def OnPaint(self, evt):
dc = wx.PaintDC(self)
#dc.Clear()
w, h = dc.GetSizeTuple()
dc.SetPen(wx.RED_PEN)
cr = ContextFromDC(dc)
cr.scale(w, h)
cr.set_source_rgb(1, 0, 1)
cr.set_line_width(0.002)
path = self.path.send(cr)
x, y = self.data.next()
#dc.DrawLines(numpy.array([x*w,y*h]).T)
cairo_tools.polyline(cr, x, y)
cairo_tools.stamp_at(cr, path, x, y)
cr.stroke()
class TextEdit(DNApyBaseDrawingClass):
'''
new Text editor that allows to display dna and
complementary dna in a usefull manner
Also it can and should show:
- features (done, buggy)
- restriction enzymes (partly)
- dna modifications (todo)
- primer (todo)
'''
def __init__(self, parent, id):
#parent
self.parent = parent
# get data
self.dna = genbank.gb.GetDNA()
self.cdna = genbank.gb.GetDNA()
# settings for the editor
self.sY = 60 # offset top
self.dX = 8 # border left and right
self.textSpacing = 80 # seperation of lines
self.fontsize = 9 # line size
self.lineGap = 6
# interactive cursor
self.PositionPointer = 1
self.PositionPointerEnd = False
# initial minimal height of the editor
self.minHeight = 200
# storage dict, to prevent recalculating to much
self.cairoStorage = {
'features' : None, # feature Object
'fPaths' : [], # path of alls features as List
'cursorPath': None,
'cursor' : None,
'enzymes' : {}, # enzymes object
'ePaths' : [], # enzymes drawn
'ticks' : None, # ticks object --> self.dna
'tPaths' : [] # ticks drawn
}
# call window
DNApyBaseDrawingClass.__init__(self, parent, wx.ID_ANY)
# bind events
self.Bind(wx.EVT_LEFT_DCLICK, self.OnLeftDouble)
self.Bind(wx.EVT_LEFT_DOWN, self.OnLeftDown)
self.Bind(wx.EVT_LEFT_UP, self.OnLeftUp)
self.Bind(wx.EVT_MOTION, self.OnMotion) # drag and drop, selection etc.
self.Bind(wx.EVT_KEY_DOWN, self.OnKeyPress) #This is important for controlling the input into the editor
####### Modify methods from base calss to fit current needs #########
def update_globalUI(self):
'''
Method should be modified as to update other panels in response to changes in own panel.
'''
MSG_CHANGE_TEXT = "change.text"
pub.sendMessage(MSG_CHANGE_TEXT, text="DNA view says update!")
def update_ownUI(self):
"""
This would get called if the drawing needed to change, for whatever reason.
The idea here is that the drawing is based on some data generated
elsewhere in the system. If that data changes, the drawing needs to
be updated.
This code re-draws the buffer, then calls Update, which forces a paint event.
"""
#####################
# remove buffered features, to force redraw:
self.cairoStorage['features'] = None
# The Buffer init is done here, to make sure the buffer is always
# the same size as the Window
wC, hC = self.parent.GetClientSize()
wP, hP = self.parent.GetSize()
self.SetSize(wx.Size(wC, self.minHeight))
self.parent.SetVirtualSize(wx.Size(wC-30, self.minHeight))
# Make new offscreen bitmap: this bitmap will always have the
# current drawing in it, so it can be used to save the image to
# a file, or whatever.
# if wC != 0 and hC !=0:
# self._Buffer = wx.EmptyBitmap(wC, self.minHeight)
# else:
# self._Buffer = wx.EmptyBitmap(wP, hP)
##########################
# start dc
dc = wx.MemoryDC()
dc.SelectObject(self._Buffer)
dc.SetBackground(wx.Brush("White"))
dc.Clear()
# make a cairo context
self.ctx = ContextFromDC(dc)
# start pango as a font backend
self.pango = pangocairo.CairoContext(self.ctx)
self.pango.set_antialias(cairo.ANTIALIAS_SUBPIXEL)
# reload dna
self.dna = genbank.gb.GetDNA()
if self.dna != None:
self.cdna = dna.C(self.dna)
else:
self.dna = '' # no dna, if there is nothing
self.cdna = '' # empty cdna
# render the text
self.displayText()
# create colorful features here
self.drawFeatures()
# draw enzymes
self.drawEnzymes()
# draw a cursor
self.drawCursor()
# draw Tics above all!
self.drawTicks()
# end of canvas handling
dc.SelectObject(wx.NullBitmap) # need to get rid of the MemoryDC before Update() is called.
self.Refresh()
self.Update()
return None
def displayText(self):
''' main function for the editors text capabilities
here the text gets positioned and all its color.
