# Path: picrust/util.py
# def get_picrust_project_dir():
#     """ Returns the top-level PICRUST directory
#     """
#     # Get the full path of util.py
#     current_file_path = abspath(__file__)
#     # Get the directory containing util.py
#     current_dir_path = dirname(current_file_path)
#     # Return the directory containing the directory containing util.py
#     return dirname(current_dir_path)


from cogent.util.table import Table
from os.path import split, splitext
from os import remove, environ
from glob import glob
from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
from cogent.app.parameters import ValuedParameter, FilePath
from cogent import LoadTable
from picrust.util import get_picrust_project_dir
from os.path import join
from cogent.parse.tree import DndParser
#!/usr/bin/env python
# Author: Morgan Langille (morgan.g.i.langille@gmail.com)
# count_wagner.py

""" Application controller for Count (ancestral state resconstruction)

File created on 24 Jan 2012.

"""
from __future__ import division
#from cogent import LoadTree

__author__ = "Morgan Langille"
__copyright__ = "Copyright 2015, The PICRUSt Project"
__credits__ = ["Morgan Langille"]
__license__ = "GPL"
__version__ = "1.1.4"
__maintainer__ = "Morgan Langille"
__email__ = "morgan.g.i.langille@gmail.com"
__status__ = "Development"


class Count(CommandLineApplication):
    """ Application controller for Count an ASR tool."""

    #count_fp = environ['COUNT_JAR']

# Path: picrust/util.py
# def get_picrust_project_dir():
#     """ Returns the top-level PICRUST directory
#     """
#     # Get the full path of util.py
#     current_file_path = abspath(__file__)
#     # Get the directory containing util.py
#     current_dir_path = dirname(current_file_path)
#     # Return the directory containing the directory containing util.py
#     return dirname(current_dir_path)


# Path: picrust/count.py
from cogent.util.table import Table
from os.path import split, splitext
from os import remove, environ
from glob import glob
from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
from cogent.app.parameters import ValuedParameter, FilePath
from cogent import LoadTable
from picrust.util import get_picrust_project_dir
from os.path import join
from cogent.parse.tree import DndParser

#!/usr/bin/env python
# Author: Morgan Langille (morgan.g.i.langille@gmail.com)
# count_wagner.py

""" Application controller for Count (ancestral state resconstruction)

File created on 24 Jan 2012.

"""
from __future__ import division
#from cogent import LoadTree

__author__ = "Morgan Langille"
__copyright__ = "Copyright 2015, The PICRUSt Project"
__credits__ = ["Morgan Langille"]
__license__ = "GPL"
__version__ = "1.1.4"
__maintainer__ = "Morgan Langille"
__email__ = "morgan.g.i.langille@gmail.com"
__status__ = "Development"


class Count(CommandLineApplication):
    """ Application controller for Count an ASR tool."""

    #count_fp = environ['COUNT_JAR']

    count_fp = join(get_picrust_project_dir(),'picrust','support_files','jar','Count.jar')