def __init__(self, path):
Tree.__init__(self, path)
for root, dirs, files in os.walk(path):
node = self.find_node(self.root, str(root))
for dir_ in dirs:
node.add_child(os.path.join(root, dir_))
for file_ in files:
node.add_child(os.path.join(root, file_))
def __init__(self):
Tree.__init__(self,
root=HyperCategory(hid=Autogen.root_hid,
name='All goods'))
self.add_children({
HyperCategory(hid=Autogen.default_hid, name='Default category'):
{}
})
def __init__(self, tree, mp='', ml=''):
"""
Convert sequences in MSA file into ancestral state for each site and attach them to each node
@param tree: string, a newick format string or a filename of a newick format file (in this version this only accept a newick format file generated by FastML instead of a untouched newick format file which only contains aligned sequence for all terminal nodes)
@param mp: string, filename of a MSA file, MP method only
@param ml: string, filename of a MSA file, ML method only
"""
Tree.__init__(self, tree, mp, ml)
def __init__(self, tree, mp='', ml='', save=False, outdir=''):
"""
Reconstruct ancestral state by MP method for a given tree in newick format and a MSA file in fasta format
@param tree: string, a newick format string or a filename of a newick format file
@param mp: string, filename of a MSA file, MP method only
@param ml: string, filename of a MSA file, ML method only
@param save: bool, save result to a file or print it out (default), default: False
@param outdir: string, a directory name (with absoluter or relative path) to save result.
"""
Tree.__init__(self, tree, mp, ml)
self.save = save
self.outdir = outdir if outdir else os.getcwd()
def __init__(self,
master,
root,
iconsManager=None,
idleRedraw=True,
nodeHeight=15,
headerHeight=0,
treeWidth=160,
**kw):
Tree.__init__(self,
master,
root,
iconsManager=iconsManager,
idleRedraw=idleRedraw,
nodeHeight=nodeHeight,
headerHeight=headerHeight,
**kw)
self.objectToNode = {} # key is object, values if Node instance
self.objectToNode[root.object] = root
self.nbCol = 0 # number of columns of buttons
self.columns = [] # list of ColumnDescriptor instance
self.balloon = Balloon(master)
self.colLabIds = []
self.colWidth = 17 # width of each column in pixels
w = self.treeWidth = treeWidth # width of the tree part of the widget
self.newTreeWidth = 0 # used to widen tree whebn labels gets long
self.prevX = 0
self.prevY = 0
# draw the divider between tree and buttons
canvas = self.canvas
id_ = canvas.create_line(w - 6, 0, w - 6, 1000, fill='grey75', width=3)
self.dividerCanvasId = id_
canvas.tag_bind(id_, "<Enter>", self.enterDivider_cb)
canvas.tag_bind(id_, "<Leave>", self.leaveDivider_cb)
canvas.tag_bind(id_, "<Button-1>", self.dividePress_cb)
canvas.tag_bind(id_, "<ButtonRelease-1>", self.divideRelease_cb)
#id_ = canvas.create_line( w+1, 0, w+1, 1000, fill='grey75')
#self.dividerCanvasIds.append(id_)
self.crosshairTk = None
self.canvas.bind("<Leave>", self.leave_cb)
self.circlesForOnOff = True
self.lastHighligted = None
self.minTreeWidth = 0 # width of buttons above tree
def __init__(self, client, *args, **kwargs):
kwargs['draw_zebra'] = False
self.client = client
self.directory = get_platform_root_dir()
self.content = content = os.walk(self.directory)
if client is not None and hasattr(client, 'directory'):
self.directory = client.directory
self.directory = kwargs.pop('directory', self.directory)
self.data = data = {}
d = {}
for dirpath, dirnames, filenames in content:
for name in dirnames:
d[name] = self.parse_path(name, os.path.join(dirpath, name))
data[dirpath] = d
break
kwargs['data'] = data
Tree.__init__(self, *args, **kwargs)
del self.menu
self.set_directory(self.directory)
def __init__(self, client, *args, **kwargs):
kwargs["draw_zebra"] = False
self.client = client
self.directory = get_platform_root_dir()
self.content = content = os.walk(self.directory)
if client is not None and hasattr(client, "directory"):
self.directory = client.directory
self.directory = kwargs.pop("directory", self.directory)
self.data = data = {}
d = {}
for dirpath, dirnames, filenames in content:
for name in dirnames:
d[name] = self.parse_path(name, os.path.join(dirpath, name))
data[dirpath] = d
break
kwargs["data"] = data
Tree.__init__(self, *args, **kwargs)
del self.menu
self.set_directory(self.directory)
def __init__(self, master, root, iconsManager=None, idleRedraw=True,
nodeHeight=20, **kw):
Tree.__init__(self, master, root, iconsManager=None, idleRedraw=True,
