# Path: simdna/synthetic/core.py
# class DefaultNameMixin(object):
#     """Basic functionality for classes that have a self.name attribute.
#     
#     The self.name attribute is typically used to leave a trace in
#     an instance of :class:`.AdditionalInfo`
#     
#     Arguments:
#         name: string
#     """
# 
#     def __init__(self, name):
#         if (name == None):
#             name = self.getDefaultName()
#         self.name = name
# 
#     def get_default_name(self):
#         self.getDefaultName()
# 
#     def getDefaultName(self):
#         return type(self).__name__
# 
# Path: simdna/simdnautil/util.py
# DEFAULT_LETTER_TO_INDEX = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
# DEFAULT_BACKGROUND_FREQ = OrderedDict(
#     [('A', 0.3), ('C', 0.2), ('G', 0.2), ('T', 0.3)])
# DEFAULT_DINUC_FREQ = OrderedDict([
#  ('AA',0.095),
#  ('AC',0.050),
#  ('AG',0.071),
#  ('AT',0.075),
#  ('CA',0.073),
#  ('CC',0.054),
#  ('CG',0.010),
#  ('CT',0.072),
#  ('GA',0.060),
#  ('GC',0.044),
#  ('GG',0.054),
#  ('GT',0.050),
#  ('TA',0.064),
#  ('TC',0.060),
#  ('TG',0.073),
#  ('TT',0.095),
# ])
# DEFAULT_BASE_DISCRETE_DISTRIBUTION = DiscreteDistribution(
#     DEFAULT_BACKGROUND_FREQ)
# class DiscreteDistribution(object):
# class VariableWrapper():
#     class Enum(object):
# class FileNameParts(object):
# class ArgumentToAdd(object):
# class FloatArgument(ArgumentToAdd):
# class BooleanArgument(ArgumentToAdd):
# class CoreFileNameArgument(ArgumentToAdd):
# class ArrArgument(ArgumentToAdd):
# class ArrOfFileNamesArgument(ArrArgument):
#     def __init__(self, valToFreq):
#     def sample(self):
# def get_file_handle(filename, mode="r"):
# def default_tab_seppd(s):
# def trim_newline(s):
# def perform_action_on_each_line_of_file(
#     file_handle, action, transformation=default_tab_seppd, ignore_input_title=False):
# def process_line(line, i, ignore_input_title,
#                  transformation, action):
#     def __init__(self, var):
# def enum(**enums):
# def combine_enums(*enums):
# def sampleFromProbsArr(arrWithProbs):
# def reverseComplement(sequence):
# def sampleWithoutReplacement(arr, numToSample):
# def swapIndices(arr, idx1, idx2):
# def get_file_name_parts(file_name):
#     def __init__(self, directory, core_file_name, extension):
#     def get_full_path(self):
#     def get_core_file_name_and_extension(self):
#     def get_transformed_core_file_name(self, transformation, extension=None):
#     def get_transformed_file_path(self, transformation, extension=None):
# def format_as_json(jsonable_data):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def transform(self):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+", toStringFunc=str):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+"):
# def addArguments(string, args, joiner="_"):
# 
# Path: simdna/simdnautil/pwm.py
# class PWM(object):
#     def __init__(self, name, letterToIndex=DEFAULT_LETTER_TO_INDEX,
#                        probMatrix=None, pseudocountProb=None):
#     def add_row(self, weights):
#     def addRow(self, weights):
#     def add_rows(self, matrix):
#     def addRows(self, matrix):
#     def finalize(self, pseudocountProb=0.001):
#     def finalise(self, pseudocountProb=0.001):
#     def get_best_hit(self):
#     def getBestHit(self):
#     def compute_best_hit_given_matrix(self, matrix):
#     def computeBestHitGivenMatrix(self, matrix):
#     def get_rows(self):
#     def getRows(self):
#     def sample_from_pwm(self, bg=None):
#     def sampleFromPwm(self, bg=None):
#     def sample_from_pwm_and_score(self, bg):
#     def sampleFromPwmAndScore(self, bg):
#     def __str__(self):


from simdna.synthetic.core import DefaultNameMixin
from simdna.simdnautil import util, pwm
from collections import OrderedDict
import numpy as np
class LoadedJasparRawPFMMotifs(AbstractLoadedMotifsFromFile):
    """A class for reading in a motifs file in the Jaspar Raw motifs format.

    This class is specifically for reading files in the Jaspar motif
    format.

    Basically, the motif declarations start with a >, the first
    characters after > until the first space are taken as the motif name,
    the lines after the line with a > have the format:
        P(A) "<nuc 1> <nuc 2> ... <nuc n>"
        P(C) "<nuc 1> <nuc 2> ... <nuc n>"
        P(T) "<nuc 1> <nuc 2> ... <nuc n>"
        P(G) "<nuc 1> <nuc 2> ... <nuc n>"

    Likely if you need to load your own motifs you will use this import
    script.
    """

    def getReadPwmAction(self, loadedMotifs):
        """See superclass.
        """
        currentPwm = util.VariableWrapper(None)
        _pwm = []
        def action(inp, lineNumber):
            if (inp.startswith(">")):
                inp = inp.lstrip(">")
                inpArr = inp.split()
                motifName = inpArr[1]
                while len(_pwm) > 0:
                    _pwm.pop()