Also the selection highlight is done here'''
# get window size to wrap text
width, height = self.parent.GetVirtualSize()
if width > 30:
w = width - self.dX
else:
w = width
# save with for other functions
self.w = w
# start layout
layout = self.pango.create_layout()
layout.set_wrap(pango.WRAP_WORD_CHAR)
layout.set_width(pango.SCALE * w)
layout.set_spacing(pango.SCALE *self.textSpacing)
layout.set_alignment(pango.ALIGN_LEFT)
# new attr list for the dna
dnaAttr = pango.AttrList()
# color
gray = 56 * 65535/255
fg_color = pango.AttrForeground(gray,gray,gray, 0, len(self.dna))
spacing = pango.AttrLetterSpacing(1500, 0, len(self.dna))
# add attr
dnaAttr.insert(fg_color)
dnaAttr.insert(spacing)
# set attr
layout.set_attributes(dnaAttr)
#set font
font = pango.FontDescription("monospace normal "+ "1")
font.set_size(pango.SCALE * self.fontsize)
layout.set_font_description(font)
# font and color are prepared for the DNA
# get selection, if any
start, end, zero = self.get_selection()
if end != -1:
# correct direktion of selection
if start > end:
s = end - 1
e = start
else:
s = start - 1
e = end
# make markup selection
if abs(end-start) >= 0 and zero == -1 and end != -1 :
senseText = self.dna[0:s] + '<span background="#0082ED">'+self.dna[s:e] + '</span>' + self.dna[e:]
antiText = self.cdna[0:s] + '<span background="#0082ED">'+self.cdna[s:e] + '</span>' + self.cdna[e:]
elif abs(end-start) >= 0 and zero == 1 and end != -1:
senseText = '<span background="#0082ED">'+self.dna[0:s] + '</span>' + self.dna[s:e] + '<span background="#0082ED">'+self.dna[e:] + '</span>'
antiText = '<span background="#0082ED">'+self.cdna[0:s] + '</span>' + self.cdna[s:e] + '<span background="#0082ED">'+self.cdna[e:] + '</span>'
else:
senseText = self.dna
antiText = self.cdna
# output dna
self.ctx.move_to(self.dX,self.sY)
layout.set_markup(senseText)
self.pango.update_layout(layout)
self.pango.show_layout(layout)
# copy sense layout
self.senseLayout = layout.copy()
# determine the length and height of a line
self.lineLength = layout.get_line(0).length
x1, y1, w1, h1 = self.senseLayout.index_to_pos(1)
x2, y2, w2, h2 = self.senseLayout.index_to_pos(1+self.lineLength)
self.lineHeight = abs(y1 - y2) / pango.SCALE
# print anti sense strain
self.ctx.move_to(self.dX,self.sY + self.fontsize + self.lineGap)
layout.set_markup(antiText)
self.pango.update_layout(layout)
self.pango.show_layout(layout)
# update the height of the context, based on the inserted dna
w, h = layout.get_pixel_size()
self.minHeight = h + 2*self.sY
# resize window
# w,h = self.GetSize() # prevents missfomration on resize
# self.SetSize(wx.Size(w,self.minHeight)) # prevents missfomration on resize
return None
def drawFeatures(self):
features = genbank.gb.get_all_feature_positions()
paths = {} # (color, path)
featureheight = 10
if self.cairoStorage['features'] != features :
# something changed, we have to draw the paths new
self.drawn_fw_locations = []
self.drawn_rv_locations = []
# font settings
# draw the name somewhere at the start
nameheight = 9 # px
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
self.ctx.set_font_size(nameheight)
for feature in features:
featuretype, complement, start, finish, name, index = feature
if featuretype != "source":
# get names
hname = self.hitName(name, index)
name = self.nameBeautiful(name)
#get position
xs, ys, ws, hs = self.senseLayout.index_to_pos(start)
xf, yf, wf, hf = self.senseLayout.index_to_pos(finish+1)
# linecount:
# if ys and yf are not the same, we have feature over multiple lines!
dy = abs(ys - yf) / pango.SCALE
ySteps = dy / self.lineHeight # number of lines!
