def __init__(self, A_f, numLevels, theta=0.25, verb=0, graph=False):
timer = Timer('AMG setup')
self.seqA = [None]*numLevels
self.updates = [None]*numLevels
self.downdates = [None]*numLevels
self.seqA[numLevels-1] = A_f
tab1 = Tab()
tab2 = Tab()
for i in reversed(range(numLevels-1)):
Debug.msg1(verb, '-------------------------------------------------------------')
Debug.msg1(verb, tab1, 'coarsening level %d to level %d' % (i+1,i))
np.set_printoptions(threshold=np.inf)
Debug.msg4(verb, tab2, 'operator is A[%d]\n' % i, self.seqA[i+1].tolil())
C = coarsen(self.seqA[i+1], theta = theta, verb=verb)
Debug.msg2(verb, tab2, '#vertices: %d' % len(C))
if graph:
matrixGraph(self.seqA[i+1], C, name='graph-%d.gv' % i)
Debug.msg1(verb, tab1, 'making update operator: level %d to level %d' % (i+1,i))
I_up = smoothUpdate(self.seqA[i+1], C, verb)
Debug.msg1(verb, tab1, 'making downdate operator: level %d to level %d' % (i,i+1))
I_down = makeDowndate(I_up, verb)
self.updates[i] = I_up
self.downdates[i] = I_down
self.seqA[i] = self.downdates[i]*(self.seqA[i+1]*self.updates[i])
def setUpClass(self):
username = os.getenv(constants.USERNAME, "")
password = os.getenv(constants.PASSWORD, "")
"""Start web browser"""
self._browser = Tab()
self._browser.login_on_page(constants.DERA_SCM_URL, username, password)
def __init__(self, nb):
Tab.__init__(self, nb)
self.project_list = wx.ListCtrl(self, -1, style=wx.LC_REPORT, size=(700, 400))
self.project_list.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self._load_project)
self._il = wx.ImageList(16,16)
self._il.Add(bitmaps.fetch_icon_bitmap("actions", "agt_action_success", scale=(16,16)))
self.project_list.SetImageList(self._il, wx.IMAGE_LIST_SMALL)
titles = ['', 'Title', '# Jobs', 'Last Action']
sizes = [20,400, 100,140]
for i,t in enumerate(titles):
self.project_list.InsertColumn(i, t)
self.project_list.SetColumnWidth(i, sizes[i])
self.sidebar = wx.BoxSizer(wx.VERTICAL)
new = metallicbutton.MetallicButton(self, -1, 'New', '', bitmaps.fetch_icon_bitmap("actions", "folder_new"), size=(120,40))
delete = metallicbutton.MetallicButton(self, -1, 'Delete', '', bitmaps.fetch_icon_bitmap("actions", "fileclose"), size=(120,40))
load = metallicbutton.MetallicButton(self, -1, 'Load', '', bitmaps.fetch_icon_bitmap("actions", "folder"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._new_project, new)
self.Bind(wx.EVT_BUTTON, self._load_project, load)
self.Bind(wx.EVT_BUTTON, self._delete_project, delete)
self.sidebar.Add(new, 0, wx.EXPAND|wx.ALL, 5)
self.sidebar.Add(load, 0, wx.EXPAND|wx.ALL, 5)
self.sidebar.Add(delete, 0, wx.EXPAND|wx.ALL, 5)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.project_list, 0, wx.EXPAND | wx.ALL, 5)
self.sizer.Add(self.sidebar, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizer(self.sizer)
def render_graphs(self):
# If MDF loaded iterate through tabs and render each plot onto their graphs.
if self.mdf_extracted != None:
# Delete old tab wigets. Redraw leads to ugly behavior.
for i in reversed(range(self.tabs.count())):
self.tabs.removeTab(i)
new_tabs = []
# Create new tab widgets, add to new tab list.
for tab_obj in self.tab_list:
newTab = Tab(tab_obj.get_title(), self.play_slider)
for plot in tab_obj.get_plots():
group = plot[0]
signal = plot[1]
try:
mdf_obj = self.channel_dict[group][signal]
if mdf_obj is not None:
newTab.add_plot(group, signal, mdf_obj.timestamps,
mdf_obj.samples, mdf_obj.unit)
except Exception:
newTab.add_plot(group, signal)
self.tabs.addTab(newTab.get_tab_widget(), newTab.get_title())
new_tabs.append(newTab)
newTab.render_multiplot()
# Replace old tab list with new and redraw features.
self.tab_list.clear()
self.tab_list = new_tabs
self.redraw_slider()
def __init__(self, nb):
Tab.__init__(self, nb)
Refinement.set_proot(self.s.proot)
# plot
self.dpi = 100
self.fig = Figure((5.0, 4.0), dpi=self.dpi)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.115,0.17,0.80,0.79])
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.ax2 = self.ax1.twinx()
self.ax2.set_position([0.115,0.17,0.80,0.79])
self._clear_figure()
# stats
self.stats_sizer = wx.FlexGridSizer(cols=2, rows=9, hgap=5, vgap=5)
self._labels = [
wx.StaticText(self, -1, 'Title'),
wx.StaticText(self, -1, 'Status'),
wx.StaticText(self, -1, 'Cycle'),
wx.StaticText(self, -1, 'Resolution (A)'),
wx.StaticText(self, -1, 'R-work (%)'),
wx.StaticText(self, -1, 'R-free (%)'),
wx.StaticText(self, -1, '# of Reflections'),
wx.StaticText(self, -1, 'Parameters'),
wx.StaticText(self, -1, 'Data:Parameter')
]
self._labels[0].Wrap(200)
self._values = [ wx.StaticText(self, -1, '') for x in range(len(self._labels)) ]
rows = [1,2,3,4,6]
for i in range(len(self._labels)):
self.stats_sizer.Add(self._labels[i], 0, wx.EXPAND|wx.TOP, i in rows and 15 or 5)
self.stats_sizer.Add(self._values[i], 0, wx.EXPAND|wx.TOP, i in rows and 15 or 5)
self.vbox = wx.BoxSizer(wx.VERTICAL)
self.vbox.Add(self.stats_sizer, 0, wx.ALL, 10)
self.button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.vbox.Add(self.button_sizer, 0, wx.EXPAND|wx.CENTER, 10)
self.hbox = wx.BoxSizer(wx.HORIZONTAL)
self.hbox.Add(self.vbox, 1, wx.EXPAND|wx.ALL, 10)
self.hbox.Add(self.canvas, 4, wx.EXPAND|wx.ALL, 10)
self.SetSizer(self.hbox)
self.hbox.Fit(self)
self._refinement = None
def populate(self, categories_list):
self.favorites_tab = FavoriteTab(self.notebook, self,
self.favorites_image)
self.expired_tab = ExpiredTab(self.notebook, self, self.expired_image,
self.favorites_tab)
self.favorites_tab.set_expired_tab(self.expired_tab)
for i in range(len(categories_list)):
new_tab = Tab(self.notebook, categories_list[i], self,
self.favorites_tab, self.expired_tab)
new_tab.populate_tab()
self.tabs_list.append(new_tab)
def __init__(self, window):
self.databaseWindow = window
store = Gtk.TreeStore(str)
Tab.__init__(self, store)
renderer = Gtk.CellRendererText()
column = Gtk.TreeViewColumn("Name", renderer, text=0)
column.set_resizable(True)
column.set_expand(True)
self.tree.append_column(column)
def generateTab(self):
self.error_window = QtWidgets.QErrorMessage()
error_count = 0
message = ""
tab_idx = -1
# Check empty fields.
if self.title.text() == "":
error_count += 1
message += "ERROR {}: You must enter a title.".format(error_count)
if len(self.added_dict) == 0:
error_count += 1
message += "ERROR {}: You must apply at least one signal.".format(
error_count)
# Check if tab name unique. If no check if intent is to edit,
if self.title.text() in [
tab.get_title() for tab in self.main.tab_list
]:
if self.edit == True:
tab_idx = [
idx if self.title.text() == tab.get_title() else -1
for idx, tab in enumerate(self.main.tab_list)
]
tab_idx = tab_idx[0]
else:
error_count += 1
message += "ERROR {}: Tab title \"{}\" is already taken.".format(
error_count, self.title.text())
# If errors then present else add tab to main window and close.
if error_count > 0:
self.error_window.showMessage(message)
else:
newTab = Tab(self.title.text(), self.main.play_slider)
newTab.add_plots(self.added_dict)
newTab.render_multiplot()
# If editing delete old tab and replace with new at same index. Else append.
if tab_idx != -1:
self.main.tabs.removeTab(tab_idx)
self.main.tabs.insertTab(tab_idx, newTab.get_tab_widget(),
newTab.get_title())
self.main.tab_list.pop(tab_idx)
self.main.tab_list.insert(tab_idx, newTab)
else:
self.main.tabs.addTab(newTab.get_tab_widget(),
newTab.get_title())
self.main.tab_list.append(newTab)
self.main.render_graphs()
self.close()
def LoadWorkspace(self):
# On "Import Workspace" load JSON and generate tab objects in tab_list.
file_path = QtWidgets.QFileDialog.getOpenFileName(
self, 'Import Workspace',
os.getcwd() + "/" + self.workspace_file, "JSON (*.json)")
try:
with open(file_path[0]) as fd:
# Remove any old tabs. Clean slate.
for i in reversed(range(self.tabs.count())):
self.tabs.removeTab(i)
self.tab_list.clear()
# Generate new tabs.
tab_data = json.load(fd)
for tab, groups in tab_data.items():
new_tab = Tab(tab, self.play_slider)
new_tab.add_plots(groups)
new_tab.render_multiplot()
self.tabs.addTab(new_tab.get_tab_widget(),
new_tab.get_title())
self.tab_list.append(new_tab)
self.workspace_file = os.path.split(file_path[0])[1]
except Exception:
