All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class AssemblyHaplotypesPlugin
extends AbstractPlugin
                    
```
This Class is DEPRECATED!! Should not be used anymore. It will not create or store the genome_file_data table entries. Process Assemblies - both anchor and interanchor. This class exercises the following tools: mummer4 scripts: (nucmer, delta-filter, show-coords, show-snps) Algorithm when processing all steps: 1. run mummer4:nucmer with the parameters -c 250 --mum 2. run mummer4:show-coords with parameters -T -r (tab-delimited, sorted by ref) 3. run mummer4:show-snps with parameters -T -r (tab-delimited, sorted by ref ID and SNP positions) 4. Interanchors. a. Processed the same as the anchors. The VariantContext code grabs sequence aligning to both. We expect a certain linearity to the alignments. There will be large indels between sequences that are picked up as inter-genic regions. 5. The DB is loaded in batches of 3000 reference_ranges at a time. Assumptions/requirements: 1. alignments are on a per-chromosome basis: I expect fastas to be broken down by chromosome, 1 chrom per fasta 2. Id lines in fasta must start with >X, or >chrX or >chromosomeX where X is the chromosome number. Additional data is allowed after a space, but the first data must identify the chromosome as above. 3. The assembly and reference chromosomes need to be named in a similar fashion to allow for db matching of genome_interval_ids IE, if the ref chrom name has a number without leading 0's, so must the assembly. IE, chr1 for ref, then chr1 for assembly. 4. For populating the DB per Ed: ploidy=1, genes/chroms phased=TRUE (put the confidence at 1) NOTE: Entry points There are now 3 places where the user may enter this code. The default is to run all steps. - "all": entryPoint parameter is "all", all steps are run - "refilter": entryPoint parameter is "refilter" Processing begins with the call to MummerScriptProcessing.refilterCoords() It is assumed the alignment directory contains mummer output for nucmer, delta-filter and show-coords on both the original and filtered delta files. - "haplotypes": entryPoint parameter is "haplotypes" Processing begins after all mummer4 scripts have finished, and the coordinates and snps files have been filtered. Only the VariantContext/sequence creation and db loading steps are performed. It is assumed the algin directory contains the necessary mummer files for processing.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`public enum`	`AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT`

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`static Map<Integer, AnchorDataPHG>`	`createAndLoadAssemblyData(Map<Integer, ReferenceRange> idByRangeMap, List<VariantContext> fullVC, GenomeSequence refSequence, Connection dbConn, String assemblyName, String chrom, int clusterSize, String method, Map<String, String> pluginParams)`	Create the assembly genotype/haplotype data and load to the PHG database
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`static void`	`main(Array<String> args)`
`String`	`ref()`	Input reference fasta file for single chromosome
`AssemblyHaplotypesPlugin`	`ref(String value)`	Set Reference Fasta File.
`String`	`assembly()`	Assembly fasta file for a single chromosome to align against the reference
`AssemblyHaplotypesPlugin`	`assembly(String value)`	Set Assembly Fasta File.
`String`	`outputDir()`	Output directory including trailing / for writing files
`AssemblyHaplotypesPlugin`	`outputDir(String value)`	Set Output Directory.
`String`	`dbConfigFile()`	File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
`AssemblyHaplotypesPlugin`	`dbConfigFile(String value)`	Set DB Config File.
`String`	`assemblyName()`	Name of Assembly Taxon, to be stored as taxon name in the DB
`AssemblyHaplotypesPlugin`	`assemblyName(String value)`	Set Assembly Name.
`String`	`chrom()`	Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
`AssemblyHaplotypesPlugin`	`chrom(String value)`	Set Chromosome Name.
`String`	`mummer4Path()`	Path to mummer4 binaries
`AssemblyHaplotypesPlugin`	`mummer4Path(String value)`	Set Mummer4 binary path
`Integer`	`clusterSize()`	Cluster size to use with mummer4 nucmer script.
`AssemblyHaplotypesPlugin`	`clusterSize(Integer value)`	Set Mummer4 Nucmer Cluster Size .
`String`	`gVCFOutputDir()`	Directory for gvcf files to be output for later use
`AssemblyHaplotypesPlugin`	`gVCFOutputDir(String value)`	Set GVCF Output Dir.
`AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT`	`entryPoint()`	Where to begin processing.
`AssemblyHaplotypesPlugin`	`entryPoint(AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT value)`	Set Assembly Entry Point.
`Integer`	`minInversionLen()`	Minimum length of inversion for it to be kept as part of the alignment.
`AssemblyHaplotypesPlugin`	`minInversionLen(Integer value)`	Set Minimum Inversion Length.
`String`	`assemblyMethod()`	Method name to load to db for assembly processing, default is mummer4
`AssemblyHaplotypesPlugin`	`assemblyMethod(String value)`	Set Assembly Method.

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
  - AssemblyHaplotypesPlugin
```
AssemblyHaplotypesPlugin()
```
  - AssemblyHaplotypesPlugin
```
AssemblyHaplotypesPlugin(Frame parentFrame)
```
  - AssemblyHaplotypesPlugin
```
AssemblyHaplotypesPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - createAndLoadAssemblyData
```
 static Map<Integer, AnchorDataPHG> createAndLoadAssemblyData(Map<Integer, ReferenceRange> idByRangeMap, List<VariantContext> fullVC, GenomeSequence refSequence, Connection dbConn, String assemblyName, String chrom, int clusterSize, String method, Map<String, String> pluginParams)
```
    Create the assembly genotype/haplotype data and load to the PHG database
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - main
```
 static void main(Array<String> args)
```
  - ref
```
 String ref()
```
    Input reference fasta file for single chromosome
  - ref
```
 AssemblyHaplotypesPlugin ref(String value)
```
    Set Reference Fasta File. Input reference fasta file for single chromosome
    
