconds, for this builder, as an optional.
    
    Returns:
    
    how long to let a single partition run for, in seconds, for this builder, as an optional
  - getSudo
```
public final boolean getSudo()
```
    Return true to run via sudo for this command builder.
    
    Returns:
    
    true to run via sudo for this command builder
  - isSudo
```
public final boolean isSudo()
```
    Return true to run via sudo for this command builder.
    
    Returns:
    
    true to run via sudo for this command builder
  - getArguments
```
public final List<String> getArguments()
```
    Return an immutable list of command arguments for this command builder.
    
    Returns:
    
    an immutable list of command arguments for this command builder
  - getEnvironment
```
public final Map<String,String> getEnvironment()
```
    Return an immutable map of environment variables for this command builder.
    
    Returns:
    
    an immutable map of environment variables for this command builder
  - getFiles
```
public final List<String> getFiles()
```
    Return an immutable list of files to make available locally for this command builder.
    
    Returns:
    
    an immutable list of files to make available locally for this command builder
  - getMounts
```
public final Map<String,String> getMounts()
```
    Return the map of mount points for this command builder.
    
    Returns:
    
    the map of mount points for this command builder
  - reset
```
public final CommandBuilder reset()
```
    Reset this command builder.
    
    Returns:
    
    this command builder
  - build
```
public abstract List<String> build()
```
    Build and return the command for this command builder as a list of strings.
    
    Returns:
    
    the command for this command builder as a list of strings.
    
    Throws:
    
    IllegalStateException - if this builder is in an illegal state, e.g. if required values are not set

Class CommandBuilder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CommandBuilder

CommandBuilder

Method Detail

setExecutable

setFlankSize

setImage

setSudo

setTimeout

setTimeout

add

add

addArgument

addArguments

addArguments

addEnvironment

addEnvironment

addFile

addFiles

addFiles

addMount

addMount

addMounts

getExecutable

getFlankSize

getOptFlankSize

getImage

getTimeout

getOptTimeout

getSudo

isSudo

getArguments

getEnvironment

getFiles

getMounts

reset

build