rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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try: url = 'http://localhost:7080/rhq-rhq-enterprise-server-ejb3/WebServiceTestBean?wsdl' start(url) client = Client(url, faults=False) print 'testExceptions() faults=No' result = client.service.testExceptions() sent = client.last_sent() rcvd = client.last_received() print '\nreply( %s )\n' % str(result) except WebFaul... | def basic_doc_literal(): global errors try: url = 'http://localhost:7080/rhq-rhq-enterprise-server-ejb3/WebServiceTestBean?wsdl' start(url) client = Client(url, transport=mytransport) print client # # create name # name = client.factory.create('name') name.first = u'Jeff'+unichr(1234) name.last = 'Ortel < Comp... | |
basic_doc_literal() basic_rpc_literal() authentication() perspectives() content_source() | rhqTest() | def content_source(): global subject, errors try: url = 'http://localhost:7080/rhq-rhq-enterprise-server-ejb3/ContentSourceManagerBean?wsdl' start(url) client = Client(url, xstq=False) print client # # create a configuration # configuration = client.factory.create('configuration') entry = client.factory.create('confi... |
LOCAL = ( 0-time.timezone/60/60 ) | LOCAL = ( 0-time.timezone/60/60 ) + time.daylight | def __init__(self, date=None): if date is None: date = dt.datetime.utcnow() DateTime.__init__(self, date) self.tz.local = 0 |
child_vals = [l.get() for l in self.get().keys()] | child_vals = [listvar.get() for listvar in self.listvars.values()] | def get_args(self): """Return a list of arguments for the contained list(s). """ args = [] # Add parent args, if parent was defined here if not self.parent_is_copy: args.extend(self.parent.get_args()) # FIXME: Most of this is a total hack to support 'index' and # 'repeat' keywords # If child list(s) are nonempty, and w... |
if not self.repeat: | child_vals = [l.get() for l in self.mapped] if any(child_vals) and not self.repeat: | def get_args(self): """Return a list of arguments for the contained list(s). """ args = [] # Add parent args, if parent was defined here if not self.parent_is_copy: args.extend(self.parent.get_args()) # Add child args, for one or many children if self.correspondence == '1:*': # FIXME: Most of this is a total hack to su... |
print("Installing tovid to %s" % self.prefix) | def run(self): """Install tovid, and write a list of installed files to $prefix/lib/tovid/.install.log. """ print("Installing tovid to %s" % self.prefix) install.run(self) # Move temporary install log to $prefix/lib/tovid install_log = os.path.join(self.prefix, 'lib', 'tovid', '.install.log') print("Moving install.log ... | |
install_log = os.path.join(self.prefix, 'lib', 'tovid', '.install.log') | install_log = os.path.join(prefix, 'lib', 'tovid', '.install.log') | def run(self): """Install tovid, and write a list of installed files to $prefix/lib/tovid/.install.log. """ print("Installing tovid to %s" % self.prefix) install.run(self) # Move temporary install log to $prefix/lib/tovid install_log = os.path.join(self.prefix, 'lib', 'tovid', '.install.log') print("Moving install.log ... |
rev_line = os.popen('svn info 2>/dev/null | grep ^Revision').read() | from commands import getoutput rev_line = getoutput('svn info 2>/dev/null | grep ^Revision') | def svn_version(): """Return the current SVN revision number, as reported by 'svn info', as a string like 'svn-r1234'. If svn is not installed, or if something goes wrong, return 'svn-unknown' """ rev_line = os.popen('svn info 2>/dev/null | grep ^Revision').read() # If rev_line is empty, either svn is missing or the co... |
return 'svn-unknown' | rev_line = getoutput('bzr log -l 1 2>/dev/null | grep "^svn revno"') if rev_line: return 'svn-r' + rev_line.split(':')[1].strip().split(' ')[0] return 'svn-unknown' | def svn_version(): """Return the current SVN revision number, as reported by 'svn info', as a string like 'svn-r1234'. If svn is not installed, or if something goes wrong, return 'svn-unknown' """ rev_line = os.popen('svn info 2>/dev/null | grep ^Revision').read() # If rev_line is empty, either svn is missing or the co... |
self.args.append(str(arg)) | self.args.append(unicode(arg)) | def add(self, *args): """Append one or more arguments to the command. Each argument passed to this function is converted to string form, and treated as a single argument in the command. No special quoting or escaping of argument contents is necessary. """ for arg in args: self.args.append(str(arg)) |