xs = xs / pango.SCALE
xf = xf / pango.SCALE
ys = (ys / pango.SCALE) + self.sY
yf = yf / pango.SCALE
# first sense strain over the text
if complement == False:
self.drawn_fw_locations, l = self.find_overlap(self.drawn_fw_locations, (start, finish))
level = l * (featureheight+6)
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(name)
ys = ys - level - 5
self.ctx.move_to(xs + 10, ys )
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# end name
# box for name
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys-featureheight, TextWidth + 20 , nameheight + 5)
# lines above the dna
while ySteps >= 0:
if ySteps == 0:
xE = xf
else:
xE = self.w + 5 # TODO: figure out, why we need to add 5 px, to make it look correct
# make a box-path
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys-5, xE-xs , 5)
# the second x start is always 8px, or what we will opt for
xs = self.dX
ys = ys + self.lineHeight
ySteps = ySteps - 1
# path
fillpath = self.ctx.copy_path()
self.ctx.new_path()
# get color
color = eval(featuretype)['fw'] #get the color of feature (as string)
else:
self.drawn_rv_locations, l = self.find_overlap(self.drawn_rv_locations, (start, finish))
level = l * (featureheight+6)
# set y
ys = ys + 2*self.fontsize + self.lineGap + 9 + level
# lines below the dna
while ySteps >= 0:
if ySteps == 0:
xE = xf
else:
xE = self.w
# make the path
#self.ctx.move_to(xs, ys)
#self.ctx.line_to(xE, ys)
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys+5, xE-xs , 5)
xs = self.dX
ys = ys + self.lineHeight
ySteps = ySteps - 1
# change y:
ys = ys - self.lineHeight
# buffer path
bufferPath = self.ctx.copy_path()
self.ctx.new_path()
# name at the end:
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(name)
self.ctx.move_to(xf - TextWidth - 10, ys + 10 )
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# end name
# box for name
self.ctx.append_path(bufferPath)
self.ctx.move_to(xf - TextWidth, ys + featureheight)
self.ctx.rectangle(xf - TextWidth - 20, ys, TextWidth + 20 , nameheight + 5)
# get path
fillpath = self.ctx.copy_path()
self.ctx.new_path()
# get color
color = eval(featuretype)['fw'] #get the color of feature (as string)
paths[hname] = (color,fillpath ,textpath)
self.ctx.new_path() # clear canvas
# save the paths
self.cairoStorage['fPaths'] = paths
# update storage status
self.cairoStorage['features'] = features
# draw the beautiful features
for a in self.cairoStorage['fPaths']:
color, path, tpath = self.cairoStorage['fPaths'][a]
# get color
assert type(color) == str
r,g,b = colcol.hex_to_rgb(color)
r = float(r)/255
g = float(g)/255
b = float(b)/255
# append and draw path
self.ctx.append_path(path)
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(r ,g ,b , 1) # Solid color
#self.ctx.stroke_preserve()
self.ctx.fill()
# write text
self.ctx.append_path(tpath)
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(1 ,1 ,1 , 1) # Solid color
self.ctx.fill()
return None
def drawEnzymes(self):
# load enzymes
enzymes = genbank.gb.restrictionEnzymes.selection
# create hash of selection and DNA
hashable = "%s%s" % (frozenset(enzymes), genbank.gb.gbfile['dna'])
e1 = hashlib.md5(hashable).hexdigest()
if e1 != self.cairoStorage['enzymes']:
nameheight = 9 # px
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
self.ctx.set_font_size(nameheight)
dna = self.dna
length = len(dna)
index = 0 # same as in plasmid_GUI.py
enzymesPaths = {}
# loop enzymes ordered dict
for e in enzymes:
for site in enzymes[e].restrictionSites:
name, start, end, cut51, cut52, dnaMatch = site
startRef = start - 1
hitname = self.hitName(name, index)
# get position to draw
xs, ys, ws, hs = self.senseLayout.index_to_pos(startRef)
xs = xs / pango.SCALE + self.dX
ys = ys / pango.SCALE + self.sY
hs = hs / pango.SCALE
# move there, but above the line
y = ys# - hs
self.ctx.move_to(xs,y)
# print text as path
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# make a line, representing the cut
xC51, yC51, wC51, hC51 = self.senseLayout.index_to_pos(startRef + enzymes[e].c51)
xC31, yC31, wC31, hC31 = self.senseLayout.index_to_pos(startRef + enzymes[e].c31)
xC51 = xC51 / pango.SCALE + self.dX
yC51 = yC51 / pango.SCALE + self.sY
tHeight = hC51 / pango.SCALE
xC31 = xC31 / pango.SCALE + self.dX
yC31 = yC31 / pango.SCALE + self.sY
if yC51 == yC31:
self.ctx.move_to(xC51, yC51)
self.ctx.line_to(xC51, yC51 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31, yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31, yC31 + 2 * tHeight + 0.5* self.lineGap)
else:
if yC51 <= yC31:
lineend = self.dX + self.w
linestart = self.dX
else:
# switch
linestart = self.dX + self.w
lineend = self.dX
# split the drawing in two parts
self.ctx.move_to(xC51, yC51)
self.ctx.line_to(xC51, yC51 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(lineend, yC51 + tHeight + 0.25 * self.lineGap)