pass
# Display data immediately upon upload if MDF already uploaded.
self.render_graphs()
def addNewTab(self, modus, tabData=None):
"""adds new tab"""
if (tabData is None):
tab = Tab(
modus,
QtCore.QCoreApplication.translate("MainWindow", "Neuer Tab"))
self.tabWidget.insertTab(
self.tabWidget.count() - 1, tab,
QtCore.QCoreApplication.translate("MainWindow", "Neuer Tab"))
else:
tab = Tab(modus, tabData.name, tabData)
self.tabWidget.insertTab(
self.tabWidget.count() - 1, tab,
QtCore.QCoreApplication.translate("MainWindow", tabData.name))
self.tabWidget.setCurrentIndex(self.tabWidget.count() - 2)
def __init__(self, nb):
Tab.__init__(self, nb)
Holder.set_finished_callback(self._job_finished)
self._tabs = wx.aui.AuiNotebook(self, -1, size=(700,750))
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self._tabs, 1 , wx.EXPAND)
self.SetSizer(self.main)
self._auto_manager = AutoProcessManager()
AutoProcess.set_start_refinement(self.start_new_refinement)
self._running = 0
def __init__(self, windowDatabase):
self.windowDatabase = windowDatabase
store = Gtk.ListStore(int, str, str)
Tab.__init__(self, store)
for i, value in enumerate(itemModel):
renderer = Gtk.CellRendererText()
if value != "ID":
renderer.set_property("editable", True)
renderer.connect("edited", self.editRenderer, value)
column = Gtk.TreeViewColumn(value, renderer, text=i)
column.set_resizable(True)
column.set_expand(True)
self.tree.append_column(column)
self.itemCapacities = list()
def __init__(self, nb):
Tab.__init__(self, nb)
self._tabs = wx.aui.AuiNotebook(self, -1, style=wx.NB_TOP, size=(850,750))
self.sheet1 = Projects(self._tabs)
self.sheet2 = Jobs(self._tabs)
self._tabs.AddPage(self.sheet1, "Projects")
self._tabs.AddPage(self.sheet2, "Job List")
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self._tabs, 1, wx.EXPAND)
self.SetSizer(self.main)
def __init__(self, nb):
Tab.__init__(self, nb)
#Process.set_finished_callback(self.refinement_finished)
self._tabs = wx.aui.AuiNotebook(self, -1, style=wx.NB_TOP, size=(850,750))
self._tab_list = []
self._stats = Process(self)
self._stats.set_finished_callback(self.refinement_finished)
self._tabs.AddPage(self._stats, 'Refinement')
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self._tabs, 1, wx.EXPAND)
self.SetSizer(self.sizer)
def dup_tab(self):
t = Tab.create(self, self.gettab().path())
if t:
self.tablist.append(t)
self.curtab = len(self.tablist) - 1
self.UI.draw()
return True
def __init__(self, nb):
Tab.__init__(self, nb)
self.job_list = wx.ListCtrl(self, -1, style=wx.LC_REPORT|wx.LC_SINGLE_SEL, size=(700, 400))
self.job_list.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self._load_job)
titles = ['ID', 'Date', 'Title', 'Type', 'Status', 'R']
sizes = [65,135,225,130,80,60]
for i,t in enumerate(titles):
self.job_list.InsertColumn(i, t, width=sizes[i])
new = metallicbutton.MetallicButton(self, -1, 'New', '', bitmaps.fetch_icon_bitmap("actions", "window_new"), size=(120,40))
load = metallicbutton.MetallicButton(self, -1, 'Load', '', bitmaps.fetch_icon_bitmap("actions", "fileopen"), size=(120,40))
delete = metallicbutton.MetallicButton(self, -1, 'Delete', '', bitmaps.fetch_icon_bitmap("actions", "fileclose"), size=(120,40))
sum = metallicbutton.MetallicButton(self, -1, 'Summary', '', bitmaps.fetch_icon_bitmap("actions", "info"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._new_job, new)
self.Bind(wx.EVT_BUTTON, self._load_job, load)
self.Bind(wx.EVT_BUTTON, self._delete_job, delete)
self.Bind(wx.EVT_BUTTON, self._show_summary, sum)
import_cif = metallicbutton.MetallicButton(self, -1, 'Import HKL', '', icons.hkl_file.GetBitmap(), size=(120,40))
import_pdb = metallicbutton.MetallicButton(self, -1, 'Import PDB', '', icons.pdb_file.GetBitmap(), size=(120,40))
rcsb_dl = metallicbutton.MetallicButton(self, -1, 'RCSB PDB', '', bitmaps.fetch_icon_bitmap("actions", "down"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._import_pbd, import_pdb)
self.Bind(wx.EVT_BUTTON, self._import_cif, import_cif)
self.Bind(wx.EVT_BUTTON, self._download_files, rcsb_dl)
self.sidebar = wx.BoxSizer(wx.VERTICAL)
self.sidebar.Add(new, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(load, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(sum, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(delete, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.AddSpacer(20)
self.sidebar.Add(import_cif, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(import_pdb, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.AddSpacer(10)
self.sidebar.Add(rcsb_dl, 0, wx.EXPAND | wx.ALL, 5)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.job_list, 0, wx.EXPAND|wx.ALL, 5)
self.main.Add(self.sidebar, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
def describe(self):
tab0 = Tab()
tab1 = Tab()
print(tab0, '=' * 60)
print(tab0, 'Newton-Krylov solver')
print(tab1, 'Max iters: ', self.maxIters)
print(
tab1,
'Tolerance: tau_r=%12.5g, tau_a=%12.5g' % (self.tau_r, self.tau_a))
print(tab1, 'Verbosity: ', self.verb)
print(
tab1, 'Newton-Krylov tolerance multiplier=%12.5g, min tol=%12.5g' %
(self.tolFudge, self.minLinTol))
print(tab1, 'use tolerance adjustment: ', not self.fixLinTol)
print(tab1, 'Linear solver: GMRES, maxIters=', self.maxLinIters)
print(
tab1, 'Preconditioner: ILU(drop=%12.5g, fill=%d)' %
(self.iluDrop, self.iluFill))
print(tab1, 'Recycle initial preconditioner ', self.reusePrecond)
def __init__(self, shell, plugin):
GObject.Object.__init__(self)
self.shell = shell
self.sp = shell.get_property('shell-player')
self.db = shell.get_property('db')
self.plugin = plugin
self.settings = Gio.Settings("org.gnome.rhythmbox.plugins.tabsearch")
self.sites = self.get_sites()
self.nr_sites = len(self.sites)
self.tab_list = []
self.info_tab = Tab('Info', 'Infos\n=====')
self.stock = self.get_stock_icon(ICON_FILENAME)
self.visible = True
self.init_gui()
self.connect_signals()
self.action_toggle = (
'ToggleTabSearch', self.stock, _('TabSearch'), None,
_('Change the visibility of the tab search pane'),
self.toggle_visibility, True)
self.action_group = Gtk.ActionGroup('TabSearchActions')
self.action_group.add_toggle_actions([self.action_toggle])
# since the visibility toggle is per default set to TRUE,
# click it once, if visibility in gconf is set to false!
if self.settings.get_boolean('visible') == False:
action = self.action_group.get_action('ToggleTabSearch')
action.activate()
uim = self.sp.get_property('ui-manager')
uim.insert_action_group(self.action_group, 0)
self.ui_id = uim.add_ui_from_string(tab_search_ui)
uim.ensure_update()
def clean(self):
used = False
for tab in self.application.tabs_list:
if tab.get_category().get_name() == self.entry.get():
used = True
if used:
window = InvalidInputWindow(self.master, self.application,
"This category already exists.")
else:
if self.valid_input_checker(self.entry.get()):
self.value = self.entry.get()
DatabaseHandler.create_category_database(self.entry.get())
new_tab = Tab(self.application.get_notebook(),
Category(self.entry.get()), self.application,
self.favorites_tab, self.expired_tab)
new_tab.populate_tab()
self.application.tabs_list.append(new_tab)
self.top.destroy()
else:
window = InvalidInputWindow(
self.master, self.application,
"Use only capital and lowercase letters,\nnumbers or apostrophe, please."
)
def add_tab_to_notebook(self, data, params):
#print data
#print "add_tab_to_notebook !!!!"
if not self.settings.get_boolean('preventautoweblookup'):
doAutoLookup = True
else:
doAutoLookup = False
# local file not found
if data is None:
if params['source'] == 'hdd':
data = "\t No tabs found on your hard disk."
if doAutoLookup:
data = data + "\n\t Try checking the tab sites on the internet\n\t by clicking on the 'load from web' button above."
else:
data = data + "\n\t Wait for the plugin research from web..."
self.update_info_tab('\t-> Nothing found!\n' + data)
self.load_tabs('web')
else:
data = "you should not see this, check source code!"
self.update_info_tab('\t-> Nothing found!\n' + data)
else:
if params['source'] == 'hdd':
if doAutoLookup:
self.load_tabs('web')
else:
self.update_info_tab('\t-> You choose not to lookup when local tab is found...');
else:
# inform user on info tab about success at fetching data
self.update_info_tab('\t-> tabs found on ' + params['source'] + ' for \'' + params['artist'] + '\' - \'' + params['title'] + '\'.')