print(self) | print(unicode(self)) | def run_redir(self, stdin=None, stdout=None, stderr=None): """Execute the command using the given stream redirections. |
commands = [str(cmd) for cmd in self.commands] | commands = [unicode(cmd) for cmd in self.commands] | def __str__(self): """Return a string representation of the Pipe. """ commands = [str(cmd) for cmd in self.commands] return ' | '.join(commands) |
'normal|oval|plectrum|egg|wave|galaxy|boomerang|spiral|flattube|tilde|none', 'dropdown') | thumb_masks, 'dropdown') | def strip_all(filename): return '' |
self.commands = [] | def __init__(self, master, text, icon): Frame.__init__(self, master) self.pages = [] self.index = IntVar() self.text = text self.icon = icon self.master = master self.commands = [] self.is_running = BooleanVar() self.is_running.set(True) self.waitVar = BooleanVar() self.waitVar.set(False) | |
print index | def next(self): index = wizard.index.get() print index try: self.pages[index].hide_page() wizard.index.set(index + 1) self.pages[index+1].frame.pack(side='right') self.pages[index+1].show_page() except IndexError: pass | |
set_env = [] | def run_gui(self, args=[], index='', script=''): """Run the tovid GUI, collecting options, and saving to wizard """ title = 'load saved script' script = 'todisc_commands.bash' set_env = [] if index: print "DEBUG: setting os.environ['METAGUI_WIZARD'] =", "%s" %index os.environ['METAGUI_WIZARD'] = '%s' %index cmd = ['tod... | |
yscroll = Scrollbar(frame1, command=self.listbox.yview, orient='vertica') | yscroll = Scrollbar(frame1, command=self.listbox.yview, \ orient='vertical') | def draw(self): text = '''ROOT MENU (VMGM) |
def get_id(self): | def set(self, program): | def get_id(self): """Create and pack container frame, then get X11 identifier for it (converted to base 10). Return the identifier """ self.frame = Frame(self.master, container=1, borderwidth=1, width=self.width, height=self.height) id = self.tk.call('winfo', 'id', self.frame) self.frame_id = '%s' %int(id, 16) return s... |
id = self.tk.call('winfo', 'id', self.frame) self.frame_id = '%s' %int(id, 16) return self.frame_id | _id = self.tk.call('winfo', 'id', self.frame) if program == 'mplayer': return _id else: return '%s' %int(_id, 16) | def get_id(self): """Create and pack container frame, then get X11 identifier for it (converted to base 10). Return the identifier """ self.frame = Frame(self.master, container=1, borderwidth=1, width=self.width, height=self.height) id = self.tk.call('winfo', 'id', self.frame) self.frame_id = '%s' %int(id, 16) return s... |
cmd = Popen(command, stderr=PIPE, stdout=PIPE) | cmd = Popen(command, stderr=PIPE) | def run(self, command): """Execute self.command, call the callback from self.master""" self.is_running.set(True) self.frame.pack() cmd = Popen(command, stderr=PIPE, stdout=PIPE) self.after(200, self.poll()) self.callback() |
def demo(app): | def demo(program): | def demo(app): def callback(): """Called upon creation and exiting of container app, Set a BooleanVar() to track whether the app is running. """ if container.is_running.get() == True: app_is_running.set(True) else: app_is_running.set(False) root_frame.pack_forget() label.pack(side='top', fill='both', expand=1) label.c... |
if container.is_running.get() == True: | if app.is_running.get() == True: | def callback(): """Called upon creation and exiting of container app, Set a BooleanVar() to track whether the app is running. """ if container.is_running.get() == True: app_is_running.set(True) else: app_is_running.set(False) root_frame.pack_forget() label.pack(side='top', fill='both', expand=1) label.configure(text='... |
root_frame.pack(fill='both', expand=1) xid = container.get_id() | root_frame.pack(side='top', fill='both', expand=1) xid = app.set(program) | def execute(): label.pack_forget() button.pack_forget() root_frame.pack(fill='both', expand=1) xid = container.get_id() font = '-misc-fixed-medium-r-normal--13-100-100-100-c-70-iso8859-1' if app == 'xterm': geometry = '80x40+0+0' command = 'xterm -geometry %s -fn %s -into %s &' \ %(geometry, font, xid) |
if app == 'xterm': | if program == 'xterm': | def execute(): label.pack_forget() button.pack_forget() root_frame.pack(fill='both', expand=1) xid = container.get_id() font = '-misc-fixed-medium-r-normal--13-100-100-100-c-70-iso8859-1' if app == 'xterm': geometry = '80x40+0+0' command = 'xterm -geometry %s -fn %s -into %s &' \ %(geometry, font, xid) |
