All Implemented Interfaces:
```
public class RMethods

                    
```
The purpose of this class is hold static methods that generate results that can be used by R

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`public class`	`RMethods.DataFrameVectors`	A data class holding columnNames, rowNames, and a dataVectors List as public fields in a format that can be easily used by rJava to create R objects
`public class`	`RMethods.MatrixWithNames`	A data class holding columnNames, rowNames, and a matrix List as public fields in a format that can be easily used by rJava to create R objects. It is expected that the matrix will be a 2-D primitive Java array of some type that is converted correctly by rJava.

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static RMethods.MatrixWithNames`	`hapidTableAsMatrix(HaplotypeGraph graph)`
`static RMethods.DataFrameVectors`	`hapidTableAsDF(HaplotypeGraph graph)`
`static RMethods.DataFrameVectors`	`referenceRanges(HaplotypeGraph graph)`
`static RMethods.MatrixWithNames`	`pathHapids(String configFile, Array<String> pathFileNames)`
`static RMethods.MatrixWithNames`	`pathsForMethod(String configFile, String pathMethod)`
`static RMethods.DataFrameVectors`	`readMappingsForLineName(String configFile, String lineName, String readMappingMethodName, String haplotypeMethodName)`
`static RMethods.DataFrameVectors`	`readMappingsForLineName(String configFile, String lineName, String readMappingMethodName, String haplotypeMethodName, String fileGroup)`
`static RMethods.DataFrameVectors`	`readMappingTableInfo(String configFile)`
`static Set<Integer>`	`hapidSetFromReadMappings(Map<List<Integer>, Integer> readMappings)`
`static Set<Integer>`	`rangeSetFromHapidSet(Set<Integer> hapids, Map<Integer, Integer> hapidRangeMap)`
`static void`	`exportPHGToFlapjack(HaplotypeGraph graph, String filename)`
`static RMethods.MatrixWithNames`	`testMatrix()`	A test function to verify that MatrixWithNames works correctly for R
`static RMethods.DataFrameVectors`	`testDataFrame()`	A test function to verify that DataFrameVectors works correctly for R

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

- Constructor Detail
- Method Detail
  - hapidTableAsMatrix
```
 static RMethods.MatrixWithNames hapidTableAsMatrix(HaplotypeGraph graph)
```
    Parameters:
    
    graph - a HaplotypeGraph
  - hapidTableAsDF
```
 static RMethods.DataFrameVectors hapidTableAsDF(HaplotypeGraph graph)
```
    Parameters:
    
    graph - a HaplotypeGraph
  - referenceRanges
```
 static RMethods.DataFrameVectors referenceRanges(HaplotypeGraph graph)
```
    Parameters:
    
    graph - a HaplotypeGraph
  - pathHapids
```
 static RMethods.MatrixWithNames pathHapids(String configFile, Array<String> pathFileNames)
```
    Parameters:
    
    configFile - a config file of PHG database connection parameters
    
    pathFileNames - a String array of path file names
  - pathsForMethod
```
 static RMethods.MatrixWithNames pathsForMethod(String configFile, String pathMethod)
```
    Parameters:
    
    configFile - the database configuration file
    
    pathMethod - the name of the path method in the PHG DB
  - readMappingsForLineName
```
 static RMethods.DataFrameVectors readMappingsForLineName(String configFile, String lineName, String readMappingMethodName, String haplotypeMethodName)
```
    Parameters:
    
    configFile - a database configuration file
    
    lineName - the name of the line (taxon) for which the read mapping information is to be retrieved.
    
    readMappingMethodName - the method name for the read mappings (only takes a single method)
    
    haplotypeMethodName - optional: one or more colon-delimited haplotype method names
  - readMappingsForLineName
```
 static RMethods.DataFrameVectors readMappingsForLineName(String configFile, String lineName, String readMappingMethodName, String haplotypeMethodName, String fileGroup)
```
    Parameters:
    
    configFile - the database configuration file
    
    lineName - the name of the line (taxon) for which the read mapping information is to be retrieved.
    
    readMappingMethodName - the name of the read mapping method from the database
    
    haplotypeMethodName - the name of the haplotype method used to write the pangenome fasta used to map reads
    
    fileGroup - the name of the file group for the line from the database.
  - readMappingTableInfo
```
 static RMethods.DataFrameVectors readMappingTableInfo(String configFile)
```
    Parameters:
    
    configFile - a config file containing the DB name and connection information
  - hapidSetFromReadMappings
```
 static Set<Integer> hapidSetFromReadMappings(Map<List<Integer>, Integer> readMappings)
```
  - rangeSetFromHapidSet
```
 static Set<Integer> rangeSetFromHapidSet(Set<Integer> hapids, Map<Integer, Integer> hapidRangeMap)
```
  - exportPHGToFlapjack
```
 static void exportPHGToFlapjack(HaplotypeGraph graph, String filename)
```
  - testMatrix
```
 static RMethods.MatrixWithNames testMatrix()
```
    A test function to verify that MatrixWithNames works correctly for R
  - testDataFrame
```
 static RMethods.DataFrameVectors testDataFrame()
```
    A test function to verify that DataFrameVectors works correctly for R

Class RMethods

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Method Detail

hapidTableAsMatrix

hapidTableAsDF

referenceRanges

pathHapids

pathsForMethod

readMappingsForLineName

readMappingsForLineName

readMappingTableInfo

hapidSetFromReadMappings

rangeSetFromHapidSet

exportPHGToFlapjack

testMatrix

testDataFrame