tab = Tab('#' + str(len(self.notebook.get_children())) + ' ' + params['source'], data)
tab.set_meta('artist', params['artist'])
tab.set_meta('title', params['title'])
self.tab_list.append(tab)
self.update_notebook(params['source'], params['artist'], params['title'])
def open_dir(self, new_tab = False, background = False):
if new_tab:
curt = self.gettab()
dentry = curt.dentry()
if dentry.isdir():
t = Tab.create(self, dentry.path())
if t:
self.tablist.append(t)
if not background: self.curtab = len(self.tablist) - 1
curt.winexit()
self.UI.draw()
else:
self.gettab().open_dir()
self.UI.draw(False)
return True
def goto_path(self, path, new_tab = False, background = False):
if not os.path.exists(path): return True
if new_tab:
curt = self.gettab()
t = Tab.create(self, path)
if t:
self.tablist.append(t)
if not background: self.curtab = len(self.tablist) - 1
curt.winexit()
self.UI.draw()
else:
self.gettab().goto_path(path)
self.UI.draw(False)
return True
class TestBase(unittest.TestCase):
# Method getting the test name
def getTestName(self):
testMethodName = re.sub(constants.TEST_NUMBER_PATTERN, constants.EMPTY,
self._testMethodName, 1)
return testMethodName.replace(constants.UNDERSCORE, constants.SPACE)
# setup method, called once before all the tests
@classmethod
def setUpClass(self):
username = os.getenv(constants.USERNAME, "")
password = os.getenv(constants.PASSWORD, "")
"""Start web browser"""
self._browser = Tab()
self._browser.login_on_page(constants.DERA_SCM_URL, username, password)
# setup method, called before each test
def setUp(self):
time.sleep(2)
Log.info(constants.STARS_START_LINE)
Log.info(constants.TEST_START + self.getTestName())
# This will run at end of each test
def tearDown(self):
Log.info(constants.TEST_FINSIH + self.getTestName())
self.logResult()
Log.info(constants.STARS_END_LINE)
# This will run at end of all tests
@classmethod
def tearDownClass(self):
"""Logout browser"""
try:
time.sleep(2)
self._browser.logout()
except Exception as ex:
raise Exception("Tear Down Failed : {}.".format(ex))
time.sleep(4)
self._browser.quit()
# Method to log the result
def logResult(self):
if sys.exc_info() == (None, None, None):
Log.info(constants.TEST_PASS)
else:
Log.info(constants.TEST_FAIL)
def __init__(self, shell, plugin):
GObject.Object.__init__(self)
self.shell = shell
self.sp = shell.get_property('shell-player')
self.db = shell.get_property('db')
self.plugin = plugin
self.settings = Gio.Settings("org.gnome.rhythmbox.plugins.tabsearch")
self.sites = self.get_sites()
self.nr_sites = len(self.sites)
self.tab_list = []
self.info_tab = Tab('Info', 'Infos\n=====')
self.stock = self.get_stock_icon(ICON_FILENAME)
self.visible = True
self.init_gui()
self.connect_signals()
self.action_toggle = ('ToggleTabSearch', self.stock, _('TabSearch'),
None, _('Change the visibility of the tab search pane'),
self.toggle_visibility, True)
self.action_group = Gtk.ActionGroup('TabSearchActions')
self.action_group.add_toggle_actions([self.action_toggle])
# since the visibility toggle is per default set to TRUE,
# click it once, if visibility in gconf is set to false!
if self.settings.get_boolean('visible') == False:
action = self.action_group.get_action('ToggleTabSearch')
action.activate();
uim = self.sp.get_property('ui-manager')
uim.insert_action_group (self.action_group, 0)
self.ui_id = uim.add_ui_from_string(tab_search_ui)
uim.ensure_update()
def add_tab_to_notebook(self, data, params):
#print data
#print "add_tab_to_notebook !!!!"
if not self.settings.get_boolean('preventautoweblookup'):
doAutoLookup = True
else:
doAutoLookup = False
# local file not found
if data is None:
if params['source'] == 'hdd':
data = "\t No tabs found on your hard disk."
if doAutoLookup:
data = data + "\n\t Try checking the tab sites on the internet\n\t by clicking on the 'load from web' button above."
else:
data = data + "\n\t Wait for the plugin research from web..."
self.update_info_tab('\t-> Nothing found!\n' + data)
self.load_tabs('web')
else:
data = "you should not see this, check source code!"
self.update_info_tab('\t-> Nothing found!\n' + data)
else:
if params['source'] == 'hdd':
if doAutoLookup:
self.load_tabs('web')
else:
self.update_info_tab(
'\t-> You choose not to lookup when local tab is found...'
)
else:
# inform user on info tab about success at fetching data
self.update_info_tab('\t-> tabs found on ' + params['source'] +
' for \'' + params['artist'] + '\' - \'' +
params['title'] + '\'.')
tab = Tab(
'#' + str(len(self.notebook.get_children())) + ' ' +
params['source'], data)
tab.set_meta('artist', params['artist'])
tab.set_meta('title', params['title'])
self.tab_list.append(tab)
self.update_notebook(params['source'], params['artist'],
params['title'])
def __init__(self, parent, id, title):
self._settings = Settings()
if self._settings.val('phenix'):
import sys
p = self._settings.val('phenix')
base = p + '/Contents/' + os.path.basename(p).lower()
if os.path.exists(base):
sys.path.append(base + '/elbow')
sys.path.append(base)
libtbx.env.add_repository(base)
libtbx.env.process_module(None, 'elbow', False)
CootClient.set_start_coot(self.start_coot)
SettingsDialog.set_settings(self._settings)
HelpDialog.set_settings(self._settings)
wx.Frame.__init__(self, parent, id, title, size=(850,540))
self.Bind(wx.EVT_CLOSE, self._on_close)
self.toolbar = wx.ToolBar(self, style=wx.TB_3DBUTTONS|wx.TB_TEXT)
quit = self.toolbar.AddLabelTool(wx.ID_ANY, 'Quit', wxtbx.bitmaps.fetch_icon_bitmap('actions', 'exit'))
settings = self.toolbar.AddLabelTool(wx.ID_ANY, 'Settings', wxtbx.bitmaps.fetch_icon_bitmap('actions', 'configure'))
about = self.toolbar.AddLabelTool(wx.ID_ANY, 'About', wxtbx.bitmaps.fetch_icon_bitmap('actions', 'info'))
help = self.toolbar.AddLabelTool(wx.ID_ANY, 'Help', wxtbx.bitmaps.fetch_icon_bitmap('actions', 'agt_support'))
self.toolbar.AddSeparator()
coot = self.toolbar.AddLabelTool(wx.ID_ANY, 'Coot', wx.Bitmap(self._settings.proot + 'Resources/gui_resources/coot.png'))
ligand = self.toolbar.AddLabelTool(wx.ID_ANY, 'Ligands', wx.Bitmap(self._settings.proot + 'Resources/gui_resources/ligand_32.png'))
self.SetToolBar(self.toolbar)
self.toolbar.Realize()
self.Bind(wx.EVT_TOOL, self._on_close, quit)
self.Bind(wx.EVT_TOOL, self.start_coot, coot)
self.Bind(wx.EVT_TOOL, self._show_settings, settings)
self.Bind(wx.EVT_TOOL, self._show_about, about)
self.Bind(wx.EVT_TOOL, self._show_help, help)
self.Bind(wx.EVT_TOOL, self._view_ligand, ligand)
self._coot_timer = None
self._coot_process = None
self._coot_client = CootClient()
nb = wx.aui.AuiNotebook(self, -1, style=wx.NB_TOP)
self.sheet1 = Manager(nb)
Tab.set_settings(self._settings)
CootClient.set_p8(self._settings.proot)
Tab.set_coot_client(self._coot_client)
Tab.set_start_coot(self.start_coot)
Tab.set_update_sb(self.set_status)
self.sheet2 = ProcessManager(nb)
self.sheet3 = Compare(nb)
Jobs.set_new_refinement(self.sheet2.new_refinement)
Jobs.set_load_refinement(self.sheet2.load_refinement)
Jobs.set_auto_refinement(self.sheet2.auto_refinement)
nb.AddPage(self.sheet1, 'Manage')
nb.AddPage(self.sheet2, 'Process')
nb.AddPage(self.sheet3, 'Compare')
self.sb = self.CreateStatusBar()
self.sb.SetFieldsCount(2)
self.sb.SetStatusWidths([-4, -1])
self.sheet2.SetFocus()
self.sheet1.load_project()
self.sheet1.refresh_tabs()
def smoothUpdate(A, C, verb=0):
'''
Create an update operator from a coarse mesh to a fine mesh, based on
a matrix A and a set of coarse-mesh nodes C
'''
tab0 = Tab()
timer = Timer('AMG update formation')
Debug.msg3(verb, tab0, 'forming update operator')
Debug.msg3(verb, tab0, 'C=', C)
if not sp.isspmatrix_csr(A):
raise ValueError('makeUpdate() expected a CSR matrix as input')
M = A.shape[0]
if A.shape[1] != A.shape[0]:
raise ValueError('Non-square matrix in makeUpdate(): size is %d by %d' %
(A.shape[0], A.shape[1]))
c_to_f, f_to_c = makeIndexMaps(C)
Debug.msg3(verb, tab0, 'f2c map is ', f_to_c)
I_up = sp.dok_matrix((M,len(C)))
ip = A.indptr
allVals = A.data
allCols = A.indices
tab1 = Tab()
tab2 = Tab()
tab3 = Tab()
tab4 = Tab()
tab5 = Tab()
# Main loop over rows
for i in range(M):
Debug.msg3(verb, tab0, 'row %d' % i)
# If the current index is in the coarse mesh, take its value directly
# from the fine mesh
if i in C:
I_up[i, f_to_c[i]] = 1.0
Debug.msg3(verb, tab1, 'coarse-coarse connection, entry is 1')
continue
Debug.msg3(verb, tab1, 'interpolating value for fine row ', i)
# Get arrays of column indices and values for this row
cols_i = allCols[ip[i] : ip[i+1]]
vals_i = allVals[ip[i] : ip[i+1]]
# Find diagonal
diag = vals_i[np.where(cols_i==i)]
Debug.msg3(verb, tab1, 'diagonal is %g' % diag)
# Diagonal must be nonzero!
if diag == 0.0:
raise ValueError('zero diagonal detected in row %d' % i)
# build interpolation matrix
for j, a_ij in zip(cols_i, vals_i):
if j==i:
continue
if j not in C:
continue
Debug.msg3(verb, tab2, 'contrib from coarse node f=%d, c=%d' % (j, f_to_c[j]))
w_ij = a_ij
Debug.msg3(verb, tab2, 'direct connection: (%d,%d)=%g' % (i,j,w_ij))
Debug.msg3(verb, tab2, 'finding indirect contributions')
Debug.msg3(verb, tab2, 'looking at neighbors ', cols_i)
for m, a_im in zip(cols_i, vals_i):
if m==i: # <--- I forgot this on first pass!
