def finishInit(self):
global decodeFile
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.decode import decodeFile
from cadnano.controllers.documentcontroller import DocumentController
from cadnano.views.pathview import pathstyles as styles
styles.setFontMetrics()
doc = Document()
self._document = self.createDocument(base_doc=doc)
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
self.dontAskAndJustDiscardUnsavedChanges = True
util.loadAllPlugins()
if self.argns.interactive:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self._document
print("\tw()\tshortcut for d().controller().window()")
def w():
return self._document.controller().window()
print("\tp()\tshortcut for d().selectedInstance().reference()")
def p():
return self._document.selectedInstance().reference()
print("\tpi()\tthe PartItem displaying p()")
def pi():
part_instance = self._document.selectedInstance()
return w().pathroot.partItemForPart(part_instance)
print("\tvh(i)\tshortcut for p().reference().getStrandSets(i)")
def strandsets(id_num):
return p().reference().getStrandSets(id_num)
print("\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(id_num):
partitem = pi()
return partitem.vhItemForIdNum(id_num)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a': self, 'd': d, 'w': w,
'p': p, 'pi': pi, 'vhi': vhi,
})
def finishInit(self):
global decodeFile
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.nnodecode import decodeFile
from cadnano.gui.controllers.documentcontroller import DocumentController
from cadnano.gui.views.pathview import pathstyles as styles
doc = Document()
self._document = self.createDocument(base_doc=doc)
styles.setFontMetrics()
os.environ['CADNANO_DISCARD_UNSAVED'] = 'True' # added by Nick
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
util.loadAllPlugins()
if self.argns.interactive:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self._document
print("\tw()\tshortcut for d().controller().window()")
def w():
return self._document.controller().window()
print("\tp()\tshortcut for d().selectedInstance().reference()")
def p():
return self._document.selectedInstance().reference()
print("\tpi()\tthe PartItem displaying p()")
def pi():
part_instance = self._document.selectedInstance()
return w().pathroot.partItemForPart(part_instance)
print("\tvh(i)\tshortcut for p().reference().getStrandSets(i)")
def strandsets(id_num):
return p().reference().getStrandSets(id_num)
print("\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(id_num):
partitem = pi()
return partitem.vhItemForIdNum(id_num)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a': self, 'd': d, 'w': w,
'p': p, 'pi': pi, 'vhi': vhi,
})
def finishInit(self):
global decode
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.nnodecode import decode
from cadnano.gui.controllers.documentcontroller import DocumentController
from cadnano.gui.views.pathview import pathstyles as styles
doc = Document()
self.d = self.newDocument(base_doc=doc)
styles.setFontMetrics()
os.environ['CADNANO_DISCARD_UNSAVED'] = 'True' ## added by Nick
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
if os.environ.get('CADNANO_DEFAULT_DOCUMENT', False) and not self.ignoreEnv():
self.shouldPerformBoilerplateStartupScript = True
util.loadAllPlugins()
if "-i" in self.argv:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self.d
print("\tw()\tshortcut for d().controller().window()")
def w():
return self.d.controller().window()
print("\tp()\tshortcut for d().selectedPart()")
def p():
return self.d.selectedPart()
print("\tpi()\tthe PartItem displaying p()")
def pi():
return w().pathroot.partItemForPart(p())
print( "\tvh(i)\tshortcut for p().virtualHelix(i)")
def vh(vhref):
return p().virtualHelix(vhref)
print( "\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(vhref):
partitem = pi()
vHelix = vh(vhref)
return partitem.vhItemForVH(vHelix)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a':self, 'd':d, 'w':w,\
'p':p, 'pi':pi, 'vh':vh, 'vhi':vhi,\
})
def finishInit(self):
global decode
global Document
global DocumentController
from cadnano.document import Document
from cadnano.fileio.nnodecode import decode
from cadnano.gui.controllers.documentcontroller import DocumentController
from cadnano.gui.views import styles
doc = Document()
self.d = self.newDocument(base_doc=doc)
styles.setFontMetrics()
os.environ['CADNANO_DISCARD_UNSAVED'] = 'True' ## added by Nick
if os.environ.get('CADNANO_DISCARD_UNSAVED', False) and not self.ignoreEnv():
self.dontAskAndJustDiscardUnsavedChanges = True
if os.environ.get('CADNANO_DEFAULT_DOCUMENT', False) and not self.ignoreEnv():
self.shouldPerformBoilerplateStartupScript = True
util.loadAllPlugins()
if "-i" in self.argv:
print("Welcome to cadnano's debug mode!")
