JobBatch (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
- - net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

All Implemented Interfaces:: Job

public class JobBatch
extends AbstractJob

Field Summary
- Fields inherited from class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
  hasMetadataWriteback

Constructor Summary

Constructors
Constructor and Description

JobBatch(String algo)

Constructors
Constructor and Description
`JobBatch(String algo)`

Method Summary

Methods
Modifier and Type	Method and Description
`Job`	`createBashJob(String algo)`
`Command`	`getCommand()`
`List<Job>`	`getJobList()`
`int`	`getThreads()`
`boolean`	`hasMetadataWriteback()` job specific metadata is not supported yet
`boolean`	`isLocal()` Whether this job should run locally instead of out on a cluster.
`Command`	`setCommand(String cmd)` set the job command
`void`	`setHasMetadataWriteback(boolean metadata)` job specific metadata is not supported yet
`void`	`setLocal()` Sets this job to run locally.
`void`	`setLocal(boolean runLocal)` Sets whether this job should run locally.
`void`	`setParentAccessions(Collection<String> parentAccessions)` set parent accessiosns for the job
`Job`	`setQueue(String queue)` set the queue
`AbstractJob`	`setThreads(int count)` set the max thread number

Methods inherited from class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
addFile, addParent, addParent, addRequirement, getAlgo, getAnnotations, getClassPath, getFiles, getMainClass, getMaxMemory, getParentAccessions, getParents, getQsubOptions, getQueue, getRequirements, setAlgo, setMaxMemory, setParents, setQsubOptions, setRequirements

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

- Constructor Detail
  - JobBatch
```
public JobBatch(String algo)
```
- Method Detail
  - createBashJob
```
public Job createBashJob(String algo)
```
  - setCommand
```
public Command setCommand(String cmd)
```
    Description copied from interface: Job
    
    set the job command
    
    Specified by:
    
    setCommand in interface Job
    
    Overrides:
    
    setCommand in class AbstractJob
    
    Returns:
  - getCommand
```
public Command getCommand()
```
    Specified by:
    
    getCommand in interface Job
    
    Overrides:
    
    getCommand in class AbstractJob
    
    Returns:
    a job command object
  - setThreads
```
public AbstractJob setThreads(int count)
```
    Description copied from interface: Job
    
    set the max thread number
    
    Specified by:
    
    setThreads in interface Job
    
    Overrides:
    
    setThreads in class AbstractJob
    
    Returns:
  - getThreads
```
public int getThreads()
```
    Specified by:
    
    getThreads in interface Job
    
    Overrides:
    
    getThreads in class AbstractJob
    
    Returns:
    the max thread number
  - setQueue
```
public Job setQueue(String queue)
```
    Description copied from interface: Job
    
    set the queue
    
    Specified by:
    
    setQueue in interface Job
    
    Overrides:
    
    setQueue in class AbstractJob
    
    Returns:
  - setHasMetadataWriteback
```
public void setHasMetadataWriteback(boolean metadata)
```
    Description copied from interface: Job
    
    job specific metadata is not supported yet
    
    Specified by:
    
    setHasMetadataWriteback in interface Job
    
    Overrides:
    
    setHasMetadataWriteback in class AbstractJob
  - hasMetadataWriteback
```
public boolean hasMetadataWriteback()
```
    Description copied from interface: Job
    
    job specific metadata is not supported yet
    
    Specified by:
    
    hasMetadataWriteback in interface Job
    
    Overrides:
    
    hasMetadataWriteback in class AbstractJob
    
    Returns:
  - setParentAccessions
```
public void setParentAccessions(Collection<String> parentAccessions)
```
    Description copied from interface: Job
    
    set parent accessiosns for the job
    
    Specified by:
    
    setParentAccessions in interface Job
    
    Overrides:
    
    setParentAccessions in class AbstractJob
  - isLocal
```
public boolean isLocal()
```
    Description copied from interface: Job
    
    Whether this job should run locally instead of out on a cluster.
    
    Specified by:
    
    isLocal in interface Job
    
    Overrides:
    
    isLocal in class AbstractJob
    
    Returns:
    true if it will run locally
  - setLocal
```
public void setLocal()
```
    Description copied from interface: Job
    
    Sets this job to run locally.
    
    Specified by:
    
    setLocal in interface Job
    
    Overrides:
    
    setLocal in class AbstractJob
  - setLocal
```
public void setLocal(boolean runLocal)
```
    Description copied from interface: Job
    
    Sets whether this job should run locally.
    
    Specified by:
    
    setLocal in interface Job
    
    Overrides:
    
    setLocal in class AbstractJob
    
    Parameters:
    runLocal - true to run locally, false otherwise
  - getJobList
```
public List<Job> getJobList()
```

Class JobBatch

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

Methods inherited from class java.lang.Object

Constructor Detail

JobBatch

Method Detail

createBashJob

setCommand

getCommand

setThreads

getThreads

setQueue

setHasMetadataWriteback

hasMetadataWriteback

setParentAccessions

isLocal

setLocal

setLocal

getJobList