continue
if m not in C: # Approximate values on F by averaging
Debug.msg3(verb, tab3, 'approximating fine node m=%d' % m)
cols_m = allCols[ip[m] : ip[m+1]]
vals_m = allVals[ip[m] : ip[m+1]]
denom = 0.0
num = 0.0
Debug.msg3(verb, tab3, 'neighbors of m=%d are ' % m, cols_m)
count = 0
for k,a_mk in zip(cols_m, vals_m):
if k in C and k in cols_i:
Debug.msg3(verb, tab4, 'indirect contribution from coarse node k=', k)
denom += a_mk
count += 1
if k==j:
num = a_im * a_mk
Debug.msg3(verb, tab4, 'numerator=%g, denominator=%g' % (num,denom))
if count>0:
if denom==0.0:
raise ValueError('zero denominator detected in (%d,%d)' %(i,j))
Debug.msg3(verb, tab3, 'indirect connection through fine node %d: %g' % (m,num/denom))
w_ij += num/denom
else: # No need to approximate coarse node values
Debug.msg3(verb, tab3, 'no need to approximate value at coarse node m=', m)
continue
Debug.msg3(verb, tab2, '(%d,%d), val=%g' %(i,j,w_ij))
I_up[i, f_to_c[j]] = -w_ij/diag
# end second pass through row i
# end loop over rows
Debug.msg3(verb, tab0, 'done forming update operator')
return I_up.tocsr()
def solve(self, func, uInit):
# Report all parameters
if self.verb > 0:
self.describe()
# Set up formatting
tab0 = Tab()
tab1 = Tab()
# Make a copy of the initial estimate
u0 = uInit.copy()
# Evaluate residual and its norm at initial iterate
F0 = func.evalF(u0)
r0 = npla.norm(F0)
# Newton step vector. Initialize to all ones (this will be overwritten
# before use)
du = np.ones_like(u0)
# We'll keep a count of the total Krylov iterations
totalKrylovIters = 0
# Run the loop!
if self.verb > 0:
print('\n', tab0, 'Newton-Krylov loop')
for i in range(self.maxIters):
# Evaluate residual at current iterate (already done if i=0)
if i > 0:
F0 = func.evalF(u0)
# Compute residual norm
r = npla.norm(F0)
# Output convergence information if desired
if self.verb > 0:
print(
tab1, 'iter %6d r=%12.5g r/r0=%12.5g dx=%12.5g' %
(i, r, r / r0, npla.norm(du)))
# Check for convergence
if r <= r0 * self.tau_r + self.tau_a:
print(tab0, 'Converged!')
print(tab0, 'totalKrylovIters=', totalKrylovIters)
return (True, u0)
# Compute Jacobian at current iterate
J = func.evalJ(u0)
# Update tolerance for linear solve
if self.fixLinTol: # Use fixed tolerance if desired (for testing)
tau_lin = self.minLinTol
else: # Adjust linear tol according to nonlinear resid
# new linear tolerance is the larger of:
# (*) "fudge factor" times relative residual of nonlinear solve
# (*) a minimum linear tolerance.
# The minimum tolerance avoids pointlessly small tolerances
# for the linear solver
tau_lin = max(self.tolFudge * r / r0, self.minLinTol)
# Update the preconditioner if desired
if i == 0 or not self.reusePrecond:
print(tab1, 'Building ILU prec')
drop = self.iluDrop
fill = self.iluFill
ILU = ILURightPreconditioner(J,
drop_tol=drop,
fill_factor=fill)
(conv, krylovIters, du) = GMRES(J,
-F0,
maxiters=self.maxLinIters,
tol=tau_lin,
verb=self.linVerb,
precond=ILU)
totalKrylovIters += krylovIters
if not conv:
if self.verb > 0:
print('Newton-Krylov: linear solver failed to converge')
return (False, u0)
# Update solution estimate
u0 = u0 + du
if self.verb > 0:
print(tab0, 'Newton-Krylov failed to converge!')
return (False, u0)
def func(verb):
tab = Tab()
Debug.msg1(verb, tab, 'verb=%s, message 1' % verb)
Debug.msg2(verb, tab, 'verb=%s, message 2' % verb)
Debug.msg3(verb, tab, 'verb=%s, message 3' % verb)
Debug.msg4(verb, tab, 'verb=%s, message 4' % verb)
def __init__(self, store):
Tab.__init__(self, store)
if verb >= 3:
Debug._write(args)
@classmethod
def msg4(cls, verb, *args):
'''Write the arguments when verb >= 4.'''
if verb >= 4:
Debug._write(args)
@classmethod
def _write(cls, args):
for a in args:
print(a, end='', file=Debug.outstream)
print('', file=Debug.outstream)
if __name__ == '__main__':
t = Tab()
def func(verb):
tab = Tab()
Debug.msg1(verb, tab, 'verb=%s, message 1' % verb)
Debug.msg2(verb, tab, 'verb=%s, message 2' % verb)
Debug.msg3(verb, tab, 'verb=%s, message 3' % verb)
Debug.msg4(verb, tab, 'verb=%s, message 4' % verb)
for i in range(1, 5):
print('i=', i)
func(i)
class TabSearch(GObject.Object):
def __init__(self, shell, plugin):
GObject.Object.__init__(self)
self.shell = shell
self.sp = shell.get_property('shell-player')
self.db = shell.get_property('db')
self.plugin = plugin
self.settings = Gio.Settings("org.gnome.rhythmbox.plugins.tabsearch")
self.sites = self.get_sites()
self.nr_sites = len(self.sites)
self.tab_list = []
self.info_tab = Tab('Info', 'Infos\n=====')
self.stock = self.get_stock_icon(ICON_FILENAME)
self.visible = True
self.init_gui()
self.connect_signals()
self.action_toggle = (
'ToggleTabSearch', self.stock, _('TabSearch'), None,
_('Change the visibility of the tab search pane'),
self.toggle_visibility, True)
self.action_group = Gtk.ActionGroup('TabSearchActions')
self.action_group.add_toggle_actions([self.action_toggle])
# since the visibility toggle is per default set to TRUE,
# click it once, if visibility in gconf is set to false!
if self.settings.get_boolean('visible') == False:
action = self.action_group.get_action('ToggleTabSearch')
action.activate()
uim = self.sp.get_property('ui-manager')
uim.insert_action_group(self.action_group, 0)
self.ui_id = uim.add_ui_from_string(tab_search_ui)
uim.ensure_update()
def init_gui(self):
print "TabSearch->init_gui"
self.vbox = Gtk.VBox()
self.toolbar = Gtk.Toolbar()
self.toolitemSave = Gtk.ToolButton()
self.toolitemSave.set_label('Save')
self.toolitemSave.set_stock_id(Gtk.STOCK_SAVE)
self.toolitemSave.connect('clicked', self.save_tabs)
self.toolitemSave.set_sensitive(False)
self.toolbar.add(self.toolitemSave)
self.toolitemEdit = Gtk.ToolButton()
self.toolitemEdit.set_label('Edit')
self.toolitemEdit.set_stock_id(Gtk.STOCK_EDIT)
self.toolitemEdit.connect('clicked', self.edit_tabs)
self.toolitemEdit.set_sensitive(False)
self.toolbar.add(self.toolitemEdit)
self.toolitemLoad = Gtk.ToolButton()
self.toolitemLoad.set_label('Load From Web')
self.toolitemLoad.set_stock_id(Gtk.STOCK_FIND)
self.toolitemLoad.connect('clicked', self.load_tabs_from_web)
self.toolitemLoad.set_sensitive(False)
self.toolbar.add(self.toolitemLoad)
self.vbox.pack_start(self.toolbar, expand=False, fill=True, padding=0)
self.notebook = Gtk.Notebook()
self.notebook.set_scrollable(True)
self.progressbar = Gtk.ProgressBar()
self.timeout = GObject.timeout_add(100, self.start_pulse)
self.vbox.set_size_request(250, -1)
self.shell.add_widget(self.vbox,
RB.ShellUILocation.RIGHT_SIDEBAR,
expand=True,
fill=True)
self.vbox.show_all()
def show_pulse(self):
if self.progressbar is not None:
self.vbox.remove(self.progressbar)
GObject.source_remove(self.timeout)
self.vbox.pack_end(self.progressbar,
expand=False,
fill=True,
padding=0)
self.timeout = GObject.timeout_add(100, self.start_pulse)
self.start_pulse()
def hide_pulse(self):
self.nr_sites = self.nr_sites - 1
print "Sites left to stop progressbar: " + str(self.nr_sites)
if self.nr_sites == 0:
self.vbox.remove(self.progressbar)
GObject.source_remove(self.timeout)
def start_pulse(self):
self.progressbar.pulse()
return True
def get_stock_icon(self, filename):
icon_file_path = rb.find_plugin_file(self.plugin, filename)
#icon_file_path = os.path.join(plugin.plugin_info.get_data_dir(), filename)
if icon_file_path is None:
print filename + " not found in " + self.plugin.plugin_info.get_data_dir(
)
return Gtk.STOCK_INFO
else:
iconsource = Gtk.IconSource()
iconsource.set_filename(icon_file_path)
iconset = Gtk.IconSet()
iconset.add_source(iconsource)
iconfactory = Gtk.IconFactory()
iconfactory.add(STOCK_IMAGE, iconset)
iconfactory.add_default()
return STOCK_IMAGE
# set the callback function 'playing_changed_cb'
def connect_signals(self):
self.player_cb_ids = (self.sp.connect('playing-song-changed',
self.playing_changed_cb))
# which sites did the user check in the configuration dialog?
def get_sites(self):
try:
sites = self.settings['sites']
if sites is None:
sites = []
except:
print "Error: can't load the sites from configuration"
sites = []
print "tabs sites: " + str(sites)
return sites
# which folder did the user specify in the configuration dialog?
# TODO: what's happening when the path is not valid?
def get_tabfolder(self):
try:
# folder = gconf.client_get_default().get_string(self.gconf_keys['folder'])
folder = self.settings.get_string('folder')
except:
print "Error: can't load the tab folder path from configuration"
print "tabs folder: " + folder
return folder
def load_tabs_from_web(self, action):
return self.load_tabs('web')
# callback function that is triggered whenever there's
# a change in played song title
def playing_changed_cb(self, playing, user_data):
print "There's been a change in playback ..."
