Source code for TASSELpy.net.maizegenetics.taxa.TaxaListBuilder

from TASSELpy.net.maizegenetics.taxa.Taxon import Taxon
from TASSELpy.net.maizegenetics.taxa.TaxaList import TaxaList
from TASSELpy.net.maizegenetics.dna.snp.GenotypeTable import GenotypeTable
from TASSELpy.java.util.Collection import Collection
from TASSELpy.javaObj import javaObj
from TASSELpy.javaObj import javaArray
from TASSELpy.utils.helper import make_sig
from TASSELpy.utils.Overloading import javaOverload,javaConstructorOverload
import numpy as np
from TASSELpy.java.lang.String import String

java_imports = {'Collection':'java/util/Collection',
                'GenotypeTable':'net/maizegenetics/dna/snp/GenotypeTable',
                'String':'java/lang/String',
                'TaxaListBuilder':'net/maizegenetics/taxa/TaxaListBuilder',
                'TaxaList':'net/maizegenetics/taxa/TaxaList',
                'Taxon':'net/maizegenetics/taxa/Taxon'}

## A builder for creating immutable TaxaList instances
class TaxaListBuilder(javaObj):
    """
    A builder for creating immutable TaxaList instances

    Example:

    tlb = TaxaListBuilder()
    for i in xrange(10):
        at = Taxon.Builder("Z"+i+":Line:mays:Zea").inbreedF(0.99)\
             .parents("B73","B97")\
             .pedigree("(B73xB97)S6I1")\
             .build()
        tlb.add(at)
    tl = tlb.build()
    """
    _java_name = java_imports['TaxaListBuilder']
    @javaConstructorOverload(java_imports['TaxaListBuilder'],
                (make_sig([],'void'),()))
    def __init__(self, *args, **kwargs):
        pass
    ## Adds a taxon to the builder
    # @param taxon taxon
    # @return TaxaListBuilder with taxon added
    @javaOverload("add",
                  (make_sig([java_imports['Taxon']],java_imports['TaxaListBuilder']),
                   (Taxon,),lambda x: TaxaListBuilder(obj=x)))
    def add(self, *args):
        """
        Adds a taxon to the builder
        
        Signatures:

        TaxaListBuilder add(Taxon taxon)

        Arguments:

        taxon -- taxon

        Returns:

        TaxaListBuilder with taxon added
        """
        pass
    ## Adds multiple taxa to the builder
    # @param taxa A collection of taxa (either collection of Taxons or Strings)
    # @param a GenotypeTable from which to add taxa
    # @return TaxaListBuilder with taxa added
    @javaOverload("addAll",
            (make_sig([java_imports['Collection']],java_imports['TaxaListBuilder']),
                (Collection,),lambda x: TaxaListBuilder(obj=x)),
            (make_sig([java_imports['GenotypeTable']],java_imports['TaxaListBuilder']),
                (GenotypeTable,),lambda x: TaxaListBuilder(obj=x)),
            (make_sig([java_imports['String']+'[]'],java_imports['TaxaListBuilder']),
                (javaArray.get_array_type(String),),lambda x: TaxaListBuilder(obj=x)),
            (make_sig([java_imports['Taxon']+'[]'],java_imports['TaxaListBuilder']),
                (javaArray.get_array_type(Taxon),), lambda x: TaxaListBuilder(obj=x)))
    def addAll(self, *args):
        """
        Adds multiple taxa to the builder

        Signatures:

        TaxaListBuilder addAll(Collection<Taxon> taxa)
        TaxaListBuilder addAll(GenotypeTable a)
        
        Arguments:

        TaxaListBuilder addAll(Collection<Taxon> taxa)
           taxa -- taxa
        TaxaListBuilder addAll(GenotypeTable a)
           a -- GenotypeTable from which to add taxa
        TaxaListBuilder addAll(String[] taxa)
           taxa -- taxa
        TaxaListBuilder addAll(Taxon[] taxa)
           taxa -- taxa
        
        Returns:

        TaxaListBuilder with taxa added
        """
        pass
    ## Builds the TaxaList
    # @return A TaxaList
    @javaOverload("build",
        (make_sig([],java_imports['TaxaList']),(),lambda x: TaxaList(obj=x)))
    def build(self, *args):
        """
        Builds the TaxaList

        Signatures:

        TaxaList build()

        Returns:

        A TaxaList
        """
        pass