nodeHeight=20, **kw)
self.objectToNode = {} # key is object, values if Node instance
self.objectToNode[root.object] = root
self.nbCol = 0 # number of columns of buttons
self.columns = [] # list of ColumnDescriptor instance
self.balloon = Balloon(master)
self.colLabIds = []
self.colWidth = 25 # width of each column in pixels
self.treeWidth = 180 # width of the tree part of the widget
self.prevX = 0
self.prevY = 0
self.crosshairTk = None
self.canvas.bind("<Leave>", self.leave_cb)
def __init__(self, master, root, iconsManager=None, idleRedraw=True,
nodeHeight=15, headerHeight=30, treeWidth=160, **kw):
Tree.__init__(self, master, root, iconsManager=iconsManager,
idleRedraw=idleRedraw, nodeHeight=nodeHeight,
headerHeight=headerHeight, **kw)
self.objectToNode = {} # key is object, values if Node instance
self.objectToNode[root.object] = root
self.nbCol = 0 # number of columns of buttons
self.columns = [] # list of ColumnDescriptor instance
self.balloon = Balloon(master)
self.colLabIds = []
self.colWidth = 17 # width of each column in pixels
w = self.treeWidth = treeWidth # width of the tree part of the widget
self.newTreeWidth = 0 # used to widen tree whebn labels gets long
self.prevX = 0
self.prevY = 0
# draw the divider between tree and buttons
canvas = self.canvas
id_ = canvas.create_line( w-6, 0, w-6, 1000, fill='grey75', width=3)
self.dividerCanvasId = id_
canvas.tag_bind(id_,"<Enter>", self.enterDivider_cb)
canvas.tag_bind(id_,"<Leave>", self.leaveDivider_cb)
canvas.tag_bind(id_,"<Button-1>", self.dividePress_cb)
canvas.tag_bind(id_,"<ButtonRelease-1>", self.divideRelease_cb)
#id_ = canvas.create_line( w+1, 0, w+1, 1000, fill='grey75')
#self.dividerCanvasIds.append(id_)
self.crosshairTk = None
self.canvas.bind("<Leave>", self.leave_cb)
self.circlesForOnOff = True
self.lastHighligted = None
def __init__(self):
Tree.__init__(self)
def __init__(self):
Tree.__init__(self)
self._n_nodes = 0
self._nodes = [] # _nodes is a list of dictionaries.
def __init__(self):
Tree.__init__(self)
self.root = None # Set up the tree with no root
self._n_nodes = 0
def __init__(self):
Tree.__init__(self, get_widget_by_name('Project Explorer Tree'))
def __init__(self):
Tree.__init__(self)
self._n_nodes = 0
self._nodes = [] # _nodes is a list of dictionaries.
def __init__(self):
""""""
DownloadManager.__init__(self, lambda x: x, [])
Tree.__init__(self, [None], self)
self.config = shared.configuration
def __init__(self):
Tree.__init__(self, get_widget_by_name('Project Explorer Tree'))
def __init__(self, directory_or_file):
Tree.__init__(self)
self.counter = Counter(directory_or_file)
def __init__(self, json):
"""
Constructor.
It simply calls GeneralTree constructor with specified json.
"""
Tree.__init__(self, "", json)
def __init__(self):
Tree.__init__(self, root=HyperCategory(hid=Autogen.root_hid, name='All goods'))
self.add_children({HyperCategory(hid=Autogen.default_hid, name='Default category'): {}})
def __init__(self):
Tree.__init__(self)
self.root = None # Set up the tree with no root
self._n_nodes = 0
def __init__(self):
Tree.__init__(
self, Region(name='Russia', type='country', rid=Autogen.root_rid))
def __init__(self, end_node, prec, index, index_list=None):
Tree.__init__(self, end_node, prec)
if index_list is None:
self._index_list = [index]
else:
self._index_list = index_list
def __init__(self, height=0):
Tree.__init__(self, height)
self.type = "FoxtailPine"
def __init__(self, height=0):
Tree.__init__(self, height)
self.type = "WhitebarkPine"
def __init__(self, datasets, feature):
Tree.__init__(self, datasets, feature)
self.tree = None
def __init__(self, label = "Genome", myObject = None):
'''
'''
Tree.__init__(self, label, myObject)
self.exonCnt, self.intronCnt, self.cdsCnt = 0, 0, 0
self.splices = True # Print out splicing variants by default
def __init__(self, id=0, **kwargs):
Tree.__init__(self, root=NavCategory(**kwargs))
self.__id = id
self.__primaries = set()
if self._root.primary:
self.__primaries.add(self._root.hid)
def __init__(self):
Tree.__init__(self, Region(name='Russia', type='country', rid=Autogen.root_rid))
def __init__(self): """""" DownloadManager.__init__(self, lambda x: x, []) Tree.__init__(self, [None], self) self.config = shared.configuration
def __init__(self):
Tree.__init__(self)
self.root = None
self.count = 0
def __init__(self, end_node, prec, index):
Tree.__init__(self, end_node, prec)
self._index = index
