gov.usda.gdpc.pal
Class PALUtil

java.lang.Object
  gov.usda.gdpc.pal.PALUtil

public class PALUtil

extends java.lang.Object

Author:

terryc

Method Summary

static pal.alignment.SimpleAnnotatedAlignment	createAnnotationAlignment(GenotypeTable table) Converts the given GDPC GenotypeTable to a PAL SimpleAnnotatedAlignment.
static pal.alignment.SimpleAnnotatedAlignment	createAnnotationAlignment(GenotypeTable table, int tableIndex)
static pal.alignment.SimpleCharacterAlignment	createCharacterAlignment(PhenotypeTable phenoTable)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createAnnotationAlignment

public static pal.alignment.SimpleAnnotatedAlignment createAnnotationAlignment(GenotypeTable table)

Converts the given GDPC GenotypeTable to a PAL SimpleAnnotatedAlignment. This defaults to using the first column (index 0) in the genotype table.

Parameters:

table - the genotype table

Returns:

the simple annotated alignment

createAnnotationAlignment

public static pal.alignment.SimpleAnnotatedAlignment createAnnotationAlignment(GenotypeTable table,
                                                                               int tableIndex)

createCharacterAlignment

public static pal.alignment.SimpleCharacterAlignment createCharacterAlignment(PhenotypeTable phenoTable)