# part 2
self.ctx.move_to(linestart, yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31, yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31, yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31, yC31 + 2 * tHeight + 0.5* self.lineGap)
linepath = self.ctx.copy_path()
self.ctx.new_path()
enzymesPaths[hitname] = (textpath, linepath)
# raise index
index = index + 1
# update storage
self.cairoStorage['enzymes'] = e1
self.cairoStorage['ePaths'] = enzymesPaths
# draw enzymes:
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(0.6,0.3,0.3 , 1) # Solid color
for e in self.cairoStorage['ePaths']:
path, pathc = self.cairoStorage['ePaths'][e]
self.ctx.append_path(path)
self.ctx.fill()
self.ctx.append_path(pathc)
self.ctx.stroke()
def drawTicks(self):
''' draw the nice infos about the dna position in each line'''
nameheight = 9 # px
self.ctx.set_font_size(nameheight)
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
# number of lines:
if len(self.dna) != 0 and self.cairoStorage['ticks'] != self.dna:
# count the lines:
nLines = math.ceil((len(self.dna)-1) / self.lineLength)
# empty paths:
self.cairoStorage['tPaths'] = []
n = 0 # counter
y = self.sY -2 #- self.fontsize - 2
# clear paths
self.ctx.new_path()
while n <= nLines:
self.ctx.move_to(self.dX + 3, y)
# make the tick
text = "%d" % (n * self.lineLength + 1)
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(text)
self.ctx.text_path(text)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# make a box
boxPath = self.carioRoundBox(self.dX,y - TextHeight - 2, TextWidth + 6, TextHeight + 4, 0.6)
self.ctx.new_path()
#save paths
self.cairoStorage['tPaths'].append((textpath, boxPath))
# raise counter
y = y + self.lineHeight
n = n + 1
# set storage:
self.cairoStorage['ticks'] = self.dna
# print the ticks:
self.ctx.set_line_width(0)
for i in self.cairoStorage['tPaths']:
textpath, boxPath = i
# draw box
self.ctx.set_source_rgba(1,1,1, 0.6) # white, transparent
self.ctx.append_path(boxPath)
self.ctx.fill()
# draw position
self.ctx.set_source_rgba(0,0,0,1) # dark black
self.ctx.append_path(textpath)
self.ctx.fill()
return None
def carioRoundBox(self, x, y, width=10, height=10, aspect=0.8):
''' draw a box with rounded corners '''
# from http://cairographics.org/samples/rounded_rectangle/
corner_radius = height / 10.0
radius = corner_radius / aspect
degrees = math.pi / 180.0
self.ctx.new_sub_path()
self.ctx.arc( x + width - radius, y + radius, radius, -90 * degrees, 0 * degrees)
self.ctx.arc( x + width - radius, y + height - radius, radius, 0 * degrees, 90 * degrees)
self.ctx.arc(x + radius, y + height - radius, radius, 90 * degrees, 180 * degrees)
self.ctx.arc(x + radius, y + radius, radius, 180 * degrees, 270 * degrees)
self.ctx.close_path()
path = self.ctx.copy_path()
self.ctx.new_path()
return path
def drawCursor(self):
''' draw and display cursor in the textfield'''
indexO = self.cairoStorage['cursor']
index = self.PositionPointer
pos1, pos2, zero = self.get_selection()
if indexO != index and pos2 == -1:
index = index - 1 # we save the genetic curors 1-len(), but mean the cursor 0-len()-1
# turn index to x,y
x, y, w, h = self.senseLayout.index_to_pos(index)
x = x / pango.SCALE + self.dX
y = (y / pango.SCALE) + self.sY
y1 = y
y2 = y + 0.5 * self.lineHeight
# move cursor if its the line end:
if self.PositionPointerEnd == True:
x = x + self.dX
self.ctx.move_to(x,y1)
self.ctx.line_to(x,y2)
self.cairoStorage['cursorPath'] = self.ctx.copy_path()
self.ctx.new_path()
elif pos2 != -1:
# there is a selection, so no cursor:
self.cairoStorage['cursorPath'] = None
if self.cairoStorage['cursorPath'] != None:
# draw cursor:
self.ctx.append_path(self.cairoStorage['cursorPath'])
self.ctx.set_line_width(0.3)
self.ctx.set_source_rgba(0,0,0, 1) # Solid color
self.ctx.stroke()
######################################################
def OnLeftDown(self, event):
# remove selection:
self.set_dna_selection()
# get position
x, y = self.ScreenToClient(wx.GetMousePosition())
xp = (x - self.dX) * pango.SCALE
yp = int(y - self.sY - self.fontsize) * pango.SCALE
self.LeftDownIndex = None
index = self.senseLayout.xy_to_index(xp,yp)
if index != False:
# click can be left or right of the center of the char
if index[1] == 0:
self.LeftDownIndex = index[0] + 1
else:
self.LeftDownIndex = index[0] + 2
# update cursor
self.PositionPointer = self.LeftDownIndex
self.set_cursor_position()
event.Skip() #very important to make the event propagate and fulfill its original function
def OnLeftUp(self, event):
# get selection
pos1, pos2, zero = self.get_selection()
if pos2 == -1:
# reset selection
#self.set_dna_selection()
# maybe we cliked on a feature, label or a line?
hit = self.HitTest()
if hit != None:
