Source code for TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D
from TASSELpy.utils.helper import make_sig
from TASSELpy.utils.Overloading import javaConstructorOverload, javaOverload
from TASSELpy.net.maizegenetics.dna.snp.score.SiteScore import SiteScore
from TASSELpy.java.lang.Object import Object
from TASSELpy.java.lang.Integer import metaInteger
from TASSELpy.utils.primativeArray import javaPrimativeArray
from TASSELpy.java.lang.Enum import Enum
import numpy as np
java_imports = {'Byte2D':'net/maizegenetics/dna/snp/byte2d/Byte2D',
'SiteScore':'net/maizegenetics/dna/snp/score/SiteScore'
}
[docs]class Byte2D(Object):
_java_name = java_imports['Byte2D']
@javaConstructorOverload(java_imports['Byte2D'])
[docs] def __init__(self, *args, **kwargs):
pass
@javaOverload("valueForAllele",
(make_sig(['int','int'],'byte'),(metaInteger,metaInteger),np.int8))
[docs] def valueForAllele(self, *args):
""" Gets the byte value for a particular allele in the matrix
Signatures:
byte valueForAllele(int taxon, int site)
Arguments:
taxon -- taxon
site -- site
Returns:
The byte value for the allele
"""
pass
@javaOverload("valuesForAllSites",
(make_sig(['int'],'byte[]'),(metaInteger,),
lambda x: javaPrimativeArray.make_array_from_obj('byte', x)))
[docs] def valuesForAllSites(self, *args):
""" Gets the byte values for all sites on a taxon
Signatures:
byte[] valuesForAllSites(int taxon)
Arguments:
taxon -- taxon
Returns:
The array of bytes for a taxon, where each entry is a genotype
"""
pass
@javaOverload("numTaxa",
(make_sig([],'int'),(),None))
[docs] def numTaxa(self, *args):
""" The number of taxa in the matrix
Signatures:
int numTaxa()
Returns:
The number of taxa in the matrix
"""
pass
@javaOverload("numSites",
(make_sig([],'int'),(),None))
[docs] def numSites(self, *args):
""" The number of sites in the matrix
Signatures:
int numSites()
Returns:
The number of sites in the matrix
"""
pass
@javaOverload("siteScoreType",
(make_sig([],java_imports['SiteScore']+'$SITE_SCORE_TYPE'),
(), lambda x: Enum(obj=x)))
[docs] def siteScoreType(self, *args):
""" The site score type for sites
Signatures:
SiteScore.SITE_SCORE_TYPE siteScoreType()
Returns:
The SITE_SCORE_TYPE
"""
pass