elif app == 'mplayer': | elif program == 'mplayer': | def execute(): label.pack_forget() button.pack_forget() root_frame.pack(fill='both', expand=1) xid = container.get_id() font = '-misc-fixed-medium-r-normal--13-100-100-100-c-70-iso8859-1' if app == 'xterm': geometry = '80x40+0+0' command = 'xterm -geometry %s -fn %s -into %s &' \ %(geometry, font, xid) |
container.frame.destroy() | app.frame.destroy() | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
time.sleep(1) | time.sleep(0.2) | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
times.pop(-1) | if times: times.pop(-1) | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
command = 'mplayer -nomouseinput -xy 400 \ | command = 'mplayer -nomouseinput \ | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
%s -wid %s %s > /tmp/mplayer.log 2>&1' %(cmd_pipe, editlist, xid, media_file) but_frame = Frame(root_frame) | %s -wid %s %s ' %(cmd_pipe, editlist, xid, media_file) | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
b1 = Button(but_frame, command=set_chapter, text='set chapter') | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... | |
b2 = Button(but_frame, command=exit_mplayer, text='Exit') | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... | |
container.frame.configure(width=600, height=450) container.run(command) | app.frame.configure(width=600, height=450) app.run(command) | def exit_mplayer(): # send bogus edl command so mplayer sends last edl_mark send_command('edl_mark') # send quit and destroy frame send_command('quit') container.frame.destroy() # need a sleep to make sure mplayer gives up its data time.sleep(1) f = open(editlist) c = f.read() f.close() # convert text from opened file ... |
if app == 'xterm': | if program == 'xterm': | def confirm_exit(): if app_is_running.get() == 1: if app == 'xterm': text = "Close the xterm by typing 'exit', before exiting this demo" elif app == 'mplayer': text = "Close mplayer first, before exiting this demo" showerror(message=text) return quit() |
elif app == 'mplayer': | elif program == 'mplayer': | def confirm_exit(): if app_is_running.get() == 1: if app == 'xterm': text = "Close the xterm by typing 'exit', before exiting this demo" elif app == 'mplayer': text = "Close mplayer first, before exiting this demo" showerror(message=text) return quit() |
container = AppContainer(root_frame, 640, 480, callback) | app = AppContainer(root_frame, 640, 480, callback) | def confirm_exit(): if app_is_running.get() == 1: if app == 'xterm': text = "Close the xterm by typing 'exit', before exiting this demo" elif app == 'mplayer': text = "Close mplayer first, before exiting this demo" showerror(message=text) return quit() |
HPanel('', _thumb_columns, _align), | _thumb_columns, _align, | def nodupes(seq): noDupes = [] [noDupes.append(i) for i in seq if not noDupes.count(i)] return noDupes |
_thumb_rows = Choice('Rows', '', 'none', 'tooltip text ....', 'none|-tile-3x1|-tile-4x1', 'dropdown') | _thumb_columns = Choice('Thumb columns', '-thumb-columns', 'none', 'Use a montage tile of 3x1 or 4x1 instead of the usual 2x2 for 3 videos. ' 'If you want 1 row with 3 thumbs choose "3", or for 1 row with 4 thumbs ' 'choose "4".', 'none|3|4', 'dropdown') | def nodupes(seq): noDupes = [] [noDupes.append(i) for i in seq if not noDupes.count(i)] return noDupes |
HPanel('', _thumb_rows, _align), | HPanel('', _thumb_columns, _align), | def nodupes(seq): noDupes = [] [noDupes.append(i) for i in seq if not noDupes.count(i)] return noDupes |
_SubList.draw(self, master, allow_add_remove=False) | _SubList.draw(self, master, allow_add_remove=True) | def draw(self, master): """Draw the parent copy and related list Control, side by side in the given master. """ _SubList.draw(self, master, allow_add_remove=False) # Add callbacks to handle changes in parent self.add_callbacks() |
prefix = Command('tovid', "-prefix") prefix.run(capture=True) sys_dir = prefix.get_output() + '/masks' | os_path = os.environ['PATH'].rsplit(':') sys_dir = os_path[-1] + '/masks' | def nodupes(seq): noDupes = [] [noDupes.append(i) for i in seq if not noDupes.count(i)] return noDupes |
m = MATCHER_IMG.search(data) self._img_urls.append(m.group(1)) m = MATCHER_SHOW.search(data) | m = MATCHER_TAG.search(data) self._img_urls.append(m.group(2)) | def _upload(self, image): self._curl.setopt(pycurl.HTTPHEADER, ['Expect:']) self.post('http://imageshack.us/', [ ('fileupload', (pycurl.FORM_FILE, image)), ('uploadtype', 'on'), ('refer', 'http://www.imageshack.us/'), ('brand', ''), ('email', ''), ('MAX_FILE_SIZE', '13145728'), ('optsize', '320x320'), ('url', 'paste im... |
