from TASSELpy.utils.Overloading import javaOverload, javaConstructorOverload, javaStaticOverload
from TASSELpy.utils.helper import make_sig
from TASSELpy.java.lang.Object import Object
from TASSELpy.java.lang.String import String, metaString
from TASSELpy.utils.primativeArray import meta_double_array
from TASSELpy.utils.primativeArray import javaPrimativeArray
from TASSELpy.javaObj import javaArray
from TASSELpy.net.maizegenetics.trait.Trait import Trait
from TASSELpy.net.maizegenetics.trait.Phenotype import Phenotype
java_imports = {'Phenotype':'net/maizegenetics/trait/Phenotype',
'ReadPhenotypeUtils':'net/maizegenetics/trait/ReadPhenotypeUtils',
'String':'java/lang/String',
'Trait':'net/maizegenetics/trait/Trait'}
[docs]class ReadPhenotypeUtils(Object):
_java_name = java_imports['ReadPhenotypeUtils']
@javaConstructorOverload(java_imports['ReadPhenotypeUtils'])
[docs] def __init__(self, *args, **kwargs):
pass
@javaStaticOverload(java_imports['ReadPhenotypeUtils'], "makeCharacterTrait",
(make_sig([java_imports['String']+'[]','double[]',
java_imports['String'],java_imports['String']],
java_imports['Trait']),(javaArray.get_array_type(String),
meta_double_array, metaString,
metaString), lambda x: Trait(obj=x)))
[docs] def makeCharacterTrait(*args):
""" Makes a character trait
Signatures:
static Trait makeCharacterTrait(String[] original, double[] tonumber,
String name, String type)
Arguments:
original -- the original class or discrete data
tonumber -- a double array, the same length as the original data, which
will hold the class indices
name -- the trait name
type -- the trait type
Returns:
The new trait
"""
pass
@javaStaticOverload(java_imports["ReadPhenotypeUtils"], "doubleFromCharacterTrait",
(make_sig([java_imports['Trait'], java_imports['String']+'[]'],
'double[]'), (Trait, javaArray.get_array_type(String)),
lambda x: javaPrimativeArray.make_array_from_obj('double',x)))
[docs] def doubleFromCharacterTrait(*args):
""" Converts a character trait to doubles
Signatures:
static double[] doubleFromCharacterTrait(Trait trait, String[] textdata)
Arguments:
trait -- trait
textdata -- the current data
Returns:
The new trait
"""
pass
@javaStaticOverload(java_imports["ReadPhenotypeUtils"], "readPolymorphismAlignment",
(make_sig([java_imports['String']], java_imports['Phenotype']),
(metaString,), lambda x: Phenotype(obj=x)))
[docs] def readPolymorphismAlignment(*args):
""" Reads the polymorphism data from a TASSEL v2 polymorphism format file
Signatures:
static Phenotype readPolymorphismAlignment(String inputFile) throws IOException
Arguments:
inputFile -- The input file in TASSEL v2 polymorphism format
Returns:
a Phenotype
"""
pass
@javaStaticOverload(java_imports['ReadPhenotypeUtils'],'readNumericalAlignment',
(make_sig([java_imports['String']], java_imports['Phenotype']),
(metaString,), lambda x: Phenotype(obj=x)))
[docs] def readNumericalAlignment(*args):
""" Reads Phenotype from a file in TASSEL v2 numerical format
Signatures:
static Phenotype readNumericalAlignment(String inputFile) throws IOException
Arguments:
inputFile -- the input file in TASSEL v2 numerical format
Returns:
a Phenotype
"""
pass
@javaStaticOverload(java_imports['ReadPhenotypeUtils'],'readGenericFile',
(make_sig([java_imports['String']], java_imports['Phenotype']),
(metaString,), lambda x: Phenotype(obj=x)))
[docs] def readGenericFile(*args):
""" Reads input file with TASSEL v3 annotations or with no input directive
Signatures:
static Phenotype readGenericFile(String inputFile) throws IOException
Arguments:
inputFile -- the input file with TASSEL v3 annotations or with no input directives
Returns:
a Phenotype
"""
pass