def create_genome_map(self,phages):
self.c = db_conf.db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor()
self.db = pham.db(c = self.c)
lengths = []
for phage in phages:
length = phamerator_manage_db.get_length_of_genome(self.c,phage["PhageID"])
lengths.append(length)
length = max(lengths)
self.canvas = goocanvas.Canvas()
canvasInterface = cartographer.CanvasInterface(self.c, self.canvas)
self.canvas.set_root_item_model(canvasInterface.create_canvas_model(phages, length))
zoomFactor = 20.0
self.canvas.set_bounds(0,0,length/zoomFactor, 100000)
needs_new = True
while needs_new == True:
name = "/tmp/phageSOAP/tmp" + str(hash(str(random.randint(1,64563))+str(hash(self.canvas))))
if os.path.exists(name):
needs_new = True
else:
needs_new = False
self.current_genome_map = name
surface = cairo.SVGSurface (self.current_genome_map, (length/zoomFactor)+72, 5*72*len(phages))
cr = cairo.Context (surface)
cr.translate (36, 130)
self.canvas.render (cr, None, 0.1)
cr.show_page ()
print "\n>genome map generated\n"
return "genome map generated\n"
def get_length_of_genome(self, PhageID):
self.c = db_conf.db_conf(username=self.username,
password=self.password,
server=self.server,
db=self.database).get_cursor()
self.db = pham.db(c=self.c)
return phamerator_manage_db.get_length_of_genome(self.c, PhageID)
def create_genome_map(self, phages):
self.c = db_conf.db_conf(username=self.username,
password=self.password,
server=self.server,
db=self.database).get_cursor()
self.db = pham.db(c=self.c)
lengths = []
for phage in phages:
length = phamerator_manage_db.get_length_of_genome(
self.c, phage["PhageID"])
lengths.append(length)
length = max(lengths)
self.canvas = goocanvas.Canvas()
canvasInterface = cartographer.CanvasInterface(self.c, self.canvas)
self.canvas.set_root_item_model(
canvasInterface.create_canvas_model(phages, length))
zoomFactor = 20.0
self.canvas.set_bounds(0, 0, length / zoomFactor, 100000)
needs_new = True
while needs_new == True:
name = "/tmp/phageSOAP/tmp" + str(
hash(str(random.randint(1, 64563)) + str(hash(self.canvas))))
if os.path.exists(name):
needs_new = True
else:
needs_new = False
self.current_genome_map = name
surface = cairo.SVGSurface(self.current_genome_map,
(length / zoomFactor) + 72,
5 * 72 * len(phages))
cr = cairo.Context(surface)
cr.translate(36, 130)
self.canvas.render(cr, None, 0.1)
cr.show_page()
print "\n>genome map generated\n"
return "genome map generated\n"
def get_length_of_genome(self,PhageID): self.c = db_conf.db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor() self.db = pham.db(c = self.c) return phamerator_manage_db.get_length_of_genome(self.c,PhageID)