community this will not be what you want. | community the default behaviour is not what you want. | def __init__(self, cmap=None, inputFile=None, N_nodes=None): """Create node cover from data. |
def create_commIDs(self): | def getCommIDs(self): | def create_commIDs(self): """Construct commIDs. |
cID_A = create_commIDs(self) cID_B = create_commIDs(other) | cID_A = self.getCommIDs() cID_B = other.getCommIDs() | def _getOverlapNetwork(self, other): """Create a bipartite network from overlapping nodes. |
if src>=nNodes: | while nNodes<=src or nNodes<=dest: | def _setEdge(self,src,dest,val): nNodes=len(self._nodeList) if src>=nNodes: self._addNode() if dest>=nNodes: self._addNode() if val==0: try: del self._nodeList[src][dest,0] except KeyError: pass try: del self._nodeList[dest][src,0] except KeyError: pass else: self._nodeList[src][dest,0]=val self._nodeList[dest][src,0]=... |
if dest>=nNodes: self._addNode() | nNodes+=1 | def _setEdge(self,src,dest,val): nNodes=len(self._nodeList) if src>=nNodes: self._addNode() if dest>=nNodes: self._addNode() if val==0: try: del self._nodeList[src][dest,0] except KeyError: pass try: del self._nodeList[dest][src,0] except KeyError: pass else: self._nodeList[src][dest,0]=val self._nodeList[dest][src,0]=... |
axes.annotate(showthislabel,(xy[node][0]+nodeLabel_xOffset,xy[node][1]), | axes.annotate(showthislabel,(xy[node][0],xy[node][1]), textcoords='offset points', xytext=(nodeLabel_xOffset, 0), | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, equalshape=True, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeShape='o', nodeEdgeColor='k', nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, nodeShapes=None, bgcolor='white', maxwidth=2.0, minwidth=0.... |
""" Finds connected components of a network. | """Get connected components of a network NOTE! This method currently discards nodes with no edges (proper behaviour would be to turn them into components, so this should be fixed). | def getComponents(net): """ Finds connected components of a network. Parameters ---------- net : A network object Returns ------- Connected components as a NodePartition object. """ edges=net.edges ee=EvaluationList(edges) ee.setLastEvaluation() p=Percolator(ee,buildNet=False) for cs in p: return cs |
for neigh in self[nodeName]: self[node,neigh]=0 self[neigh,node]=0 | for neigh in list(self[nodeName]): self[nodeName,neigh]=0 self[neigh,nodeName]=0 | def _removeNodeEdges(self,nodeName): for neigh in self[nodeName]: self[node,neigh]=0 self[neigh,node]=0 |
self.result=[self.Nclones,self.clones,self.keeptheserows,self.m] | self.result=[self.Nclones,self.clones,self.keeptheserows,self.m,self.msdata] | def applyme(self): |
for i in xdict: if i!=None: for j in ydict: if j!=None: dist += float(i-j)**2*xdict[i]/NElementsX*ydict[j]/NElementsY distList.append(dist) return sum(distList)/self.getNumberofLoci() | if NElementsX!=0 and NElementsY!=0: for i in xdict: if i!=None: for j in ydict: if j!=None: dist += float(i-j)**2*xdict[i]/NElementsX*ydict[j]/NElementsY distList.append(dist) return sum(distList)/len(distList) | def getGroupwiseDistance_Goldstein(self,x,y): """ Returns the goldstein distance between two populations |
Example ------- >>> ms=eden.MicrosatelliteData(open("../data/microsatellites/microsatellites.txt",'r')) >>> ms_u = ms.getUniqueSubset() >>> ms_u.getGroupwiseDistance_Goldstein([1,2,3,4],[1,2,3,4]) == 1330.5 True | def getGroupwiseDistance_Goldstein(self,x,y): """ Returns the goldstein distance between two populations | |
for i in xdict: for j in ydict: dist += 1.0*(i-j)**2*xdict[i]/(len(x))*ydict[j]/(len(y))/self.getNumberofLoci() distList.append(dist) return sum(distList) | NElementsX=float(sum(xdict.itervalues())-xdict.get(None,0)) NElementsY=float(sum(ydict.itervalues())-ydict.get(None,0)) if NElementsX!=0 and NElementsY!=0: for i in xdict: if i!=None: for j in ydict: if j!=None: dist += float(i-j)**2*xdict[i]/NElementsX*ydict[j]/NElementsY distList.append(dist) return sum(distList)/l... | def getGroupwiseDistance_Goldstein(self,x,y): """ Returns the goldstein distance between two populations |
matrix / network using the formula W = 1 - D / max(D). | matrix / network using the formula W = 1 - D / max(D)+epsilon. | def dist_to_weights(net,epsilon=0.001): '''Transforms a distance matrix / network to a weight matrix / network using the formula W = 1 - D / max(D). Returns a matrix/network''' N=len(net._nodes) if (isinstance(net,pynet.SymmFullNet)): newmat=pynet.SymmFullNet(N) else: newmat=pynet.SymmNet() edges=list(net.edges) ma... |
