system/__init__.py

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 2.0.8
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.



from sys import version_info
if version_info >= (2,6,0):
    def swig_import_helper():
        from os.path import dirname
        import imp
        fp = None
        try:
            fp, pathname, description = imp.find_module('_IMP_system', [dirname(__file__)])
        except ImportError:
            import _IMP_system
            return _IMP_system
        if fp is not None:
            try:
                _mod = imp.load_module('_IMP_system', fp, pathname, description)
            finally:
                fp.close()
            return _mod
    _IMP_system = swig_import_helper()
    del swig_import_helper
else:
    import _IMP_system
del version_info
try:
    _swig_property = property
except NameError:
    pass # Python < 2.2 doesn't have 'property'.
def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
    if (name == "thisown"): return self.this.own(value)
    if (name == "this"):
        if type(value).__name__ == 'SwigPyObject':
            self.__dict__[name] = value
            return
    method = class_type.__swig_setmethods__.get(name,None)
    if method: return method(self,value)
    if (not static):
        self.__dict__[name] = value
    else:
        raise AttributeError("You cannot add attributes to %s" % self)

def _swig_setattr(self,class_type,name,value):
    return _swig_setattr_nondynamic(self,class_type,name,value,0)

def _swig_getattr(self,class_type,name):
    if (name == "thisown"): return self.this.own()
    method = class_type.__swig_getmethods__.get(name,None)
    if method: return method(self)
    raise AttributeError(name)

def _swig_repr(self):
    try: strthis = "proxy of " + self.this.__repr__()
    except: strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)

try:
    _object = object
    _newclass = 1
except AttributeError:
    class _object : pass
    _newclass = 0


try:
    import weakref
    weakref_proxy = weakref.proxy
except:
    weakref_proxy = lambda x: x


class IMP_SYSTEM_SwigPyIterator(_object):
    """Proxy of C++ swig::IMP_SYSTEM_SwigPyIterator class"""
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_SYSTEM_SwigPyIterator, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, IMP_SYSTEM_SwigPyIterator, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _IMP_system.delete_IMP_SYSTEM_SwigPyIterator
    __del__ = lambda self : None;
    def value(self):
        """value(IMP_SYSTEM_SwigPyIterator self) -> PyObject *"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_value(self)

    def incr(self, n=1):
        """
        incr(IMP_SYSTEM_SwigPyIterator self, size_t n=1) -> IMP_SYSTEM_SwigPyIterator
        incr(IMP_SYSTEM_SwigPyIterator self) -> IMP_SYSTEM_SwigPyIterator
        """
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_incr(self, n)

    def decr(self, n=1):
        """
        decr(IMP_SYSTEM_SwigPyIterator self, size_t n=1) -> IMP_SYSTEM_SwigPyIterator
        decr(IMP_SYSTEM_SwigPyIterator self) -> IMP_SYSTEM_SwigPyIterator
        """
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_decr(self, n)

    def distance(self, *args):
        """distance(IMP_SYSTEM_SwigPyIterator self, IMP_SYSTEM_SwigPyIterator x) -> ptrdiff_t"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_distance(self, *args)

    def equal(self, *args):
        """equal(IMP_SYSTEM_SwigPyIterator self, IMP_SYSTEM_SwigPyIterator x) -> bool"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_equal(self, *args)

    def copy(self):
        """copy(IMP_SYSTEM_SwigPyIterator self) -> IMP_SYSTEM_SwigPyIterator"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_copy(self)

    def next(self):
        """next(IMP_SYSTEM_SwigPyIterator self) -> PyObject *"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_next(self)

    def __next__(self):
        """__next__(IMP_SYSTEM_SwigPyIterator self) -> PyObject *"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___next__(self)

    def previous(self):
        """previous(IMP_SYSTEM_SwigPyIterator self) -> PyObject *"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_previous(self)

    def advance(self, *args):
        """advance(IMP_SYSTEM_SwigPyIterator self, ptrdiff_t n) -> IMP_SYSTEM_SwigPyIterator"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator_advance(self, *args)