print("Some handy locals:")
print("\ta\tcadnano.app() (the shared cadnano application object)")
print("\td()\tthe last created Document")
def d():
return self.d
print("\tw()\tshortcut for d().controller().window()")
def w():
return self.d.controller().window()
print("\tp()\tshortcut for d().selectedPart()")
def p():
return self.d.selectedPart()
print("\tpi()\tthe PartItem displaying p()")
def pi():
return w().pathroot.partItemForPart(p())
print( "\tvh(i)\tshortcut for p().virtualHelix(i)")
def vh(vhref):
return p().virtualHelix(vhref)
print( "\tvhi(i)\tvirtualHelixItem displaying vh(i)")
def vhi(vhref):
partitem = pi()
vHelix = vh(vhref)
return partitem.vhItemForVH(vHelix)
print("\tquit()\tquit (for when the menu fails)")
print("\tgraphicsItm.findChild() see help(pi().findChild)")
interact('', local={'a':self, 'd':d, 'w':w,\
'p':p, 'pi':pi, 'vh':vh, 'vhi':vhi,\
})
def addPluginAtPath(self, fname):
self.fileopendialog.close()
fname = str(fname[0])
print("Attempting to open plugin %s" % fname)
try:
zf = zipfile.ZipFile(fname, "r")
except Exception as e:
self.failWithMsg("Plugin file seems corrupt: %s." % e)
return
tdir = tempfile.mkdtemp()
try:
for f in zf.namelist():
if f.endswith("/"):
os.makedirs(os.path.join(tdir, f))
for f in zf.namelist():
if not f.endswith("/"):
zf.extract(f, tdir)
except Exception as e:
self.failWithMsg("Extraction of plugin archive failed: %s." % e)
return
files_in_zip = [(f, os.path.join(tdir, f)) for f in os.listdir(tdir)]
try:
self.confirmDestructiveIfNecessary(files_in_zip)
self.removePluginsToBeOverwritten(files_in_zip)
self.movePluginsIntoPluginsFolder(files_in_zip)
except OSError:
print(
"Couldn't copy files into plugin directory, attempting\
again after boosting privileges."
)
if platform.system() == "Darwin":
self.darwinAuthedMvPluginsIntoPluginsFolder(files_in_zip)
elif platform.system() == "Linux":
self.linuxAuthedMvPluginsIntoPluginsFolder(files_in_zip)
else:
print("Can't boost privelages on platform %s" % platform.system())
loadedAPlugin = util.loadAllPlugins()
if not loadedAPlugin:
print("Unable to load anythng from plugin %s" % fname)
self.readPreferences()
shutil.rmtree(tdir)
def addPluginAtPath(self, fname):
self.fileopendialog.close()
fname = str(fname[0])
print("Attempting to open plugin %s" % fname)
try:
zf = zipfile.ZipFile(fname, 'r')
except Exception as e:
self.failWithMsg("Plugin file seems corrupt: %s." % e)
return
tdir = tempfile.mkdtemp()
try:
for f in zf.namelist():
if f.endswith('/'):
os.makedirs(os.path.join(tdir, f))
for f in zf.namelist():
if not f.endswith('/'):
zf.extract(f, tdir)
except Exception as e:
self.failWithMsg("Extraction of plugin archive failed: %s." % e)
return
files_in_zip = [(f, os.path.join(tdir, f)) for f in os.listdir(tdir)]
try:
self.confirmDestructiveIfNecessary(files_in_zip)
self.removePluginsToBeOverwritten(files_in_zip)
self.movePluginsIntoPluginsFolder(files_in_zip)
except OSError:
print("Couldn't copy files into plugin directory, attempting\
again after boosting privileges.")
if platform.system() == 'Darwin':
self.darwinAuthedMvPluginsIntoPluginsFolder(files_in_zip)
elif platform.system() == 'Linux':
self.linuxAuthedMvPluginsIntoPluginsFolder(files_in_zip)
else:
print("Can't boost privelages on platform %s" %
platform.system())
loadedAPlugin = util.loadAllPlugins()
if not loadedAPlugin:
print("Unable to load anythng from plugin %s" % fname)
self.readPreferences()
shutil.rmtree(tdir)