maxd=maxd+epsilon | def dist_to_weights(net,epsilon=0.001): '''Transforms a distance matrix / network to a weight matrix / network using the formula W = 1 - D / max(D). Returns a matrix/network''' N=len(net._nodes) if (isinstance(net,pynet.SymmFullNet)): newmat=pynet.SymmFullNet(N) else: newmat=pynet.SymmNet() edges=list(net.edges) ma... | |
newmat[edge[0]][edge[1]]=1-edge[2]/maxd | newmat[edge[0]][edge[1]]=1-edge[2]/maxd+epsilon | def dist_to_weights(net,epsilon=0.001): '''Transforms a distance matrix / network to a weight matrix / network using the formula W = 1 - D / max(D). Returns a matrix/network''' N=len(net._nodes) if (isinstance(net,pynet.SymmFullNet)): newmat=pynet.SymmFullNet(N) else: newmat=pynet.SymmNet() edges=list(net.edges) ma... |
max_node_diameter = max(node_diameters.values()) y_coords = sorted(map(operator.itemgetter(1), coords.values())) x_coords = sorted(map(operator.itemgetter(0), coords.values())) ax_pos = axes.get_position() x_span = x_coords[-1] - x_coords[0] y_span = y_coords[-1] - y_coords[0] ax_width_inches = ax_pos.width*axes.get_fi... | if scaling: max_node_diameter = max(node_diameters.values()) y_coords = sorted(map(operator.itemgetter(1), coords.values())) x_coords = sorted(map(operator.itemgetter(0), coords.values())) ax_pos = axes.get_position() x_span = x_coords[-1] - x_coords[0] y_span = y_coords[-1] - y_coords[0] ax_width_inches = ax_pos.... | def draw_node(axes, x, y, shape, color, size, edgecolor, edgewidth, zorder): axes.plot([x], [y], shape, markerfacecolor=color, markeredgecolor=edgecolor, markeredgewidth=edgewidth, markersize=size, zorder=zorder) |
axes.set_autoscale_on(prev_autoscale) | def draw_node(axes, x, y, shape, color, size, edgecolor, edgewidth, zorder): axes.plot([x], [y], shape, markerfacecolor=color, markeredgecolor=edgecolor, markeredgewidth=edgewidth, markersize=size, zorder=zorder) | |
return self.totalDeg(nodeIndex) | return self._totalDeg(nodeIndex) | def _degIndex(self,nodeIndex): return self.totalDeg(nodeIndex) |
runTests() | test_pynet() | def test_pynet(): suite = unittest.TestSuite() #symmetric tests: suite.addTest(TestPynet("test_basic_symm_ScipySparseSymmNet")) suite.addTest(TestPynet("test_basic_symm_NumpyFullSymmNet")) suite.addTest(TestPynet("test_basic_symm_LCELibSparseSymmNet")) #dir tests: suite.addTest(TestPynet("test_basic_dir_ScipySparseDir... |
normalizedValue = normalizeValue(value,valueLimits) color = colorMap(normalizedValue) | normalizedValue = normalizeValue(value,valueLimits) print " ",normalizedValue color = colorMap(normalizedValue) | def setColor(value,valueLimits,colorMap): """Converts a numerical value to a color. The value is scaled linearly to the range (0...1) using the function normalizeValue and the limits valueLimits. This scaled value is used to pick a color from the given colormap. The colormap should take in values in the range (0...1) ... |
axes : matplotlib.axes object (default: None) If given, the network will be drawn in this axis. Otherwise a separate figure is created (which you then have to give as an argument to the pylab.FigureCanvasBase method be able to plot it.) Note that if `baseFig` is also give this parameter has no effect. | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, equalshape=True, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeShape='o', nodeEdgeColor='k', nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, nodeShapes=None, bgcolor='white', maxwidth=2.0, minwidth=0.... | |
if axes is None: axes = thisfigure.add_subplot(111) | axes = thisfigure.add_subplot(111) | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, equalshape=True, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeShape='o', nodeEdgeColor='k', nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, nodeShapes=None, bgcolor='white', maxwidth=2.0, minwidth=0.... |
cm = get_cmap() cm._segmentdata={ | cm={ | def getConstantColorMap(rgb=(0,0,0)): """Return a colormap with constant color. Parameters ---------- rgb : tuple (r, g, b) The color as RGB tuple. Each value must be between 0 and 1. Return ------ cm : colorMap The colormap that has just one constant color. """ cm = get_cmap() cm._segmentdata={ 'red': ( (0,rgb[0],r... |
return cm | return matplotlib.colors.LinearSegmentedColormap("constant colormap",cm) | def getConstantColorMap(rgb=(0,0,0)): """Return a colormap with constant color. Parameters ---------- rgb : tuple (r, g, b) The color as RGB tuple. Each value must be between 0 and 1. Return ------ cm : colorMap The colormap that has just one constant color. """ cm = get_cmap() cm._segmentdata={ 'red': ( (0,rgb[0],r... |