    def __eq__(self, *args):
        """__eq__(IMP_SYSTEM_SwigPyIterator self, IMP_SYSTEM_SwigPyIterator x) -> bool"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___eq__(self, *args)

    def __ne__(self, *args):
        """__ne__(IMP_SYSTEM_SwigPyIterator self, IMP_SYSTEM_SwigPyIterator x) -> bool"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___ne__(self, *args)

    def __iadd__(self, *args):
        """__iadd__(IMP_SYSTEM_SwigPyIterator self, ptrdiff_t n) -> IMP_SYSTEM_SwigPyIterator"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___iadd__(self, *args)

    def __isub__(self, *args):
        """__isub__(IMP_SYSTEM_SwigPyIterator self, ptrdiff_t n) -> IMP_SYSTEM_SwigPyIterator"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___isub__(self, *args)

    def __add__(self, *args):
        """__add__(IMP_SYSTEM_SwigPyIterator self, ptrdiff_t n) -> IMP_SYSTEM_SwigPyIterator"""
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___add__(self, *args)

    def __sub__(self, *args):
        """
        __sub__(IMP_SYSTEM_SwigPyIterator self, ptrdiff_t n) -> IMP_SYSTEM_SwigPyIterator
        __sub__(IMP_SYSTEM_SwigPyIterator self, IMP_SYSTEM_SwigPyIterator x) -> ptrdiff_t
        """
        return _IMP_system.IMP_SYSTEM_SwigPyIterator___sub__(self, *args)

    def __iter__(self): return self
IMP_SYSTEM_SwigPyIterator_swigregister = _IMP_system.IMP_SYSTEM_SwigPyIterator_swigregister
IMP_SYSTEM_SwigPyIterator_swigregister(IMP_SYSTEM_SwigPyIterator)

_value_types=[]
_object_types=[]
_raii_types=[]
_plural_types=[]

IMP_HAS_DEPRECATED = _IMP_system.IMP_HAS_DEPRECATED
IMP_DEBUG = _IMP_system.IMP_DEBUG
IMP_RELEASE = _IMP_system.IMP_RELEASE
IMP_SILENT = _IMP_system.IMP_SILENT
IMP_PROGRESS = _IMP_system.IMP_PROGRESS
IMP_TERSE = _IMP_system.IMP_TERSE
IMP_VERBOSE = _IMP_system.IMP_VERBOSE
IMP_NONE = _IMP_system.IMP_NONE
IMP_USAGE = _IMP_system.IMP_USAGE
IMP_INTERNAL = _IMP_system.IMP_INTERNAL
IMP_COMPILER_HAS_AUTO = _IMP_system.IMP_COMPILER_HAS_AUTO
IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_system.IMP_COMPILER_HAS_DEBUG_VECTOR
IMP_COMPILER_HAS_NULLPTR = _IMP_system.IMP_COMPILER_HAS_NULLPTR
IMP_BASE_HAS_BOOST_RANDOM = _IMP_system.IMP_BASE_HAS_BOOST_RANDOM
IMP_BASE_HAS_GPERFTOOLS = _IMP_system.IMP_BASE_HAS_GPERFTOOLS
IMP_BASE_HAS_LOG4CXX = _IMP_system.IMP_BASE_HAS_LOG4CXX
IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_system.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_system.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
import sys
class _DirectorObjects(object):
    """@internal Simple class to keep references to director objects
       to prevent premature deletion."""
    def __init__(self):
        self._objects = []
    def register(self, obj):
        """Take a reference to a director object; will only work for
           refcounted C++ classes"""
        if hasattr(obj, 'get_ref_count'):
            self._objects.append(obj)
    def cleanup(self):
        """Only drop our reference and allow cleanup by Python if no other
           Python references exist (we hold 3 references: one in self._objects,
           one in x, and one in the argument list for getrefcount) *and* no
           other C++ references exist (the Python object always holds one)"""
        objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
                                         or x.get_ref_count() > 1]
        
        
        self._objects = objs
    def get_object_count(self):
        """Get number of director objects (useful for testing only)"""
        return len(self._objects)
_director_objects = _DirectorObjects()