self.info_tab.set_content('Infos\n=====')
return self.load_tabs('hdd')
def load_tabs(self, source):
if self.visible is False:
print "no visibility -> no need to look for tabs"
return
playing_entry = None
if self.sp:
playing_entry = self.sp.get_playing_entry()
if playing_entry is None:
return
# playing_artist = self.db.entry_get (playing_entry, rhythmdb.PROP_ARTIST)
# playing_title = self.db.entry_get (playing_entry, rhythmdb.PROP_TITLE)
playing_artist = playing_entry.get_string(RB.RhythmDBPropType.ARTIST)
playing_title = playing_entry.get_string(RB.RhythmDBPropType.TITLE)
print "looking for '" + playing_artist + "' and the song '" + playing_title + "'"
# passing the song info to the tab site parser
# without removing the é and è from it.
playing_artist = remove_accents(playing_artist)
playing_title = remove_accents(playing_title)
if playing_artist.upper() == "UNKNOWN":
playing_artist = ""
# resetting notebook
if self.notebook in self.vbox.get_children():
self.vbox.remove(self.notebook)
self.vbox.show_all()
self.notebook = None
self.notebook = Gtk.Notebook()
self.notebook.set_scrollable(True)
self.notebook.connect('switch-page', self.update_toolbar)
self.vbox.pack_start(self.notebook, expand=True, fill=True, padding=0)
self.vbox.show_all()
# Remove tabs from notebook
self.tab_list = []
self.info_tab.set_meta('artist', playing_artist)
self.info_tab.set_meta('title', playing_title)
if source == 'hdd':
self.update_info_tab("\nchecking hdd for '" + playing_artist +
"' and the song '" + playing_title + "'")
self.hide_pulse()
self.open_tabs_from_hdd(playing_artist, playing_title)
if source == 'web':
self.update_info_tab("\nchecking web for '" + playing_artist +
"' and the song '" + playing_title + "'")
if not (playing_artist == ""):
# reset the number of sites in order to detect when the research finished
self.nr_sites = len(self.sites)
self.show_pulse()
self.sites = self.get_sites()
for s in self.sites:
site_id = s
if s == 'gt':
#gt = GuitareTabParser(self.add_tab_to_notebook, self.update_info_tab)
gt = GuitareTabParser(self.add_tab_to_notebook,
self.notify_finish)
gt.tabs_finder(playing_artist, playing_title)
elif s == 'ug':
#ug = UltimateGuitarParser(self.add_tab_to_notebook, self.update_info_tab)
ug = UltimateGuitarParser(self.add_tab_to_notebook,
self.notify_finish)
ug.tabs_finder(playing_artist, playing_title)
elif s == 'az':
#az = AZChordsParser(self.add_tab_to_notebook, self.update_info_tab)
az = AZChordsParser(self.add_tab_to_notebook,
self.notify_finish)
az.tabs_finder(playing_artist, playing_title)
elif s == 'ec':
#ec = EChordsParser(self.add_tab_to_notebook, self.update_info_tab)
ec = EChordsParser(self.add_tab_to_notebook,
self.notify_finish)
ec.tabs_finder(playing_artist, playing_title)
elif s == 'lc':
#lc = LacuerdaParser(self.add_tab_to_notebook, self.update_info_tab)
lc = LacuerdaParser(self.add_tab_to_notebook,
self.notify_finish)
lc.tabs_finder(playing_artist, playing_title)
def deactivate(self, shell):
print "Plugin deactivated."
self.shell = None
self.sp = None
self.db = None
self.plugin = None
shell.remove_widget(self.vbox, RB.ShellUILocation.RIGHT_SIDEBAR)
uim = self.sp.get_property('ui-manager')
uim.remove_ui(self.ui_id)
uim.remove_action_group(self.action_group)
# toggles the visibility of the tab widget
def toggle_visibility(self, action):
print "Visibility set to " + str(not self.visible)
if not self.visible:
self.shell.add_widget(self.vbox,
RB.ShellUILocation.RIGHT_SIDEBAR,
expand=True,
fill=True)
self.visible = True
self.load_tabs('hdd')
else:
self.shell.remove_widget(self.vbox,
RB.ShellUILocation.RIGHT_SIDEBAR)
self.visible = False
# gconf.client_get_default().set_bool(self.gconf_keys['visible'], self.visible)
self.settings.set_boolean('visible', self.visible)
def edit_tabs(self, action):
self.toolitemEdit.set_sensitive(False)
self.get_current_tab().set_editable(True)
self.toolitemSave.set_sensitive(True)
# (de)activates the buttons on the toolbar depending on whether
# they're useful in the current situation
def update_toolbar(self, notebook, page, page_num):
self.toolitemEdit.set_sensitive(False)
self.toolitemSave.set_sensitive(False)
self.toolitemLoad.set_sensitive(False)
if page_num == 0:
self.toolitemLoad.set_sensitive(True)
if page_num > 0:
self.toolitemEdit.set_sensitive(True)
# returns the currently selected tab content
def get_current_tab(self):
currentTab = self.notebook.get_current_page()
return self.notebook.get_nth_page(currentTab).get_child()
# returns the currently selected tab content
def get_current_tab_title(self):
currentTab = self.notebook.get_current_page()
currentTab = self.notebook.get_nth_page(currentTab)
return self.notebook.get_tab_label(currentTab).get_text()
# copies currently selected tabs to the hard disk
def save_tabs(self, action):
print 'saving tabs to hdd ...'
self.toolitemSave.set_sensitive(False)
self.toolitemEdit.set_sensitive(True)
self.get_current_tab().set_editable(False)
textbuffer = ""
try:
textbuffer = self.get_current_tab().get_buffer()
textbuffer = textbuffer.get_text(textbuffer.get_start_iter(),
textbuffer.get_end_iter(), 0)
except:
print 'Error: can\'t read current\'s tabs content'
if textbuffer is None:
print 'Error: loading current tabs failed'
return
directory = self.get_tabfolder(
) + '/' + self.info_tab.meta['artist'] + '/'
try:
os.makedirs(directory)
except os.error:
print 'Notice: directory\'s already existing'
filename = directory + self.info_tab.meta['title'] + '.txt'
try:
file = open(filename, 'w')
except:
print "Error: can't open file"
return
file.write(textbuffer)
file.close()
print "-> saved successfully to hdd"
self.load_tabs('hdd')
def open_tabs_from_hdd(self, artist, title):
filename = self.get_tabfolder() + '/' + artist + '/' + title + '.txt'
print filename
self.file_res = Gio.File.new_for_path(filename)
self.file_res.load_contents_async(None, self.open_tabs_from_hdd_cb, {
'source': 'hdd',
'artist': artist,
'title': title
})
def open_tabs_from_hdd_cb(self, gdaemonfile, result, params):
try:
result = self.file_res.load_contents_finish(result)
except GError:
print "Error: can't open file, maybe it's not there at all..."
self.add_tab_to_notebook(None, params)
return
successful = result[0]
data = result[1]
self.add_tab_to_notebook(data, params)
def add_tab_to_notebook(self, data, params):
#print data
#print "add_tab_to_notebook !!!!"
if not self.settings.get_boolean('preventautoweblookup'):
doAutoLookup = True
else:
doAutoLookup = False
# local file not found
if data is None:
if params['source'] == 'hdd':
data = "\t No tabs found on your hard disk."
if doAutoLookup:
data = data + "\n\t Try checking the tab sites on the internet\n\t by clicking on the 'load from web' button above."
else:
data = data + "\n\t Wait for the plugin research from web..."
self.update_info_tab('\t-> Nothing found!\n' + data)
self.load_tabs('web')
else:
data = "you should not see this, check source code!"
self.update_info_tab('\t-> Nothing found!\n' + data)
else:
if params['source'] == 'hdd':
if doAutoLookup:
self.load_tabs('web')
else:
self.update_info_tab(
'\t-> You choose not to lookup when local tab is found...'
)
else:
# inform user on info tab about success at fetching data
self.update_info_tab('\t-> tabs found on ' + params['source'] +
' for \'' + params['artist'] + '\' - \'' +
params['title'] + '\'.')
tab = Tab(
'#' + str(len(self.notebook.get_children())) + ' ' +
params['source'], data)
tab.set_meta('artist', params['artist'])
tab.set_meta('title', params['title'])
self.tab_list.append(tab)
self.update_notebook(params['source'], params['artist'],
params['title'])
def update_info_tab(self, new_content):
self.info_tab.add_content(new_content)
if len(self.notebook.get_children()) == 0:
# create info tab for the first time
scroll = self.create_page(self.info_tab.content)
self.notebook.prepend_page(scroll, Gtk.Label(self.info_tab.label))
else:
# update existing info tab
infoTab = self.notebook.get_nth_page(0).get_child()
textbuffer = infoTab.get_buffer()
textbuffer.set_text(self.info_tab.content)
self.notebook.show()
self.vbox.show_all()
def notify_finish(self, content):
self.update_info_tab(content)
self.hide_pulse()
def update_notebook(self, source, artist, title):
""" Update notebook """
if len(self.tab_list) == 0:
print 'no tabs in tab_list !'
else:
# data tabs
for tab in self.tab_list:
if not (tab.label == "Not Found"):
scroll = self.create_page(tab.content)
self.notebook.append_page(scroll, Gtk.Label(tab.label))
self.tab_list = []
self.notebook.show()
self.vbox.show_all()
def create_page(self, text):
fontdesc = Pango.FontDescription("Courier New 8")
textbuffer = Gtk.TextBuffer()
textbuffer.set_text(text)
textview = Gtk.TextView()
textview.set_buffer(textbuffer)
textview.set_editable(False)
textview.modify_font(fontdesc)
scroll = Gtk.ScrolledWindow()
scroll.set_policy(Gtk.PolicyType.AUTOMATIC, Gtk.PolicyType.AUTOMATIC)
scroll.set_shadow_type(Gtk.ShadowType.IN)
scroll.add(textview)
scroll.show()
return scroll
def __init__(self, nb):
Tab.__init__(self, nb)
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
#self.ax2 = self.ax1.twinx()
self.ax1.tick_params(labelsize=8)
#self.ax2.tick_params(labelsize=8)
self.hist_fig = Figure((2,1.5), dpi=100)
self.hist_fig.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.hist_canvas = FigCanvas(self, -1, self.hist_fig)
self.hist_ax1 = self.hist_fig.add_subplot(111)
self.shist_fig = Figure((2,1.5), dpi=100)
self.shist_fig.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.shist_canvas = FigCanvas(self, -1, self.shist_fig)
self.shist_ax1 = self.shist_fig.add_subplot(111)
self.refinements = wx.ListBox(self, 26, wx.DefaultPosition, (60, 100), [], wx.LB_MULTIPLE)
self.refinements.Bind(wx.EVT_LISTBOX, self._set_refinements)
self.res_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.res_sizer.Add(wx.StaticText(self, -1, 'Residue Type'), 0, wx.EXPAND)
self.res_type = wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self.res_sizer.Add(self.res_type, 0, wx.EXPAND)
self._flds = [ wx.StaticText(self, -1, '') for i in range(4) ]
self.avg_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
self.avg_info.Add(wx.StaticText(self, -1, 'Average Std Dev'), 0, wx.EXPAND)
self.avg_info.Add(self._flds[0], 0, wx.EXPAND)
#self.avg_info.Add(wx.StaticText(self, -1, 'Number of Vals'), wx.EXPAND|wx.ALL, 5)
#self.avg_info.Add(self._flds[1], wx.EXPAND|wx.ALL, 5)
self.res_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
self.res_info.Add(wx.StaticText(self, -1, 'Average Values'), 0, wx.EXPAND)
self.res_info.Add(self._flds[1], 0, wx.EXPAND)
self.res_info.Add(wx.StaticText(self, -1, 'Standard Dev'), 0, wx.EXPAND)
self.res_info.Add(self._flds[2], 0, wx.EXPAND)
#self.res_info.Add(wx.StaticText(self, -1, 'Number of Vals'), wx.EXPAND|wx.ALL, 5)
#self.res_info.Add(self._flds[3], wx.EXPAND|wx.ALL, 5)
self.side_sizer = wx.BoxSizer(wx.VERTICAL)
self.side_sizer.Add(wx.StaticText(self, -1, 'Refinements'), 0, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.refinements, 0, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.res_sizer, 0, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.avg_info, 0, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.shist_canvas, 1, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.res_info, 0, wx.EXPAND|wx.LEFT, 5)
self.side_sizer.Add(self.hist_canvas, 1, wx.EXPAND|wx.LEFT, 5)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.side_sizer, 0, wx.EXPAND|wx.ALL, 5)
self.sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL, 5)
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self._residue_type = 0
self._highlight = -1
self._selected_residue = -1
self._residue_types = []
self._all_data = []
self._averaged = []
self._files = []
self.SetSizer(self.sizer)
self.Fit()
from Tab import Tab
print("============================")
print("\tWeb Browser ")
print("============================")
active = True
tab = Tab()
while (active):
print("1. Forward")
print("2. Backward")
print("3. Reload")
print("4. Show History")
print("5. Exit")
inp = int(input("Enter your choice: "))
if inp == 1:
pageName = input("Enter URL: ")
tab.goForward(pageName)
elif inp == 2:
active = tab.goBack()
elif inp == 3:
print(tab.getCurrentPage)
elif inp == 4:
tab.getCurrentVisitedPage()
elif inp == 5:
active = False
print("Tab is clear!!!")