if colorMap=='primary': myMap=get_cmap() myMap._segmentdata={ 'red': ( (0,1,1), (0.5,0,0), (1,1,1) ), 'green': ( (0,1,1), (0.5,0.5,0.5), (1,0,0) ), 'blue': ( (0,0,0), (0.5,1,1), (1,0,0) ), } elif colorMap=='orange': myMap=get_cmap() myMap._segmentdata = { 'red' : ( (0.,.99,.99), (0.2,.98,.98), (0.4,.99,.99), (0.6,... | known_colormaps = ('primary', 'orange', 'bluered') if colorMap in known_colormaps: if colorMap == 'primary': segmentdata={'red': ( (0,1,1),(0.5,0,0), (1,1,1) ), 'green': ( (0,1,1), (0.5,0.5,0.5), (1,0,0) ), 'blue': ( (0,0,0), (0.5,1,1), (1,0,0) )} elif colorMap=='orange': segmentdata = { 'red' : ( (0.,.99,.99), (0.... | def setColorMap(colorMap): """Set a colormap for edges. Two options of our own ('orange' and 'primary') are available in addition to the 150 pylab readymade colormaps (which can be listed with help matplotlib.cm ). Usage: myMap = setColorMap('bone') """ if hasattr(colorMap, '_segmentdata'): return colorMap if colorM... |
if valueLimits[0] != valueLimits[1]: | if valueLimits[0] < valueLimits[1]: | def setColor(value,valueLimits,colorMap): """Converts a numerical value to a color. The value is scaled linearly to the range (0...1) using the function normalizeValue and the limits valueLimits. This scaled value is used to pick a color from the given colormap. The colormap should take in values in the range (0...1) ... |
minwidth=0.2, uselabels='none', edgeColorMap='winter', | minwidth=0.2, uselabels='some', edgeColorMap='winter', | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... |
uselabels : str, either 'none' or 'all' If 'all', the node index is shown as label for those nodes that are not listed in `labels`. | uselabels : either 'some' (default), 'none' or 'all' If 'some', the label is shown for the nodes whose label is given in `labels`. If 'all', the node index is shown also for those nodes that are not listed in `labels`. If 'none', no node labels are printed. | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... |
node_edgecolor='w' | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... | |
node_edgecolor='k' | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... | |
color=color, size=nodesize,edgecolor=node_edgecolor) if not (uselabels=='none'): if uselabels == 'all': axes.annotate(str(node),(xy[node][0]+nodeLabel_xOffset,xy[node][1]), | color=color, size=nodesize, edgecolor=nodeEdgeColor) if node in labels or uselabels == 'all': if node in labels: if isinstance(labels[node],float): showthislabel="%2.2f" % labels[node] else: showthislabel=labels[node] else: showthislabel = str(node) axes.annotate(showthislabel,(xy[node][0]+nodeLabel_xOffset,xy[node][... | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... |
elif node in labels: if isinstance(labels[node],float): showthislabel="%2.2f" % labels[node] else: showthislabel=labels[node] axes.annotate(showthislabel,(xy[node][0]+nodeLabel_xOffset,xy[node][1]),color=fontcolor,size=fontsize) | def VisualizeNet(net, xy, figsize=(6,6), coloredNodes=True, equalsize=False, labels=None, fontsize=7, showAllNodes=True, nodeColor=None, nodeSize=1.0, minnode=2.0, maxnode=6.0, nodeColors=None, nodeSizes=None, bgcolor='white', maxwidth=2.0, minwidth=0.2, uselabels='none', edgeColorMap='winter', weightLimits=None, setNo... | |
for nodeIndex in self.net: lenght+=len(self.net[nodeIndex].edges) | def __len__(self): lenght=0 for nodeIndex in self.net: lenght+=len(self.net[nodeIndex].edges) if self.net.isSymmetric(): return lenght/2 else: return lenght | |
self.tree[thisLevel][communityIndex]=fatherIndex self.net[self._getNameByNode((thisLevel,communityIndex)),self._getNameByNode((thisLevel-1,fatherIndex))]=len(cslist)+1-thisLevel break | bestFatherIndex=fatherIndex self.tree[thisLevel][communityIndex]=bestFatherIndex self.net[self._getNameByNode((thisLevel,communityIndex)),self._getNameByNode((thisLevel-1,bestFatherIndex))]=len(cslist)+1-thisLevel | def __init__(self,cslist): cslist.reverse() self.tree=[] self.cslist=cslist self.tree.append([]) |
order=[(0,0)] | order=map(lambda x:(0,x),range(len(self.tree[0]))) | def _getLeafOrderInTree(self): order=[(0,0)] for level in range(1,len(self.tree)): replace={} for i in range(0,len(self.tree[level])): father=(level-1,self.tree[level][i]) if father in replace: replace[father]+=[(level,i)] else: replace[father]=[(level,i)] for father in replace.keys(): fi=order.index(father) order=orde... |
