All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class RampSeqContigToGenomeIntervalPlugin
extends AbstractPlugin
                    
```
NOTE: this method created to aid Dan Ilut. It is not official part of Assembly pipeline This method is old, obsolete and only works with sqlite3 dbs This method takes a sorted/indexed BAM File or a SAM file. It uses htsjdk to read the BAM file and find locations of the assembly contigs in the reference genome. These locations are then mapped to genome_intervals (anchors or inter-anchors) in the db.. Genome Interval identification is based on the mid-point of the reference range where the contig maps. Use htsjdk to get the start/end of alignment from SamRecord, find the midpoint of this alignment, search the ReferenceRanges from the db to find the range (ie genome interval) where this read falls. Output: A tab delimited file with the headings: ContigNam GenomeIntervalRange GenomeIntervalId IsAnchor The file name is the BAM/SAM file name minus the extension, plus "_intervalMapping.txt", written to the specified user directory. For example: outputDir = /workdir/lcj34/danOutput/ BAM file = /workdir/lcj34/bamFiles/w22B73Asm10.bam output File from this plugin: /workdir/lcj34/danOutput/w22B73Asm10_intervalMapping.txt

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static void`	`main(Array<String> args)`
`DataSet`	`processData(DataSet input)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`hostname()`	Hostname where database resides
`RampSeqContigToGenomeIntervalPlugin`	`hostname(String value)`	Set Hostname.
`String`	`userid()`	Userid for database
`RampSeqContigToGenomeIntervalPlugin`	`userid(String value)`	Set Userid.
`String`	`password()`	Password for database
`RampSeqContigToGenomeIntervalPlugin`	`password(String value)`	Set Password.
`String`	`databaseName()`	Database name
`RampSeqContigToGenomeIntervalPlugin`	`databaseName(String value)`	Set Database Name.
`String`	`contigBAM()`	Name of contig BAM file to process
`RampSeqContigToGenomeIntervalPlugin`	`contigBAM(String value)`	Set Contig File.
`String`	`outputDir()`	Output Directory
`RampSeqContigToGenomeIntervalPlugin`	`outputDir(String value)`	Set Output Directory.

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

RampSeqContigToGenomeIntervalPlugin
```
RampSeqContigToGenomeIntervalPlugin()
```

RampSeqContigToGenomeIntervalPlugin

RampSeqContigToGenomeIntervalPlugin(Frame parentFrame)

RampSeqContigToGenomeIntervalPlugin

RampSeqContigToGenomeIntervalPlugin(Frame parentFrame, boolean isInteractive)

Method Detail
- main
```
 static void main(Array<String> args)
```
- processData
```
 DataSet processData(DataSet input)
```
- getIcon
```
 ImageIcon getIcon()
```
- getButtonName
```
 String getButtonName()
```
- getToolTipText
```
 String getToolTipText()
```
- hostname
```
 String hostname()
```
  Hostname where database resides
- hostname
```
 RampSeqContigToGenomeIntervalPlugin hostname(String value)
```
  Set Hostname. Hostname where database resides
  
  Parameters:
  
  value - Hostname
- userid
```
 String userid()
```
  Userid for database
- userid
```
 RampSeqContigToGenomeIntervalPlugin userid(String value)
```
  Set Userid. Userid for database
  
  Parameters:
  
  value - Userid
- password
```
 String password()
```
  Password for database
- password
```
 RampSeqContigToGenomeIntervalPlugin password(String value)
```
  Set Password. Password for database
  
  Parameters:
  
  value - Password
- databaseName
```
 String databaseName()
```
  Database name
- databaseName
```
 RampSeqContigToGenomeIntervalPlugin databaseName(String value)
```
  Set Database Name. Database name
  
  Parameters:
  
  value - Database Name
- contigBAM
```
 String contigBAM()
```
  Name of contig BAM file to process
- contigBAM
```
 RampSeqContigToGenomeIntervalPlugin contigBAM(String value)
```
  Set Contig File. Name of contig fasta file to process
  
  Parameters:
  
  value - Contig File
- outputDir
```
 String outputDir()
```
  Output Directory
- outputDir
```
 RampSeqContigToGenomeIntervalPlugin outputDir(String value)
```
  Set Output Directory. Output Directory
  
  Parameters:
  
  value - Output Directory

Class RampSeqContigToGenomeIntervalPlugin

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

RampSeqContigToGenomeIntervalPlugin

RampSeqContigToGenomeIntervalPlugin

RampSeqContigToGenomeIntervalPlugin

Method Detail

main

processData

getIcon

getButtonName

getToolTipText

hostname

hostname

userid

userid

password

password

databaseName

databaseName

contigBAM

contigBAM

outputDir

outputDir