else:
print("Look at instruction, you idiot!!!")
def __init__(self, nb):
Tab.__init__(self, nb)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.SetSizer(self.sizer)
class TabSearch(GObject.Object):
def __init__(self, shell, plugin):
GObject.Object.__init__(self)
self.shell = shell
self.sp = shell.get_property('shell-player')
self.db = shell.get_property('db')
self.plugin = plugin
self.settings = Gio.Settings("org.gnome.rhythmbox.plugins.tabsearch")
self.sites = self.get_sites()
self.nr_sites = len(self.sites)
self.tab_list = []
self.info_tab = Tab('Info', 'Infos\n=====')
self.stock = self.get_stock_icon(ICON_FILENAME)
self.visible = True
self.init_gui()
self.connect_signals()
self.action_toggle = ('ToggleTabSearch', self.stock, _('TabSearch'),
None, _('Change the visibility of the tab search pane'),
self.toggle_visibility, True)
self.action_group = Gtk.ActionGroup('TabSearchActions')
self.action_group.add_toggle_actions([self.action_toggle])
# since the visibility toggle is per default set to TRUE,
# click it once, if visibility in gconf is set to false!
if self.settings.get_boolean('visible') == False:
action = self.action_group.get_action('ToggleTabSearch')
action.activate();
uim = self.sp.get_property('ui-manager')
uim.insert_action_group (self.action_group, 0)
self.ui_id = uim.add_ui_from_string(tab_search_ui)
uim.ensure_update()
def init_gui(self) :
print "TabSearch->init_gui"
self.vbox = Gtk.VBox()
self.toolbar = Gtk.Toolbar()
self.toolitemSave = Gtk.ToolButton()
self.toolitemSave.set_label('Save')
self.toolitemSave.set_stock_id(Gtk.STOCK_SAVE)
self.toolitemSave.connect('clicked', self.save_tabs)
self.toolitemSave.set_sensitive(False)
self.toolbar.add(self.toolitemSave)
self.toolitemEdit = Gtk.ToolButton()
self.toolitemEdit.set_label('Edit')
self.toolitemEdit.set_stock_id(Gtk.STOCK_EDIT)
self.toolitemEdit.connect('clicked', self.edit_tabs)
self.toolitemEdit.set_sensitive(False)
self.toolbar.add(self.toolitemEdit)
self.toolitemLoad = Gtk.ToolButton()
self.toolitemLoad.set_label('Load From Web')
self.toolitemLoad.set_stock_id(Gtk.STOCK_FIND)
self.toolitemLoad.connect('clicked', self.load_tabs_from_web)
self.toolitemLoad.set_sensitive(False)
self.toolbar.add(self.toolitemLoad)
self.vbox.pack_start(self.toolbar, expand = False, fill = True, padding = 0)
self.notebook = Gtk.Notebook()
self.notebook.set_scrollable(True)
self.progressbar = Gtk.ProgressBar()
self.timeout = GObject.timeout_add(100, self.start_pulse)
self.vbox.set_size_request(250, -1)
self.shell.add_widget(self.vbox, RB.ShellUILocation.RIGHT_SIDEBAR, expand=True, fill=True)
self.vbox.show_all()
def show_pulse(self):
if self.progressbar is not None:
self.vbox.remove(self.progressbar)
GObject.source_remove(self.timeout)
self.vbox.pack_end(self.progressbar, expand = False, fill = True, padding = 0)
self.timeout = GObject.timeout_add(100, self.start_pulse)
self.start_pulse()
def hide_pulse(self):
self.nr_sites = self.nr_sites-1
print "Sites left to stop progressbar: "+str(self.nr_sites)
if self.nr_sites == 0:
self.vbox.remove(self.progressbar)
GObject.source_remove(self.timeout)
def start_pulse(self):
self.progressbar.pulse()
return True
def get_stock_icon(self, filename):
icon_file_path = rb.find_plugin_file(self.plugin, filename)
#icon_file_path = os.path.join(plugin.plugin_info.get_data_dir(), filename)
if icon_file_path is None:
print filename +" not found in "+self.plugin.plugin_info.get_data_dir()
return Gtk.STOCK_INFO
else:
iconsource = Gtk.IconSource()
iconsource.set_filename(icon_file_path)
iconset = Gtk.IconSet()
iconset.add_source(iconsource)
iconfactory = Gtk.IconFactory()
iconfactory.add(STOCK_IMAGE, iconset)
iconfactory.add_default()
return STOCK_IMAGE
# set the callback function 'playing_changed_cb'
def connect_signals(self):
self.player_cb_ids = (self.sp.connect('playing-song-changed', self.playing_changed_cb))
# which sites did the user check in the configuration dialog?
def get_sites(self):
try:
sites = self.settings['sites']
if sites is None:
sites = []
except:
print "Error: can't load the sites from configuration"
sites = []
print "tabs sites: " + str(sites)
return sites
# which folder did the user specify in the configuration dialog?
# TODO: what's happening when the path is not valid?
def get_tabfolder(self):
try:
# folder = gconf.client_get_default().get_string(self.gconf_keys['folder'])
folder = self.settings.get_string('folder')
except:
print "Error: can't load the tab folder path from configuration"
print "tabs folder: " + folder
return folder
def load_tabs_from_web(self, action):
return self.load_tabs('web')
# callback function that is triggered whenever there's
# a change in played song title
def playing_changed_cb (self, playing, user_data):
print "There's been a change in playback ..."
self.info_tab.set_content('Infos\n=====')
return self.load_tabs('hdd')
def load_tabs(self, source):
if self.visible is False:
print "no visibility -> no need to look for tabs"
return
playing_entry = None
if self.sp:
playing_entry = self.sp.get_playing_entry()
if playing_entry is None:
return
# playing_artist = self.db.entry_get (playing_entry, rhythmdb.PROP_ARTIST)
# playing_title = self.db.entry_get (playing_entry, rhythmdb.PROP_TITLE)
playing_artist = playing_entry.get_string(RB.RhythmDBPropType.ARTIST)
playing_title = playing_entry.get_string(RB.RhythmDBPropType.TITLE)
print "looking for '" + playing_artist + "' and the song '" + playing_title + "'"
# passing the song info to the tab site parser
# without removing the é and è from it.
playing_artist = remove_accents(playing_artist)
playing_title = remove_accents(playing_title)
if playing_artist.upper() == "UNKNOWN":
playing_artist = ""
# resetting notebook
if self.notebook in self.vbox.get_children():
self.vbox.remove(self.notebook)
self.vbox.show_all()
self.notebook = None
self.notebook = Gtk.Notebook()
self.notebook.set_scrollable(True)
self.notebook.connect('switch-page', self.update_toolbar)
self.vbox.pack_start(self.notebook, expand = True, fill = True, padding=0)
self.vbox.show_all()
# Remove tabs from notebook
self.tab_list = []
self.info_tab.set_meta('artist', playing_artist)
self.info_tab.set_meta('title', playing_title)
if source == 'hdd':
self.update_info_tab("\nchecking hdd for '" + playing_artist + "' and the song '" + playing_title + "'")
self.hide_pulse()
self.open_tabs_from_hdd(playing_artist, playing_title)
if source == 'web':
self.update_info_tab("\nchecking web for '" + playing_artist + "' and the song '" + playing_title + "'")
if not(playing_artist == ""):
# reset the number of sites in order to detect when the research finished
self.nr_sites = len(self.sites)
self.show_pulse()
self.sites = self.get_sites()
for s in self.sites:
site_id = s
if s == 'gt':
#gt = GuitareTabParser(self.add_tab_to_notebook, self.update_info_tab)
gt = GuitareTabParser(self.add_tab_to_notebook, self.notify_finish)
gt.tabs_finder(playing_artist, playing_title)
elif s == 'ug':
#ug = UltimateGuitarParser(self.add_tab_to_notebook, self.update_info_tab)
ug = UltimateGuitarParser(self.add_tab_to_notebook, self.notify_finish)
ug.tabs_finder(playing_artist, playing_title)
elif s == 'az':
#az = AZChordsParser(self.add_tab_to_notebook, self.update_info_tab)
az = AZChordsParser(self.add_tab_to_notebook, self.notify_finish)
az.tabs_finder(playing_artist, playing_title)
elif s == 'ec':
#ec = EChordsParser(self.add_tab_to_notebook, self.update_info_tab)
ec = EChordsParser(self.add_tab_to_notebook, self.notify_finish)
ec.tabs_finder(playing_artist, playing_title)
elif s == 'lc':
#lc = LacuerdaParser(self.add_tab_to_notebook, self.update_info_tab)
lc = LacuerdaParser(self.add_tab_to_notebook, self.notify_finish)
lc.tabs_finder(playing_artist, playing_title)
def deactivate (self, shell):
print "Plugin deactivated."