    Parameters:
    
    value - Reference Fasta File
  - assembly
```
 String assembly()
```
    Assembly fasta file for a single chromosome to align against the reference
  - assembly
```
 AssemblyHaplotypesPlugin assembly(String value)
```
    Set Assembly Fasta File. Assembly fasta file for a single chromosome to align against the reference
    
    Parameters:
    
    value - Assembly Fasta File
  - outputDir
```
 String outputDir()
```
    Output directory including trailing / for writing files
  - outputDir
```
 AssemblyHaplotypesPlugin outputDir(String value)
```
    Set Output Directory. Output directory including trailing / for writing files
    
    Parameters:
    
    value - Output Directory
  - dbConfigFile
```
 String dbConfigFile()
```
    File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
  - dbConfigFile
```
 AssemblyHaplotypesPlugin dbConfigFile(String value)
```
    Set DB Config File. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
    
    Parameters:
    
    value - DB Config File
  - assemblyName
```
 String assemblyName()
```
    Name of Assembly Taxon, to be stored as taxon name in the DB
  - assemblyName
```
 AssemblyHaplotypesPlugin assemblyName(String value)
```
    Set Assembly Name. Name of Assembly Taxon, to be stored as taxon name in the DB
    
    Parameters:
    
    value - Assembly Name
  - chrom
```
 String chrom()
```
    Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
  - chrom
```
 AssemblyHaplotypesPlugin chrom(String value)
```
    Set Chromosome Name. Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
    
    Parameters:
    
    value - Chromosome Name
  - mummer4Path
```
 String mummer4Path()
```
    Path to mummer4 binaries
  - mummer4Path
```
 AssemblyHaplotypesPlugin mummer4Path(String value)
```
    Set Mummer4 binary path
    
    Parameters:
    
    value - Mummer4 binary path
  - clusterSize
```
 Integer clusterSize()
```
    Cluster size to use with mummer4 nucmer script.
  - clusterSize
```
 AssemblyHaplotypesPlugin clusterSize(Integer value)
```
    Set Mummer4 Nucmer Cluster Size . Cluster size to use with mummer4 nucmer script.
    
    Parameters:
    
    value - Mummer4 Nucmer Cluster Size
  - gVCFOutputDir
```
 String gVCFOutputDir()
```
    Directory for gvcf files to be output for later use
  - gVCFOutputDir
```
 AssemblyHaplotypesPlugin gVCFOutputDir(String value)
```
    Set GVCF Output Dir. Directory for gvcf files to be output for later use
    
    Parameters:
    
    value - GVCF Output Dir
  - entryPoint
```
 AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT entryPoint()
```
    Where to begin processing. All runs everything. Refilter means run from the re-filtering of the coords files. hapltypes runs just the haplotypes processing.
  - entryPoint
```
 AssemblyHaplotypesPlugin entryPoint(AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT value)
```
    Set Assembly Entry Point. Where to begin processing. All runs everything. Refilter means run from the re-filtering of the coords files. hapltypes runs just the haplotypes processing.
    
    Parameters:
    
    value - Assembly Entry Point
  - minInversionLen
```
 Integer minInversionLen()
```
    Minimum length of inversion for it to be kept as part of the alignment. Default is 7500.
  - minInversionLen
```
 AssemblyHaplotypesPlugin minInversionLen(Integer value)
```
    Set Minimum Inversion Length. Minimum length of inversion for it to be kept as part of the alignment. Default is 7500
    
    Parameters:
    
    value - Minimum Inversion Length
  - assemblyMethod
```
 String assemblyMethod()
```
    Method name to load to db for assembly processing, default is mummer4
  - assemblyMethod
```
 AssemblyHaplotypesPlugin assemblyMethod(String value)
```
    Set Assembly Method. Method name to load to db for assembly processing, default is mummer4
    
    Parameters:
    
    value - Assembly Method

Class AssemblyHaplotypesPlugin

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

AssemblyHaplotypesPlugin

AssemblyHaplotypesPlugin

AssemblyHaplotypesPlugin

Method Detail

processData

createAndLoadAssemblyData

getIcon

getButtonName

getToolTipText

main

ref

ref

assembly

assembly

outputDir

outputDir

dbConfigFile

dbConfigFile

assemblyName

assemblyName

chrom

chrom

mummer4Path

mummer4Path

clusterSize

clusterSize

gVCFOutputDir

gVCFOutputDir

entryPoint

entryPoint

minInversionLen

minInversionLen

assemblyMethod

assemblyMethod