self.hit = hit
# we hit one, so we need to draw the selection!
# wich feature was hit?
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0,len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[i]
hName = self.hitName(name, index)
if hit == hName:
# a feature with start smaller then finish, is a featur laying over zero
if start > finish:
zero = 1 # 1 --> feature starts left and ends right of +1
# set selection
self.set_dna_selection((start,finish, zero))
self.set_cursor_position(start)
else:
self.hit = None
# update the UI maybe?
self.update_ownUI()
self.update_globalUI()
event.Skip() #very important to make the event propagate and fulfill its original function
def OnLeftDouble(self, event):
'''doubleclick aktion'''
# remove selection:
self.set_dna_selection()
# if we hit a feature, wen can open a dialog
hit = self.HitTest()
if hit != None:
# wich feature was hit?
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0,len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[i]
hName = self.hitName(name, index)
if hit == hName:
genbank.feature_selection = copy.copy(index)
dlg = featureedit_GUI.FeatureEditDialog(None, 'Edit Feature') # creation of a dialog with a title'''
dlg.ShowModal()
dlg.Center()
# update the UI maybe?
self.update_ownUI()
self.update_globalUI()
def OnMotion(self, event):
if event.Dragging() and event.LeftIsDown():
oldSel = genbank.dna_selection
# get position
x, y = self.ScreenToClient(wx.GetMousePosition())
xp = (x - self.dX) * pango.SCALE
yp = int(y - self.sY - self.fontsize) * pango.SCALE
self.LeftMotionIndex = None
index = self.senseLayout.xy_to_index(xp,yp)
# get motion cursor
if index != False:
if index[1] == 0:
self.LeftMotionIndex = index[0] + 1
else:
self.LeftMotionIndex = index[0] + 2
# update cursor
if self.LeftMotionIndex >= self.LeftDownIndex:
self.PositionPointer = self.LeftMotionIndex + 1
else:
self.PositionPointer = self.LeftMotionIndex
# end of line excepions
if (self.PositionPointer - 1) % self.lineLength == 0 and self.PositionPointer >= self.lineLength :
self.PositionPointerEnd = True
self.PositionPointer = self.PositionPointer -1
else:
self.PositionPointerEnd = False
# get selection
if self.LeftDownIndex <= self.LeftMotionIndex:
selection = (self.LeftDownIndex, self.LeftMotionIndex, -1)
else:
selection = (self.LeftMotionIndex , self.LeftDownIndex , -1)
if oldSel != selection:
self.set_dna_selection(selection) #update the varable keeping track of DNA selection
self.update_ownUI()
self.update_globalUI()
event.Skip() #very important to make the event propagate and fulfill its original function
# def OnRightUp(self, event):
# event.Skip() #very important to make the event propagate and fulfill its original function
#### rendering
####################################################################
def find_overlap(self, drawn_locations, new_range):
'''
Takes two ranges and determines whether the new range has overlaps with the old one.
If there are overlaps the overlap locations are returned.
This is used when drawing features. If two features overlap I want them drawn on different levels.
'''
assert type(drawn_locations) == list
assert type(new_range) == tuple
if drawn_locations == []:
drawn_locations.append([new_range])
return drawn_locations, 0
else:
i = 0
while i < len(drawn_locations):
overlap_found = False
for n in range(0,len(drawn_locations[i])):
if drawn_locations[i][n][0]<=new_range[0]<=drawn_locations[i][n][1] or drawn_locations[i][n][0]<=new_range[1]<=drawn_locations[i][n][1]: #if they overlap
overlap_found = True
elif new_range[0]<=drawn_locations[i][n][0]<=new_range[1] or new_range[0]<=drawn_locations[i][n][1]<=new_range[1]: #if they overlap
overlap_found = True
if overlap_found == False:
drawn_locations[i].append(new_range)
return drawn_locations, i
break
elif i+1==len(drawn_locations):
drawn_locations.append([new_range])
return drawn_locations, i+1
break
i += 1
def hitName(self, name, index):
# unique and reproducible id for each feature
name = self.nameBeautiful(name)
seq = "%s%s" % (name, index)
name = ''.join(seq.split())
return name
def HitTest(self):
'''Tests whether the mouse is over any feature or a enzyme'''
hit = None
# get the mouse positions
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
# list of all the paths:
loop = [self.cairoStorage['fPaths'], # features
self.cairoStorage['ePaths']] # enzymes
# loop over all possible paths to find the one we have under the mouse
for paths in loop:
for i in paths:
path = paths[i]
if type(path) == list or type(path) == tuple:
path = path[1]
# load the path
self.ctx.append_path(path)
self.ctx.set_line_width(0.1) # reduce linewith, so we can have nice clicking detection
inFill = self.ctx.in_fill(x2,y2)
inStroke = self.ctx.in_stroke(x2,y2)
# check if this path is hit
if inFill == True or inStroke == True:
hit = i
self.ctx.new_path()
return hit
def nameBeautiful(self, name):
# remove any '"' in front or at the end
if name[0:1] == '"':
name = name[1:]
if name[-1:] == '"':
name = name[:-1]
return name
def set_cursor_position(self, pointer=False):
if pointer == False:
pointer = self.PositionPointer
else:
self.PositionPointer = pointer
# set position of cursor for status bar:
genbank.cursor_position = pointer
def set_dna_selection(self, selection = (1,-1, -1)): # standart selection
'''
Updates DNA selection.