self.shell = None
self.sp = None
self.db = None
self.plugin = None
shell.remove_widget(self.vbox, RB.ShellUILocation.RIGHT_SIDEBAR)
uim = self.sp.get_property('ui-manager')
uim.remove_ui(self.ui_id)
uim.remove_action_group(self.action_group)
# toggles the visibility of the tab widget
def toggle_visibility(self, action):
print "Visibility set to " + str(not self.visible)
if not self.visible:
self.shell.add_widget(self.vbox, RB.ShellUILocation.RIGHT_SIDEBAR, expand=True, fill=True)
self.visible = True
self.load_tabs('hdd')
else:
self.shell.remove_widget(self.vbox, RB.ShellUILocation.RIGHT_SIDEBAR)
self.visible = False
# gconf.client_get_default().set_bool(self.gconf_keys['visible'], self.visible)
self.settings.set_boolean('visible', self.visible)
def edit_tabs(self, action):
self.toolitemEdit.set_sensitive(False)
self.get_current_tab().set_editable(True)
self.toolitemSave.set_sensitive(True)
# (de)activates the buttons on the toolbar depending on whether
# they're useful in the current situation
def update_toolbar(self, notebook, page, page_num):
self.toolitemEdit.set_sensitive(False)
self.toolitemSave.set_sensitive(False)
self.toolitemLoad.set_sensitive(False)
if page_num == 0:
self.toolitemLoad.set_sensitive(True)
if page_num > 0:
self.toolitemEdit.set_sensitive(True)
# returns the currently selected tab content
def get_current_tab(self):
currentTab = self.notebook.get_current_page()
return self.notebook.get_nth_page(currentTab).get_child()
# returns the currently selected tab content
def get_current_tab_title(self):
currentTab = self.notebook.get_current_page()
currentTab = self.notebook.get_nth_page(currentTab)
return self.notebook.get_tab_label(currentTab).get_text()
# copies currently selected tabs to the hard disk
def save_tabs(self, action):
print 'saving tabs to hdd ...'
self.toolitemSave.set_sensitive(False)
self.toolitemEdit.set_sensitive(True)
self.get_current_tab().set_editable(False)
textbuffer = ""
try:
textbuffer = self.get_current_tab().get_buffer()
textbuffer = textbuffer.get_text(textbuffer.get_start_iter() , textbuffer.get_end_iter(), 0)
except:
print 'Error: can\'t read current\'s tabs content'
if textbuffer is None:
print 'Error: loading current tabs failed'
return
directory = self.get_tabfolder() + '/' + self.info_tab.meta['artist'] + '/'
try:
os.makedirs(directory)
except os.error:
print 'Notice: directory\'s already existing'
filename = directory + self.info_tab.meta['title'] + '.txt'
try:
file = open(filename, 'w')
except:
print "Error: can't open file"
return
file.write(textbuffer)
file.close()
print "-> saved successfully to hdd"
self.load_tabs('hdd')
def open_tabs_from_hdd(self, artist, title):
filename = self.get_tabfolder() + '/' + artist + '/' + title + '.txt'
print filename
self.file_res = Gio.File.new_for_path(filename)
self.file_res.load_contents_async(None, self.open_tabs_from_hdd_cb, {'source': 'hdd', 'artist': artist, 'title': title})
def open_tabs_from_hdd_cb(self, gdaemonfile, result, params):
try:
result = self.file_res.load_contents_finish(result)
except GError:
print "Error: can't open file, maybe it's not there at all..."
self.add_tab_to_notebook(None, params)
return
successful = result[0]
data = result[1]
self.add_tab_to_notebook(data, params)
def add_tab_to_notebook(self, data, params):
#print data
#print "add_tab_to_notebook !!!!"
if not self.settings.get_boolean('preventautoweblookup'):
doAutoLookup = True
else:
doAutoLookup = False
# local file not found
if data is None:
if params['source'] == 'hdd':
data = "\t No tabs found on your hard disk."
if doAutoLookup:
data = data + "\n\t Try checking the tab sites on the internet\n\t by clicking on the 'load from web' button above."
else:
data = data + "\n\t Wait for the plugin research from web..."
self.update_info_tab('\t-> Nothing found!\n' + data)
self.load_tabs('web')
else:
data = "you should not see this, check source code!"
self.update_info_tab('\t-> Nothing found!\n' + data)
else:
if params['source'] == 'hdd':
if doAutoLookup:
self.load_tabs('web')
else:
self.update_info_tab('\t-> You choose not to lookup when local tab is found...');
else:
# inform user on info tab about success at fetching data
self.update_info_tab('\t-> tabs found on ' + params['source'] + ' for \'' + params['artist'] + '\' - \'' + params['title'] + '\'.')
tab = Tab('#' + str(len(self.notebook.get_children())) + ' ' + params['source'], data)
tab.set_meta('artist', params['artist'])
tab.set_meta('title', params['title'])
self.tab_list.append(tab)
self.update_notebook(params['source'], params['artist'], params['title'])
def update_info_tab(self, new_content):
self.info_tab.add_content(new_content)
if len(self.notebook.get_children()) == 0:
# create info tab for the first time
scroll = self.create_page(self.info_tab.content)
self.notebook.prepend_page(scroll, Gtk.Label(self.info_tab.label))
else:
# update existing info tab
infoTab = self.notebook.get_nth_page(0).get_child()
textbuffer = infoTab.get_buffer()
textbuffer.set_text(self.info_tab.content)
self.notebook.show()
self.vbox.show_all()
def notify_finish(self, content):
self.update_info_tab(content)
self.hide_pulse()
def update_notebook(self, source, artist, title):
""" Update notebook """
if len(self.tab_list) == 0:
print 'no tabs in tab_list !'
else:
# data tabs
for tab in self.tab_list:
if not(tab.label == "Not Found"):
scroll = self.create_page(tab.content)
self.notebook.append_page(scroll, Gtk.Label(tab.label))
self.tab_list = []
self.notebook.show()
self.vbox.show_all()
def create_page(self, text):
fontdesc = Pango.FontDescription("Courier New 8")
textbuffer = Gtk.TextBuffer()
textbuffer.set_text(text)
textview = Gtk.TextView()
textview.set_buffer(textbuffer)
textview.set_editable(False)
textview.modify_font(fontdesc)
scroll = Gtk.ScrolledWindow()
scroll.set_policy(Gtk.PolicyType.AUTOMATIC, Gtk.PolicyType.AUTOMATIC)
scroll.set_shadow_type(Gtk.ShadowType.IN)
scroll.add(textview)
scroll.show()
return scroll
N = int(sys.argv[1])
iterations = int(sys.argv[2])
# debug = True
debugger = Debugger(on=False, cell=False, table=False, program_info=False, history=True)
rank = comm.Get_rank()
processes = comm.Get_size()
if N % processes != 0:
print("Error - cannot partition the problem")
comm.Abort()
rows = int(N / processes)
mapper = Mapper(N, rank, rows, debugger)
table = Tab(N, rank, rows, mapper, debugger)
initial_rank = int(processes / 2)
debugger.print_program_info("initial_rank = " + str(initial_rank))
if rank == initial_rank:
target_x = int(N / 2)
target_y = int(N / 2)
debugger.print_program_info("First cell = " + str(target_x) + "," + str(target_y))
initial_bacteria = Bacteria(target_x, target_y, chance=1)
table.update_table([initial_bacteria])
def split_bacterias_per_process(bacterias_info, min_x, max_x):
send_up = list(filter(lambda bacteria: bacteria.target_x == min_x - 1, bacterias_info))
send_down = list(filter(lambda bacteria: bacteria.target_x == max_x + 1, bacterias_info))
# print(len(send_up), len(send_down), len(bacterias_info))
def __init__(self, nb):
Tab.__init__(self, nb)
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.1,0.1,0.85,0.86])
self.ax1.set_ylabel('sig(x)', fontsize=9)
self.ax1.set_xlabel('Resolution', fontsize=9)
self.ax1.tick_params(labelsize=8)
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.side_sizer = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
self.side_sizer.Add(wx.StaticText(self, -1, 'Vm'), 0, wx.EXPAND)
self._mv = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._mv, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'Solvent'), 0, wx.EXPAND)
self._s = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._s, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'Resolution'), 0, wx.EXPAND)
self._dmin = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._dmin, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'Completeness'), 0, wx.EXPAND)
self._c = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._c, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'R Factor'), 0, wx.EXPAND)
self._r = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._r, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'R Free'), 0, wx.EXPAND)
self._rfree = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._rfree, 0, wx.EXPAND)
self.side_sizer.AddSpacer(20)
self.side_sizer.AddSpacer(20)
self.side_sizer.Add(wx.StaticText(self, -1, 'sig(x) R'), 0, wx.EXPAND)
self._sigxr = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._sigxr, 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'sig(x) Rfree'), 0, wx.EXPAND)
self._sigxrf = wx.StaticText(self, -1, '')
self.side_sizer.Add(self._sigxrf, 0, wx.EXPAND)
self.side_sizer.AddSpacer(20)
self.side_sizer.AddSpacer(20)
self.side_sizer.Add(wx.StaticText(self, -1, 'sig(x) - 3sig (ASP)'), 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, '0.024'), 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, 'sig(x) - 3sig (HIS)'), 0, wx.EXPAND)
self.side_sizer.Add(wx.StaticText(self, -1, ''), 0, wx.EXPAND)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.side_sizer, 0, wx.EXPAND|wx.ALL, 10)
self.sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.sizer)
def __init__(self, names, ui, config):
self.config = config
self.tablist = []
for name in names:
tab = Tab.create(self, name)
if tab: self.tablist.append(tab)