DEFAULT_CHECK = _IMP_system.DEFAULT_CHECK
NONE = _IMP_system.NONE
USAGE = _IMP_system.USAGE
USAGE_AND_INTERNAL = _IMP_system.USAGE_AND_INTERNAL

def set_check_level(*args):
  """set_check_level(IMP::base::CheckLevel tf)"""
  return _IMP_system.set_check_level(*args)

def get_check_level():
  """get_check_level() -> IMP::base::CheckLevel"""
  return _IMP_system.get_check_level()
class _ostream(_object):
    """Proxy of C++ std::ostream class"""
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
    __repr__ = _swig_repr
    def write(self, *args):
        """write(_ostream self, char const * osa_buf)"""
        return _IMP_system._ostream_write(self, *args)

_ostream_swigregister = _IMP_system._ostream_swigregister
_ostream_swigregister(_ostream)

IMP_COMPILER_HAS_OVERRIDE = _IMP_system.IMP_COMPILER_HAS_OVERRIDE
IMP_COMPILER_HAS_FINAL = _IMP_system.IMP_COMPILER_HAS_FINAL
import IMP.base
IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_system.IMP_CGAL_HAS_BOOST_FILESYSTEM
IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_system.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
IMP_CGAL_HAS_BOOST_RANDOM = _IMP_system.IMP_CGAL_HAS_BOOST_RANDOM
IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_system.IMP_CGAL_HAS_BOOST_SYSTEM
import IMP.cgal
IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_system.IMP_ALGEBRA_HAS_IMP_CGAL
IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_system.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_system.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_system.IMP_ALGEBRA_HAS_BOOST_RANDOM
IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_system.IMP_ALGEBRA_HAS_BOOST_SYSTEM
IMP_ALGEBRA_HAS_CGAL = _IMP_system.IMP_ALGEBRA_HAS_CGAL
IMP_ALGEBRA_HAS_ANN = _IMP_system.IMP_ALGEBRA_HAS_ANN
import IMP.algebra
IMP_KERNEL_HAS_IMP_CGAL = _IMP_system.IMP_KERNEL_HAS_IMP_CGAL
IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_system.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_system.IMP_KERNEL_HAS_BOOST_RANDOM
IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_system.IMP_KERNEL_HAS_BOOST_SYSTEM
IMP_KERNEL_HAS_CGAL = _IMP_system.IMP_KERNEL_HAS_CGAL
import IMP.kernel
IMP_SYSTEM_HAS_IMP_ALGEBRA = _IMP_system.IMP_SYSTEM_HAS_IMP_ALGEBRA
IMP_SYSTEM_HAS_IMP_BASE = _IMP_system.IMP_SYSTEM_HAS_IMP_BASE
IMP_SYSTEM_HAS_IMP_CGAL = _IMP_system.IMP_SYSTEM_HAS_IMP_CGAL
IMP_SYSTEM_HAS_BOOST_FILESYSTEM = _IMP_system.IMP_SYSTEM_HAS_BOOST_FILESYSTEM
IMP_SYSTEM_HAS_BOOST_PROGRAMOPTIONS = _IMP_system.IMP_SYSTEM_HAS_BOOST_PROGRAMOPTIONS
IMP_SYSTEM_HAS_BOOST_RANDOM = _IMP_system.IMP_SYSTEM_HAS_BOOST_RANDOM
IMP_SYSTEM_HAS_BOOST_SYSTEM = _IMP_system.IMP_SYSTEM_HAS_BOOST_SYSTEM
IMP_SYSTEM_HAS_CGAL = _IMP_system.IMP_SYSTEM_HAS_CGAL
import sys
import re
import os
import os.path
from optparse import OptionParser

def _get_script_name():
    return os.path.splitext(os.path.split(sys.argv[0])[1])[0]

def _get_script_path():
    return os.path.split(sys.argv[0])[0]

def _get_is_sample():
    return _get_script_name().startswith("sample")