'''
##selection = self.get_selection()
a, b, none = selection # new to enable selections over 0
# if start after end, swap them
if a > b and b != -1:
a,b = b,a
selection = (a, b , -1)
genbank.dna_selection = selection
#self.update_globalUI()
#self.update_ownUI()
def moveCursor(self, offset, linejump = False):
### handle cursor movement:
# offset +-int
# linejump False/up/down
index = self.PositionPointer
topology = genbank.gb.gbfile['locus']['topology']
length = len(genbank.gb.GetDNA())
if linejump == False:
# check if we moved to a Line end
# if so, we first do not increase the counter:
if self.PositionPointerEnd == False and index % self.lineLength == 0:
self.PositionPointerEnd = True
elif self.PositionPointerEnd == True and index % self.lineLength == 0:
self.PositionPointerEnd = False
index = index + offset
else:
index = index + offset
elif linejump == "up":
# jump to the last row, but keep index to the left: #TODO, not correctly behaving if jumping between start and end
index = index - self.lineLength
elif linejump == "down":
index = index + self.lineLength
if topology == 'circular':
if index < 1:
index = index + length
elif index > length:
index = index - length
else:
if index < 1:
index = 1
elif index > length - 1:
index = length - 1
self.PositionPointer = index
self.set_cursor_position()
def OnKeyPress(self, evt):
key = evt.GetUniChar()
index = self.PositionPointer
shift = evt.ShiftDown() # is shift down?
if key in [97, 65, 116, 84, 99, 67, 103, 71]: # [a, A, t, T, c, C, g, G']
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it, then paste
genbank.gb.Delete(start+1, finish, visible=False)
self.PositionPointer = start
if shift == True:
genbank.gb.Paste(index, chr(key).upper())
elif shift == False:
genbank.gb.Paste(index, chr(key).lower())
# move pointer
self.PositionPointer = self.PositionPointer + 1
if finish != -1:
self.set_dna_selection()
self.update_ownUI()
self.update_globalUI()
elif key == 8: #backspace
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it
genbank.gb.Delete(start+1, finish)
self.set_dna_selection() # remove selection
self.PositionPointer = start
self.update_ownUI()
self.update_globalUI()
else:
genbank.gb.Delete(index-1, index-1)
self.PositionPointer = self.PositionPointer - 1 # set pointer back
self.update_ownUI()
self.update_globalUI()
#self.stc.SetSelection(start-1, start-1)
elif key == 127: #delete
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it
genbank.gb.Delete(start, finish)
self.PositionPointer = start
else:
genbank.gb.Delete(index, index)
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 314 and shift == False: #left
self.moveCursor(-1)
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 314 and shift == True: #left + select
start, finish, null = self.get_selection()
# start a selection
if finish == -1:
start = self.PositionPointer - 1
finish = self.PositionPointer
if finish == self.PositionPointer:
self.moveCursor(-1)
finish = self.PositionPointer
else:
self.moveCursor(-1)
start = self.PositionPointer
self.set_dna_selection((start, finish, null)) # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 316 and shift == False: #right
self.moveCursor(1)#self.PositionPointer = self.PositionPointer + 1
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 316 and shift == True: #right + select
start, finish, null = self.get_selection()
# start a selection
if finish == -1:
start = self.PositionPointer
finish = self.PositionPointer
if finish == self.PositionPointer:
self.moveCursor(1)
finish = self.PositionPointer
else:
self.moveCursor(1)
start = self.PositionPointer
self.set_dna_selection((start, finish, null)) # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 315 and shift == False: #up
self.moveCursor(1, "up")
self.update_ownUI()
self.update_globalUI()
elif key == 315 and shift == True: #up + select
print("select with keyboard")
elif key == 317 and shift == False: #down
self.moveCursor(1, "down")
self.update_ownUI()
self.update_globalUI()
elif key == 317 and shift == True: #down + select
print("select with keyboard")
#self.set_dna_selection() #update the varable keeping track of DNA selection
self.set_cursor_position() # udpate cursor position, just in case
##########################
#def make_outputpopup(self):
# '''Creates a popup window in which output can be printed'''
# self.outputframe = wx.Frame(None, title="Output Panel") # creation of a Frame with a title
# self.output = output.create(self.outputframe, style=wx.VSCROLL|wx.HSCROLL) # creation of a richtextctrl in the frame
#########################################
# def dna_output(self, featurelist):
# '''Prints output to the output panel'''
# self.make_outputpopup()
# tabtext = str(self.stc.GetPageText(self.stc.GetSelection()))
# DNA = featurelist[0]
# self.output.write('%s | DNA in clipboard, %d bp' % (tabtext, len(DNA))+'\n', 'File')
# self.output.write(DNA+'\n', 'DNA')
# if len(featurelist) > 1:
# self.output.write('With features: ', 'Text')
# for i in range(1, len(featurelist)):
# feature = featurelist[i]
# self.output.write(('>%s "%s", ' % (feature['key'], feature['qualifiers'][0].split('=')[1])), 'Text')
# self.output.write('\n', 'Text')
# self.outputframe.Show()
################ genbank methods ###############
def select_all(self):
'''Select the entire dna sequence'''
start = 1
finish = len(genbank.gb.GetDNA())+1 # TODO figure the coorect way to select. Write it in some dokumentation
self.set_dna_selection((start, finish, -1))
#self.set_dna_selection()
self.update_ownUI()
self.update_globalUI()
def get_selection(self):
'''Gets the text editor selection and adjusts it to DNA locations.'''
