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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
from utility.logger import getLogger
logger = getLogger(__name__)
import utility.tools
utility.tools.show_settings()
class webqtlCaseData:
"""one case data in one trait"""
def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
self.name = name
self.name2 = name2 # Other name (for traits like BXD65a)
self.value = value # Trait Value
self.variance = variance # Trait Variance
self.num_cases = num_cases # Number of individuals/cases
self.extra_attributes = None
self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
self.outlier = None # Not set to True/False until later
def __repr__(self):
case_data_string = "<webqtlCaseData> "
if self.value is not None:
case_data_string += "value=%2.3f" % self.value
if self.variance is not None:
case_data_string += " variance=%2.3f" % self.variance
if self.num_cases:
case_data_string += " ndata=%s" % self.num_cases
if self.name:
case_data_string += " name=%s" % self.name
if self.name2:
case_data_string += " name2=%s" % self.name2
return case_data_string
@property
def class_outlier(self):
"""Template helper"""
if self.outlier:
return "outlier"
return ""
@property
def display_value(self):
if self.value is not None:
return "%2.3f" % self.value
return "x"
@property
def display_variance(self):
if self.variance is not None:
return "%2.3f" % self.variance
return "x"
@property
def display_num_cases(self):
if self.num_cases is not None:
return "%s" % self.num_cases
return "x"
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