All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class SplitFastaByChromPlugin
extends AbstractPlugin
                    
```
Splits fasta by chromosome. IT assumes the id line has a chromosome of the form >1, >chr1 or >chromosome1 ALl of the above forms (case insensitive) will be written with an id line of just the number, e.g. >1 or >2 The "name" parameter is used as the basis of the name. To this name will be appended the "chr" and chrom number and .fa. For example: If the user gives "w22" as the name, the code will write files: w22chr1.fa, w22chr2.fa, etc. The isGca parameter: The assemblies starting with GCA have long text in the idLIne, with the chromosome stuck in the middle. This plugin will correctly parse these lines. OTher weird id lines are not supported and may need to be corrected manually before running through this plugin. Seems each set of assemblies that arrives has a different signature for the idline. So I keep customizing. Consider this code to the "base" plugin. On each run, if the idlines don't adhere to chr/chromosome/X or GCA, then user should run an altered version of this, or fix the idlines first.

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
`SplitFastaByChromPlugin()`
`SplitFastaByChromPlugin(Frame parentFrame)`
`SplitFastaByChromPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`String`	`parseChromosome(String chromString)`
`String`	`parseChromAsRomanNumerals(String chromString)`
`String`	`parseBauerFlint(String chromString)`
`String`	`parseChromFirstTab(String chromString)`
`String`	`parseGCA(String chromString)`
`static Integer`	`romanToDecimal(String romanNumber)`
`static int`	`processDecimal(int decimal, int lastNumber, int lastDecimal)`
`static void`	`main(Array<String> args)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`fasta()`	Fasta File to split by chromosome
`SplitFastaByChromPlugin`	`fasta(String value)`	Set Fasta File .
`String`	`name()`	Name to give each file, e.g w22.
`SplitFastaByChromPlugin`	`name(String value)`	Set Name .
`String`	`outputDir()`	Path to write the split files
`SplitFastaByChromPlugin`	`outputDir(String value)`	Set Output Directory.
`Boolean`	`isGca()`	GCA fastas have long text as idLines.
`SplitFastaByChromPlugin`	`isGca(Boolean value)`	Set Is GCA.

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
  - SplitFastaByChromPlugin
```
SplitFastaByChromPlugin()
```
  - SplitFastaByChromPlugin
```
SplitFastaByChromPlugin(Frame parentFrame)
```
  - SplitFastaByChromPlugin
```
SplitFastaByChromPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - parseChromosome
```
 String parseChromosome(String chromString)
```
  - parseChromAsRomanNumerals
```
 String parseChromAsRomanNumerals(String chromString)
```
  - parseBauerFlint
```
 String parseBauerFlint(String chromString)
```
  - parseChromFirstTab
```
 String parseChromFirstTab(String chromString)
```
  - parseGCA
```
 String parseGCA(String chromString)
```
  - romanToDecimal
```
 static Integer romanToDecimal(String romanNumber)
```
  - processDecimal
```
 static int processDecimal(int decimal, int lastNumber, int lastDecimal)
```
  - main
```
 static void main(Array<String> args)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - fasta
```
 String fasta()
```
    Fasta File to split by chromosome
  - fasta
```
 SplitFastaByChromPlugin fasta(String value)
```
    Set Fasta File . Fasta File to split by chromosome
    
    Parameters:
    
    value - Fasta File
  - name
```
 String name()
```
    Name to give each file, e.g w22. To this name will be appended 'chr' plus the chrom number plus .fa
  - name
```
 SplitFastaByChromPlugin name(String value)
```
    Set Name . Name to give each file, e.g w22. To this name will be appended 'chr' plus the chrom number plus .fa
    
    Parameters:
    
    value - Name
  - outputDir
```
 String outputDir()
```
    Path to write the split files
  - outputDir
```
 SplitFastaByChromPlugin outputDir(String value)
```
    Set Output Directory. Path to write the split files
    
    Parameters:
    
    value - Output Directory
  - isGca
```
 Boolean isGca()
```
    GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.
  - isGca
```
 SplitFastaByChromPlugin isGca(Boolean value)
```
    Set Is GCA. GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.
    
    Parameters:
    
    value - Is GCA

Class SplitFastaByChromPlugin

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

SplitFastaByChromPlugin

SplitFastaByChromPlugin

SplitFastaByChromPlugin

Method Detail

processData

parseChromosome

parseChromAsRomanNumerals

parseBauerFlint

parseChromFirstTab

parseGCA

romanToDecimal

processDecimal

main

getIcon

getButtonName

getToolTipText

fasta

fasta

name

name

outputDir

outputDir

isGca

isGca