'''start, finish = self.stc.GetSelection()
if start == finish: #not a selection
finish = 0
elif start > finish: #the selection was made backwards
start, finish = finish, start
selection = (start+1, finish)'''
return genbank.dna_selection
def uppercase(self):
'''Change selection to uppercase'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.Upper(start, finish)
self.update_ownUI()
self.set_dna_selection()
def lowercase(self):
'''Change selection to lowercase'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.Lower(start, finish)
self.update_ownUI()
self.set_dna_selection()
def reverse_complement_selection(self):
'''Reverse-complement current selection'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.RCselection(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def delete(self):
'''Deletes a selection and updates dna and features'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot delete an empty selection')
else:
genbank.gb.Delete(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def cut(self):
'''Cut DNA and store it in clipboard together with any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot cut an empty selection')
else:
genbank.gb.Cut(start, finish)
self.set_cursor_position(start)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def cut_reverse_complement(self):
'''Cut reverse complement of DNA and store it in clipboard together with any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot cut an empty selection')
else:
genbank.gb.CutRC(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def paste(self):
'''Paste DNA and any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
pass
else: #If a selection, remove sequence, reposition pointer
genbank.gb.Delete(start, finish, visible=False)
self.set_cursor_position(start)
genbank.gb.RichPaste(genbank.cursor_position)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection() # reset selection
def paste_reverse_complement(self):
'''Paste reverse complement of DNA and any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
pass
else: #If a selection, remove sequence, reposition pointer
genbank.gb.Delete(start, finish, visible=False)
self.set_cursor_position(start)
genbank.gb.PasteRC(genbank.cursor_position)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection() # reset selection
def copy(self):
'''Copy DNA and features into clipboard'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot copy an empty selection')
else:
#genbank.gb.Copy(start, finish)
# try the new copy:
genbank.gb.RichCopy(start, finish)
def copy_reverse_complement(self):
'''Copy reverse complement of DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot copy an empty selection')
else:
genbank.gb.CopyRC(start, finish)
#######################################################
####### Protein functions #######
def translate_output(self, protein, DNA, info):
'''Generate output in the output.panel'''
# tabtext = str(self.stc.GetPageText(self.stc.GetSelection()))
self.make_outputpopup()
self.output.write('Translate %s\n' % (info), 'File')
self.output.write(('%d AA from %d bases, %d bases left untranslated' % (len(protein), len(DNA), len(DNA)%3))+'\n', 'Text')
self.output.write(protein, 'Protein')
self.outputframe.Show()
def translate_selection(self):
'''Translate selected DNA'''
start, finish = self.get_selection()
if finish == -1:
raise ValueError('Cannot translate an empty selection')
else:
DNA = genbank.gb.GetDNA(start, finish)
protein = dna.Translate(DNA)
self.translate_output(protein, DNA, 'leading strand')
def translate_selection_reverse_complement(self):
'''Translate reverse-complement of selected DNA'''
start, finish = self.get_selection()
if finish == -1:
raise ValueError('Cannot translate an empty selection')
else:
DNA = genbank.gb.GetDNA(start, finish)
protein = dna.Translate(dna.RC(DNA))
self.translate_output(protein, DNA, 'complement strand')
#update this one...
def translate_feature(self):
'''Translate specified feature'''
feature = genbank.gb.allgbfeatures[2]
DNA = genbank.gb.getdnaforgbfeature(feature[4])
protein = dna.Translate(DNA)
self.translate_output(protein, DNA, 'feature "%s"' % feature[4][7:])
################ other functions ###############################
def OnCloseWindow(self, e):
self.close_all("")
foo=self.GetSize() ###except for the window size of file
if(self.IsMaximized()==0):
file=open(files['size'], "w")
file.write(str(foo[0])+"\n"+str(foo[1]))
file.close()
self.Destroy()
self.update_ownUI() #refresh everything
def mouse_position(self, event):
'''Get which features are at a given position'''
xposition, yposition = self.stc.ScreenToClient(wx.GetMousePosition())
if xposition > 1 and yposition > 1:
mposition = self.stc.CharPositionFromPoint(xposition, yposition)
