All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class CreateContigFastaFromAssemblyGenomePlugin
extends AbstractPlugin
                    
```
The sequence for each chromosome in the genome fasta file will be split based on N's. Read until an N is encountered, write the sequence as its own contig in the contig fastq output file. Skip past the "N's", start the next contig. This algorithm is subject to change during pipeline testing. Each sequence idline will be >assemblyChrom:assemblyStart:assemblyEnd INPUT: 1. The assembly genome file to process OUTPUT: 1. The newly created fasta file of contigs.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final static String`	`DEFAULT_CITATION`
`public final static String`	`POSITION_LIST_NONE`
`public final static String`	`TAXA_LIST_NONE`

Constructor Summary

Constructors
Constructor	Description
`CreateContigFastaFromAssemblyGenomePlugin()`
`CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)`
`CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`genomeFile()`	Input assembly genome file from which to pull sequence
`CreateContigFastaFromAssemblyGenomePlugin`	`genomeFile(String value)`	Set Assembly Genome.
`String`	`assembly()`	Output fastq file to use as input for BWA-MEM
`CreateContigFastaFromAssemblyGenomePlugin`	`assembly(String value)`	Set Output File.
`String`	`outputDir()`	Output fastq file to use as input for BWA-MEM
`CreateContigFastaFromAssemblyGenomePlugin`	`outputDir(String value)`	Set Output File.
`ImageIcon`	`getIcon()`

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CreateContigFastaFromAssemblyGenomePlugin
```
CreateContigFastaFromAssemblyGenomePlugin()
```
  - CreateContigFastaFromAssemblyGenomePlugin
```
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)
```
  - CreateContigFastaFromAssemblyGenomePlugin
```
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - genomeFile
```
 String genomeFile()
```
    Input assembly genome file from which to pull sequence
  - genomeFile
```
 CreateContigFastaFromAssemblyGenomePlugin genomeFile(String value)
```
    Set Assembly Genome. Input assembly genome file from which to pull sequence
    
    Parameters:
    
    value - Assembly Genome
  - assembly
```
 String assembly()
```
    Output fastq file to use as input for BWA-MEM
  - assembly
```
 CreateContigFastaFromAssemblyGenomePlugin assembly(String value)
```
    Set Output File. Output fastq file to use as input for BWA-MEM
    
    Parameters:
    
    value - Output File
  - outputDir
```
 String outputDir()
```
    Output fastq file to use as input for BWA-MEM
  - outputDir
```
 CreateContigFastaFromAssemblyGenomePlugin outputDir(String value)
```
    Set Output File. Output fastq file to use as input for BWA-MEM
    
    Parameters:
    
    value - Output File
  - getIcon
```
 ImageIcon getIcon()
```

Class CreateContigFastaFromAssemblyGenomePlugin

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class net.maizegenetics.plugindef.Plugin

Methods inherited from class java.lang.Object

Constructor Detail

CreateContigFastaFromAssemblyGenomePlugin

CreateContigFastaFromAssemblyGenomePlugin

CreateContigFastaFromAssemblyGenomePlugin

Method Detail

processData

getButtonName

getToolTipText

genomeFile

genomeFile

assembly

assembly

outputDir

outputDir

getIcon