# Path: simdna/synthetic/core.py
# class DefaultNameMixin(object):
#     """Basic functionality for classes that have a self.name attribute.
#     
#     The self.name attribute is typically used to leave a trace in
#     an instance of :class:`.AdditionalInfo`
#     
#     Arguments:
#         name: string
#     """
# 
#     def __init__(self, name):
#         if (name == None):
#             name = self.getDefaultName()
#         self.name = name
# 
#     def get_default_name(self):
#         self.getDefaultName()
# 
#     def getDefaultName(self):
#         return type(self).__name__
# 
# Path: simdna/simdnautil/util.py
# DEFAULT_LETTER_TO_INDEX = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
# DEFAULT_BACKGROUND_FREQ = OrderedDict(
#     [('A', 0.3), ('C', 0.2), ('G', 0.2), ('T', 0.3)])
# DEFAULT_DINUC_FREQ = OrderedDict([
#  ('AA',0.095),
#  ('AC',0.050),
#  ('AG',0.071),
#  ('AT',0.075),
#  ('CA',0.073),
#  ('CC',0.054),
#  ('CG',0.010),
#  ('CT',0.072),
#  ('GA',0.060),
#  ('GC',0.044),
#  ('GG',0.054),
#  ('GT',0.050),
#  ('TA',0.064),
#  ('TC',0.060),
#  ('TG',0.073),
#  ('TT',0.095),
# ])
# DEFAULT_BASE_DISCRETE_DISTRIBUTION = DiscreteDistribution(
#     DEFAULT_BACKGROUND_FREQ)
# class DiscreteDistribution(object):
# class VariableWrapper():
#     class Enum(object):
# class FileNameParts(object):
# class ArgumentToAdd(object):
# class FloatArgument(ArgumentToAdd):
# class BooleanArgument(ArgumentToAdd):
# class CoreFileNameArgument(ArgumentToAdd):
# class ArrArgument(ArgumentToAdd):
# class ArrOfFileNamesArgument(ArrArgument):
#     def __init__(self, valToFreq):
#     def sample(self):
# def get_file_handle(filename, mode="r"):
# def default_tab_seppd(s):
# def trim_newline(s):
# def perform_action_on_each_line_of_file(
#     file_handle, action, transformation=default_tab_seppd, ignore_input_title=False):
# def process_line(line, i, ignore_input_title,
#                  transformation, action):
#     def __init__(self, var):
# def enum(**enums):
# def combine_enums(*enums):
# def sampleFromProbsArr(arrWithProbs):
# def reverseComplement(sequence):
# def sampleWithoutReplacement(arr, numToSample):
# def swapIndices(arr, idx1, idx2):
# def get_file_name_parts(file_name):
#     def __init__(self, directory, core_file_name, extension):
#     def get_full_path(self):
#     def get_core_file_name_and_extension(self):
#     def get_transformed_core_file_name(self, transformation, extension=None):
#     def get_transformed_file_path(self, transformation, extension=None):
# def format_as_json(jsonable_data):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def transform(self):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+", toStringFunc=str):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+"):
# def addArguments(string, args, joiner="_"):
# 
# Path: simdna/simdnautil/pwm.py
# class PWM(object):
#     def __init__(self, name, letterToIndex=DEFAULT_LETTER_TO_INDEX,
#                        probMatrix=None, pseudocountProb=None):
#     def add_row(self, weights):
#     def addRow(self, weights):
#     def add_rows(self, matrix):
#     def addRows(self, matrix):
#     def finalize(self, pseudocountProb=0.001):
#     def finalise(self, pseudocountProb=0.001):
#     def get_best_hit(self):
#     def getBestHit(self):
#     def compute_best_hit_given_matrix(self, matrix):
#     def computeBestHitGivenMatrix(self, matrix):
#     def get_rows(self):
#     def getRows(self):
#     def sample_from_pwm(self, bg=None):
#     def sampleFromPwm(self, bg=None):
#     def sample_from_pwm_and_score(self, bg):
#     def sampleFromPwmAndScore(self, bg):
#     def __str__(self):


# Path: simdna/synthetic/loadedmotifs.py
from simdna.synthetic.core import DefaultNameMixin
from simdna.simdnautil import util, pwm
from collections import OrderedDict
import numpy as np

class LoadedJasparRawPFMMotifs(AbstractLoadedMotifsFromFile):
    """A class for reading in a motifs file in the Jaspar Raw motifs format.

    This class is specifically for reading files in the Jaspar motif
    format.

    Basically, the motif declarations start with a >, the first
    characters after > until the first space are taken as the motif name,
    the lines after the line with a > have the format:
        P(A) "<nuc 1> <nuc 2> ... <nuc n>"
        P(C) "<nuc 1> <nuc 2> ... <nuc n>"
        P(T) "<nuc 1> <nuc 2> ... <nuc n>"
        P(G) "<nuc 1> <nuc 2> ... <nuc n>"

    Likely if you need to load your own motifs you will use this import
    script.
    """

    def getReadPwmAction(self, loadedMotifs):
        """See superclass.
        """
        currentPwm = util.VariableWrapper(None)
        _pwm = []
        def action(inp, lineNumber):
            if (inp.startswith(">")):
                inp = inp.lstrip(">")
                inpArr = inp.split()
                motifName = inpArr[1]
                while len(_pwm) > 0:
                    _pwm.pop()

                currentPwm.var = pwm.PWM(motifName)