for j,jName in enumerate(nodeNames[i+1:]): | for j in range(i+1,numberOfSpecimens): jName=nodeNames[j] | def getDistanceMatrix(self,distance="lm",nodeNames=None): """ Computes the distance between each node and returns the corresponding distance matrix. """ if distance=="lm": getMSDistance=self.getMSDistance_linearManhattan elif distance=="nsa": getMSDistance=self.getMSDistance_nonsharedAlleles elif distance=="ap": getMSD... |
return self.getCommunitySizes()[0] | communitySizes=self.getCommunitySizes() if len(communitySizes)>0: return communitySizes[0] else: return 0 | def getGiantSize(self): """Get the size of the largest component. """ return self.getCommunitySizes()[0] |
If False, the frame and axis will be not be shown in the plot. | If False, the frame will be not be shown in the plot. You can still use axis labels. | def visualizeNet(net, coords=None, axes=None, frame=False, nodeShapes=None, defaultNodeShape='o', nodeColors=None, defaultNodeColor=None, nodeEdgeColors=None, defaultNodeEdgeColor='black', edgeColors=None, defaultEdgeColor=None, nodeSizes=None, defaultNodeSize=None, edgeWidths=None, defaultEdgeWidth=None, nodeEdgeWidth... |
axes.set_axis_off() | axes.set_frame_on(False) axes.set_xticklabels([]) axes.xaxis.set_ticks_position('none') axes.set_yticklabels([]) axes.yaxis.set_ticks_position('none') | def draw_node(axes, x, y, shape, color, size, edgecolor, edgewidth, zorder): axes.plot([x], [y], shape, markerfacecolor=color, markeredgecolor=edgecolor, markeredgewidth=edgewidth, markersize=size, zorder=zorder) |
yield self.node.net[self.node.index,index] | yield self.node.net[self.node.name,index] | def __iter__(self): for index in self.node: yield self.node.net[self.node.index,index] |
kcliqueList=kcliquesWeight(net,k,lambda x:getIntensity(x,net)) | kcliqueList=kcliquesWeight(net,k,getIntensity) | def kcliquePercolator(net,k,start,stop,evaluations,reverse=False,weightFunction=None): if weightFunction==None: edges=list(net.edges) edges.sort(lambda x, y: cmp(x[2],y[2]),reverse=reverse) edgesAndEvaluations=EvaluationList(edges) edgesAndEvaluations.setLinearEvaluations(start,stop,evaluations) kcliques=kcliquesByEdge... |
newNet = pynet.Net() | newNet = net.__class__() | def collapseIndices(net,returnIndexMap=False): """ Chances the indices of net to run from 0 to len(net)-1 """ newNet = pynet.Net() indexmap = {} index = 0 for i in net: if net[i].deg() != 0: indexmap[i] = index; index += 1 for i in net: for j in net[i]: if net[j][i] != 0: newNet[indexmap[i]][indexmap[j]] = net[i][j]... |
if net[i].deg() != 0: indexmap[i] = index; index += 1 for i in net: for j in net[i]: if net[j][i] != 0: newNet[indexmap[i]][indexmap[j]] = net[i][j] newNet[indexmap[j]][indexmap[i]] = net[j][i] | newNet.addNode(index) indexmap[i] = index; index += 1 for edge in net.edges: i,j,w=edge newNet[indexmap[i]][indexmap[j]] = w | def collapseIndices(net,returnIndexMap=False): """ Chances the indices of net to run from 0 to len(net)-1 """ newNet = pynet.Net() indexmap = {} index = 0 for i in net: if net[i].deg() != 0: indexmap[i] = index; index += 1 for i in net: for j in net[i]: if net[j][i] != 0: newNet[indexmap[i]][indexmap[j]] = net[i][j]... |
class SliderDialog(MySimpleDialog): | class SliderDialog2(MySimpleDialog): | def applyme(self): self.result=[self.scale_1.get(),self.e1.get()] |
return self._totalDeg(nodeIndex) | return self._totalDeg[nodeIndex] | def _degIndex(self,nodeIndex): return self._totalDeg(nodeIndex) |
edgesAndEvaluations=EvaluationList(edges,evaluations,evaluationType) | edgesAndEvaluations=EvaluationList(edges,evaluations=evaluations,evaluationType=evaluationType) | def cliquePercolator(net,k,evaluations,weightFunction="minweight",evaluationType="fraclist",reverse=False): """ Weighted and unweighted clique percolation with sequential clique percolation algorithm. Parameters ---------- net : Network object k : Size of the clique to be used. evaluations : The evaluation data. weigh... |
kcliques=EvaluationList(kcliqueList,evaluations,evaluationType,weightFunction=lambda x:getIntensity(x,net)) | kcliques=EvaluationList(kcliqueList,evaluations=evaluations,evaluationType=evaluationType,weightFunction=lambda x:getIntensity(x,net)) | def cliquePercolator(net,k,evaluations,weightFunction="minweight",evaluationType="fraclist",reverse=False): """ Weighted and unweighted clique percolation with sequential clique percolation algorithm. Parameters ---------- net : Network object k : Size of the clique to be used. evaluations : The evaluation data. weigh... |
