net.maizegenetics.analysis.data

Class MergeGenotypeTablesPlugin

AbstractPlugin

net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class MergeGenotypeTablesPlugin
extends AbstractPlugin

Merge alignments into a single alignment containing all taxa and positions. TODO: Add capacity for depth

Constructor Detail

MergeGenotypeTablesPlugin

public MergeGenotypeTablesPlugin(java.awt.Frame parentFrame,
                                 boolean isInteractive)

Method Detail

performFunction

public DataSet performFunction(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

mergeGenotypeTables

public static GenotypeTable mergeGenotypeTables(GenotypeTable[] alignments)

Merge an array of GenotypeTables into a single GenotypeTable

generateMasterTaxaList

public static TaxaList generateMasterTaxaList(GenotypeTable[] alignments)

Generate a list of unique taxa given an array of alignments

generateMasterPositionList

public static PositionList generateMasterPositionList(GenotypeTable[] alignments)

Generate a list of unique positions given an array of alignments

makeTaxaHashes

public static java.util.HashMap[] makeTaxaHashes(GenotypeTable[] alignments)

Takes an array of GenotypeTables and returns a matching array of HashMaps linking each Taxon to its index

makePositionHashes

public static java.util.HashMap[] makePositionHashes(GenotypeTable[] alignments)

Takes an array of GenotypeTables and returns a matching array of HashMaps linking each Position to its index

mergeCalls

public static byte mergeCalls(java.lang.Byte[] calls)

Take an array of Byte genotype calls and merge TODO: Make this smarter; currently just uses the last call (to be same as in TASSEL4)