if not self.tablist:
self.tablist = [Tab.create(self)]
self.curtab = 0
self.UI = ui
self.UI.init(self)
self.Registers = {
'a': [],
'b': [],
'c': [],
'd': [],
'e': [],
'f': [],
'g': [],
'h': [],
'i': [],
'j': [],
'k': [],
'l': [],
'm': [],
'n': [],
'o': [],
'p': [],
'q': [],
'r': [],
's': [],
't': [],
'u': [],
'v': [],
'w': [],
'x': [],
'y': [],
'z': [],
'A': [],
'B': [],
'C': [],
'D': [],
'E': [],
'F': [],
'G': [],
'H': [],
'I': [],
'J': [],
'K': [],
'L': [],
'M': [],
'N': [],
'O': [],
'P': [],
'Q': [],
'R': [],
'S': [],
'T': [],
'U': [],
'V': [],
'W': [],
'X': [],
'Y': [],
'Z': [],
'0': [],
'1': [],
'2': [],
'3': [],
'4': [],
'5': [],
'6': [],
'7': [],
'8': [],
'9': []
}
def __init__(self, nb):
Tab.__init__(self, nb)
self._pdbt = PDBTools()
self._res_size = (200,170)
self._to_save = []
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.res = wx.StaticBitmap(self, size=self._res_size)
self.res.SetBitmap(wx.EmptyImage(self._res_size[0], self._res_size[1]).ConvertToBitmap())
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
#self.ax1.set_frame_on(False)
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.ax2 = self.ax1.twinx()
self.ax2.set_position([0.10,0.153,0.80,0.81])
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
self._highlight = -2
self._bond_lengths = ''
self._std_devs = ''
self._residue_selection = []
self._chain_lookup = {}
self._residue_type = 0
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self.omitted_title = wx.StaticBox( self, -1, "Omitted" )
self.omitted_sizer = wx.StaticBoxSizer( self.omitted_title, wx.HORIZONTAL)
self.selected_title = wx.StaticBox( self, -1, "Displayed" )
self.selected_sizer = wx.StaticBoxSizer( self.selected_title, wx.HORIZONTAL)
self.residue_info_title = wx.StaticBox( self, -1, "Residue Info: " )
self.residue_info_sizer = wx.StaticBoxSizer( self.residue_info_title, wx.VERTICAL)
#self.residue_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
#self.residue_info.Add(wx.StaticText(self, -1, 'D(C-O)'))
#self._dco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._dco)
#self.residue_info.Add(wx.StaticText(self, -1, 'S(D(C-O))'))
#self._sdco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._sdco)
#self.residue_info.Add(wx.StaticText(self, -1, 'Level'))
#self._lev = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._lev)
#self.residue_info_sizer.Add(self.residue_info, 0)
self.residue_info_sizer.Add(self.res, 0)
self.residue_sel = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_MULTIPLE)
self.residue_sel.Bind(wx.EVT_LISTBOX, self._update_sel)
self.omitted_res = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_SINGLE)
self.omitted_res.Bind(wx.EVT_LISTBOX, self._goto_omitted)
self.data_box = wx.BoxSizer(wx.HORIZONTAL)
self.data_box.Add(wx.StaticText(self, -1, 'Residue Type'), 0, wx.EXPAND|wx.ALL, 5)
self.res_type = wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self.data_box.Add(self.res_type, 0, wx.EXPAND|wx.ALL, 5)
self.omitted_sizer.Add(self.omitted_res, 1, wx.EXPAND|wx.ALL, 0)
self.selected_sizer.Add(self.residue_sel, 1, wx.EXPAND|wx.ALL, 0)
self.ressel_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.ressel_sizer.Add(self.omitted_sizer, 1, wx.EXPAND|wx.ALL, 5)
self.ressel_sizer.Add(self.selected_sizer, 1, wx.EXPAND|wx.ALL, 5)
lig = metallicbutton.MetallicButton(self, -1, 'Ligands', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(75, 25))
save = metallicbutton.MetallicButton(self, -1, 'Figure', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
tab = metallicbutton.MetallicButton(self, -1, 'Data', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
self.Bind(wx.EVT_BUTTON, self._view_ligands, lig)
self.Bind(wx.EVT_BUTTON, self._save_figure, save)
self.Bind(wx.EVT_BUTTON, self._save_data, tab)
self.button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.button_sizer.Add(save, 0, wx.LEFT, 5)
self.button_sizer.Add(tab, 0, wx.LEFT, 5)
self.button_sizer.Add(lig, 0, wx.LEFT, 5)
self.residue_box = wx.BoxSizer(wx.VERTICAL)
self.residue_box.Add(self.data_box, 0)
self.residue_box.Add(self.residue_info_sizer, 0, wx.EXPAND, 10)
self.residue_box.Add(self.ressel_sizer, 0)
self.residue_box.Add(self.button_sizer, 0)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.residue_box, 1, wx.EXPAND|wx.ALL, 5)
self.averages = wx.StaticText(self, -1, '', style=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
#self.bottom_sizer.Add(self.button_sizer, 0)
self.bottom_sizer.Add(self.averages, 1, wx.EXPAND)
self.canvas_sizer = wx.BoxSizer(wx.VERTICAL)
self.canvas_sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL)
self.canvas_sizer.Add(self.bottom_sizer, 0, wx.EXPAND)
self.main.Add(self.canvas_sizer, 3, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
self.main.Fit(self)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.canvas.mpl_connect('pick_event', self._show_series)
def main():
tab = Tab()
history = History()
tab.setUrl("http://tutorialspoint.com")
history.add(tab.saveUrl())
tab.setUrl("https://www.python.org/doc/")
history.add(tab.saveUrl())
tab.setUrl("http://www.trome.com.pe")
print("Current web url: " + tab.getUrl())
print("Back button is clicked.. ")
tab.restoreFromSavedUrl(history.get(1))
print("Saved url: " + tab.getUrl())
print("Back button again.. ")
tab.restoreFromSavedUrl(history.get(0))
print("Saved url: " + tab.getUrl())
def generate_tab(self):
newTab = Tab(self.name.text())
self.main.tabList.append(newTab)
print(newTab.title)
self.main.add_tab(newTab)
self.close()
def __init__(self, nb):
Tab.__init__(self, nb)
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.res = wx.StaticBitmap(self, size=(200,237))
self.res.SetBitmap(wx.EmptyImage( 200,237 ).ConvertToBitmap())
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
self.ax2 = self.ax1.twinx()
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
self._highlight = 0
self._bond_lengths = ''
self._std_devs = ''
self._residue_selection = []
self._residue_type = 0
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self.omitted_title = wx.StaticBox( self, -1, "Omitted" )
self.omitted_sizer = wx.StaticBoxSizer( self.omitted_title, wx.HORIZONTAL)
self.selected_title = wx.StaticBox( self, -1, "Displayed" )
self.selected_sizer = wx.StaticBoxSizer( self.selected_title, wx.HORIZONTAL)
self.residue_info_title = wx.StaticBox( self, -1, "Residue Info: " )
self.residue_info_sizer = wx.StaticBoxSizer( self.residue_info_title, wx.HORIZONTAL)
self._labels = [
wx.StaticText(self, -1, 'D(C-O)'),
wx.StaticText(self, -1, 'S(D(C-O))'),
wx.StaticText(self, -1, 'Level'),
wx.StaticText(self, -1, 'Avg S'),
wx.StaticText(self, -1, 'Avg B'),
]
self._values = [ wx.StaticText(self, -1, '') for x in range(len(self._labels)) ]
self.residue_info = wx.GridSizer(rows=5, cols=2, vgap=5, hgap=5)
for i in range(len(self._labels)):
self.residue_info.Add(self._labels[i], 0, wx.EXPAND)
self.residue_info.Add(self._values[i], 0, wx.EXPAND)
self.residue_info_sizer.Add(self.residue_info, 0)
self.residue_info_sizer.Add(self.res, 0)
self.residue_sel = wx.ListBox(self, 26, wx.DefaultPosition, (80, 100), [], wx.LB_MULTIPLE)
self.residue_sel.Bind(wx.EVT_LISTBOX, self._update_sel)
self.omitted_res = wx.ListBox(self, 26, wx.DefaultPosition, (80, 100), [], wx.LB_SINGLE)
self.omitted_res.Bind(wx.EVT_LISTBOX, self._goto_omitted)
self._data_widgets = [ wx.StaticText(self, -1, 'Bond Lengths'),
wx.ComboBox(self, -1, '', choices=[], style=wx.CB_READONLY),
wx.StaticText(self, -1, 'Standard Deviations'),
wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY),
wx.StaticText(self, -1, 'Residue Type'),
wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)]
self._data_widgets[1].Bind(wx.EVT_COMBOBOX, self._set_data)
self._data_widgets[3].Bind(wx.EVT_COMBOBOX, self._set_data)
self._data_widgets[5].Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self._data_widgets[5].SetStringSelection('Aspartate')
self.data_box = wx.GridSizer(rows=3, cols=2, vgap=5, hgap=5)
for i in range(len(self._data_widgets)):
self.data_box.Add(self._data_widgets[i], 0, wx.EXPAND)
self.omitted_sizer.Add(self.omitted_res)
self.selected_sizer.Add(self.residue_sel)
self.button_sizer = wx.BoxSizer(wx.VERTICAL)
coot = wx.BitmapButton(self, 1, wx.Image('Resources/Icons/coot_logo.png', wx.BITMAP_TYPE_PNG).ConvertToBitmap())
pymol = wx.BitmapButton(self, 2, wx.Image('Resources/Icons/pymol.png', wx.BITMAP_TYPE_PNG).ConvertToBitmap())
plot = wx.BitmapButton(self, 3, wx.Image('Resources/Icons/plot_tiny.png', wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.button_sizer.Add(coot, 0, wx.EXPAND)
self.button_sizer.Add(pymol, 0, wx.EXPAND)
self.button_sizer.Add(plot, 0, wx.EXPAND)
plot.Bind(wx.EVT_BUTTON, self._save_figure)
self.ressel_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.ressel_sizer.Add(self.omitted_sizer)
self.ressel_sizer.Add(self.selected_sizer)
self.ressel_sizer.Add(self.button_sizer)
self.residue_box = wx.BoxSizer(wx.VERTICAL)
self.residue_box.Add(self.data_box)
self.residue_box.Add(self.residue_info_sizer, 0, wx.EXPAND | wx.TOP, 10)
self.residue_box.Add(self.ressel_sizer)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.residue_box, 0, wx.ALL, 10)
self.main.Add(self.canvas, 0, wx.ALL, 5)
self.SetSizer(self.main)
self.main.Fit(self)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.update_inputs()