def _get_number_of_samples():
    for i in range(0,100):
        if not os.path.exists(os.path.join(_get_script_path(),
                                           "sample_"+str(i)+".py")):
            return i

def _get_is_analysis():
    return _get_script_name().startswith("analyze")

def _get_is_setup():
    return _get_script_name() == "setup"


def _get_script_index():
    return int(_get_script_name().split("_")[1])

def _get_default_input():
    if _get_is_sample() and _get_script_index()==0:
        return "setup"
    elif _get_is_sample():
        return "sampled_"+str(_get_script_index()-1)
    elif _get_is_analysis() and _get_script_index()==0:
        return "sampled_"+str(_get_number_of_samples()-1)
    elif _get_is_analysis():
        return "analyzed_"+str(_get_script_index()-1)
    else:
        raise ValueError("bad script name, expect sample_n or analyze_n")

def _get_default_output():
    if _get_is_sample():
        return "sampled_"+str(_get_script_index())
    elif _get_is_analysis():
        return "analyzed_"+str(_get_script_index())
    elif _get_is_setup():
        return "setup"


def _is_sample():
    ptn="sample_.*.py"
    r= re.compile(ptn)
    nm= os.path.split(sys.argv[0])[1]
    #print nm, r.match(nm), ptn
    return r.search(nm)

def _is_sample_0():
    return sys.argv[0].endswith("sample_0.py")



def _create_parser():
    parser = OptionParser(usage='%prog [options]')
    parser.add_option(
        '-o', '--output-dir', dest='output_dir', default='auto',
        help='Where to put the output for the script',
        )
    if not _is_sample_0():
        parser.add_option(
            '-i', '--input-dir', dest='input_dir', default='auto',
            help='Where to find input for the script',
            )
    parser.add_option(
        '-d', '--data-dir', dest='data_dir', default='auto',
        help='Where to find data for the script',
        )
    if _is_sample():
        parser.add_option(
            '-j', '--job', dest='job_index',
            help='The index for the current job')
        parser.add_option(
            '-n', '--num-jobs', dest='num_jobs',
            help='The total number of jobs to divide things into')
        parser.add_option(
            '-t', '--test', action="store_true", default=False, dest='test',
            help='Just run a smaller version of the sampling to test things.')
    return parser

parser=_create_parser()
(options, args) = parser.parse_args()

def get_sample_parameters():
    """Return the index and the number of parts to divide the job in to."""
    if options.test:
        if options.job_index or options.num_jobs:
            parser.error("--test and -j or -n cannot be specified at "
                         "the same time.")
        return (0, 1000)
    return (int(options.job_index),int(options.num_jobs))

def get_is_test():
    """Return whether this run is called with --test. Scripts that use this
       can't don't expect -j and -n and so an error will be thrown if
       they are passed."""
    if options.job_index or options.num_jobs:
        parser.error("This sampling script cannot be broken up into jobs. "
                     "Only --test is supported.")
    return options.test



def get_input_path(name):
    """Get the path where the current script should find output of the
       last script"""
    id=options.input_dir
    if id=="auto":
        id= _get_default_input()
    return os.path.join(id, name)

def get_output_path(name):
    """Get the path to where the current script should write output files"""
    od=options.output_dir
    if od=="auto":
        od= _get_default_output()
    if not os.path.exists(od):
        os.makedirs(od)
    return os.path.join(od, name)


def get_data_input_path(name):
    """Get the path where the current script should find data files"""
    da= options.data_dir
    if da=="auto":
        da= os.path.join(os.path.split(sys.argv[0])[0], "data")
    return os.path.join(da, name)


def get_module_version():
  """get_module_version() -> std::string const"""
  return _IMP_system.get_module_version()

def get_example_path(*args):
  """get_example_path(std::string fname) -> std::string"""
  return _IMP_system.get_example_path(*args)

def get_data_path(*args):
  """get_data_path(std::string fname) -> std::string"""
  return _IMP_system.get_data_path(*args)
import _version_check
_version_check.check_version(get_module_version())

# This file is compatible with both classic and new-style classes.