return self._indexToNameIter(self.net._iterNodeIn(self.net._nodes[name])) | return self._indexToNameIter(self.net._iterNodeIn(self.net._nodes[self.name])) | def iterIn(self): if not self.name in self.net: raise KeyError, "Node not in the network." #name -> index -> backend iterator -> index -> name return self._indexToNameIter(self.net._iterNodeIn(self.net._nodes[name])) |
return self._indexToNameIter(self.net._iterNodeOut(self.net._nodes[name])) | return self._indexToNameIter(self.net._iterNodeOut(self.net._nodes[self.name])) | def iterOut(self): if not self.name in self.net: raise KeyError, "Node not in the network." #name -> index -> backend iterator -> index -> name return self._indexToNameIter(self.net._iterNodeOut(self.net._nodes[name])) |
for neigh in self._nodeList[nodeIndex]: yield neigh | for neigh in self._nodeList[nodeIndex].iterkeys(): yield neigh[0] | def _iterNode(self,nodeIndex): #First iter through all outgoing neighbors: for neigh in self._nodeList[nodeIndex]: yield neigh #Then iter through only incoming neighbors for neigh in self._backNodeList[nodeIndex]: if not (neigh,0) in self._nodeList[nodeIndex]: yield neigh |
for neigh in self._backNodeList[nodeIndex]: if not (neigh,0) in self._nodeList[nodeIndex]: yield neigh | for neigh in self._backNodeList[nodeIndex].iterkeys(): if not neigh in self._nodeList[nodeIndex]: yield neigh[0] | def _iterNode(self,nodeIndex): #First iter through all outgoing neighbors: for neigh in self._nodeList[nodeIndex]: yield neigh #Then iter through only incoming neighbors for neigh in self._backNodeList[nodeIndex]: if not (neigh,0) in self._nodeList[nodeIndex]: yield neigh |
def getNumberOfLines(filename,nfields): | def getNumberOfLines(input,nfields): | def getNumberOfLines(filename,nfields): """ Returns length of the given file in lines. Throws IOError if the file does not exist. """ theFile=open(filename,'rU') i=0 for line in theFile: fields=line.split(splitterChar) if len(fields)!=nfields: f.close() raise Exception("Invalid number of fields on row: "+str(i+1)) i+=1... |
theFile=open(filename,'rU') | if isinstance(input, str): theFile = open(input, 'rU') else: theFile = input | def getNumberOfLines(filename,nfields): """ Returns length of the given file in lines. Throws IOError if the file does not exist. """ theFile=open(filename,'rU') i=0 for line in theFile: fields=line.split(splitterChar) if len(fields)!=nfields: f.close() raise Exception("Invalid number of fields on row: "+str(i+1)) i+=1... |
def checkNodes(filename,net,fieldNames,hasHeader,splitterChar): | def checkNodes(input,net,fieldNames,hasHeader,splitterChar): | def checkNodes(filename,net,fieldNames,hasHeader,splitterChar): """ Returns ------- A tuple where: The first element is True if each node in a network is in the property file, and otherwise False The second element is True if each node in the property file is in the network, and otherwise False """ |
f=open(filename,'rU') | def checkNodes(filename,net,fieldNames,hasHeader,splitterChar): """ Returns ------- A tuple where: The first element is True if each node in a network is in the property file, and otherwise False The second element is True if each node in the property file is in the network, and otherwise False """ | |
fileHasAllNodes,netHasAllNodes=checkNodes(filename,net,fieldNames,propertyNames==None,splitterChar) | fileHasAllNodes,netHasAllNodes=checkNodes(input,net,fieldNames,propertyNames==None,splitterChar) | def addProperty(net,node,propertyName,theString): if isanum(theString): # if it is a number net.nodeProperty[propertyName][node]=float(theString) if isint(theString): # if it is integer net.nodeProperty[propertyName][node]=int(theString) else: # if it is a string net.nodeProperty[propertyName][node]=theString |
nPropertyLines=getNumberOfLines(filename,nfields) | nPropertyLines=getNumberOfLines(input,nfields) | def addProperty(net,node,propertyName,theString): if isanum(theString): # if it is a number net.nodeProperty[propertyName][node]=float(theString) if isint(theString): # if it is integer net.nodeProperty[propertyName][node]=int(theString) else: # if it is a string net.nodeProperty[propertyName][node]=theString |
self._alleles[i/2].append(None) | self._alleles[i/2].append((None,fields[i])) | def __init__(self,input,missingValue="999999"): """ The microsatellite data must be given as a input where each row has microsatellites for one node/specimen. Alleles should be given as integer numbers representing the number of repetitions. The data should have even number of columns where each pair represents two hom... |
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