# #which feature corresponds to this pos?
Feature = genbank.gb.get_featurename_for_pos(mposition)
return mposition, Feature
else:
return None, None
class TextEdit(DNApyBaseDrawingClass):
'''
new Text editor that allows to display dna and
complementary dna in a usefull manner
Also it can and should show:
- features (done, buggy)
- restriction enzymes (partly)
- dna modifications (todo)
- primer (todo)
'''
def __init__(self, parent, id):
#parent
self.parent = parent
# get data
self.dna = genbank.gb.GetDNA()
self.cdna = genbank.gb.GetDNA()
# settings for the editor
self.sY = 60 # offset top
self.dX = 8 # border left and right
self.textSpacing = 80 # seperation of lines
self.fontsize = 9 # line size
self.lineGap = 6
# interactive cursor
self.PositionPointer = 1
self.PositionPointerEnd = False
# initial minimal height of the editor
self.minHeight = 200
# storage dict, to prevent recalculating to much
self.cairoStorage = {
'features': None, # feature Object
'fPaths': [], # path of alls features as List
'cursorPath': None,
'cursor': None,
'enzymes': {}, # enzymes object
'ePaths': [], # enzymes drawn
'ticks': None, # ticks object --> self.dna
'tPaths': [] # ticks drawn
}
# call window
DNApyBaseDrawingClass.__init__(self, parent, wx.ID_ANY)
# bind events
self.Bind(wx.EVT_LEFT_DCLICK, self.OnLeftDouble)
self.Bind(wx.EVT_LEFT_DOWN, self.OnLeftDown)
self.Bind(wx.EVT_LEFT_UP, self.OnLeftUp)
self.Bind(wx.EVT_MOTION,
self.OnMotion) # drag and drop, selection etc.
self.Bind(
wx.EVT_KEY_DOWN, self.OnKeyPress
) #This is important for controlling the input into the editor
####### Modify methods from base calss to fit current needs #########
def update_globalUI(self):
'''
Method should be modified as to update other panels in response to changes in own panel.
'''
MSG_CHANGE_TEXT = "change.text"
pub.sendMessage(MSG_CHANGE_TEXT, text="DNA view says update!")
def update_ownUI(self):
"""
This would get called if the drawing needed to change, for whatever reason.
The idea here is that the drawing is based on some data generated
elsewhere in the system. If that data changes, the drawing needs to
be updated.
This code re-draws the buffer, then calls Update, which forces a paint event.
"""
#####################
# remove buffered features, to force redraw:
self.cairoStorage['features'] = None
# The Buffer init is done here, to make sure the buffer is always
# the same size as the Window
wC, hC = self.parent.GetClientSize()
wP, hP = self.parent.GetSize()
self.SetSize(wx.Size(wC, self.minHeight))
self.parent.SetVirtualSize(wx.Size(wC - 30, self.minHeight))
# Make new offscreen bitmap: this bitmap will always have the
# current drawing in it, so it can be used to save the image to
# a file, or whatever.
# if wC != 0 and hC !=0:
# self._Buffer = wx.EmptyBitmap(wC, self.minHeight)
# else:
# self._Buffer = wx.EmptyBitmap(wP, hP)
##########################
# start dc
dc = wx.MemoryDC()
dc.SelectObject(self._Buffer)
dc.SetBackground(wx.Brush("White"))
dc.Clear()
# make a cairo context
self.ctx = ContextFromDC(dc)
# start pango as a font backend
self.pango = pangocairo.CairoContext(self.ctx)
self.pango.set_antialias(cairo.ANTIALIAS_SUBPIXEL)
# reload dna
self.dna = genbank.gb.GetDNA()
if self.dna != None:
self.cdna = dna.C(self.dna)
else:
self.dna = '' # no dna, if there is nothing
self.cdna = '' # empty cdna
# render the text
self.displayText()
# create colorful features here
self.drawFeatures()
# draw enzymes
self.drawEnzymes()
# draw a cursor
self.drawCursor()
# draw Tics above all!
self.drawTicks()
# end of canvas handling
dc.SelectObject(
wx.NullBitmap
) # need to get rid of the MemoryDC before Update() is called.
self.Refresh()
self.Update()
return None
def displayText(self):
''' main function for the editors text capabilities
here the text gets positioned and all its color.
Also the selection highlight is done here'''
# get window size to wrap text
width, height = self.parent.GetVirtualSize()
if width > 30:
w = width - self.dX
else:
w = width
# save with for other functions
self.w = w
# start layout
layout = self.pango.create_layout()
layout.set_wrap(pango.WRAP_WORD_CHAR)
layout.set_width(pango.SCALE * w)
layout.set_spacing(pango.SCALE * self.textSpacing)
layout.set_alignment(pango.ALIGN_LEFT)
# new attr list for the dna
dnaAttr = pango.AttrList()
# color
gray = 56 * 65535 / 255
fg_color = pango.AttrForeground(gray, gray, gray, 0, len(self.dna))
spacing = pango.AttrLetterSpacing(1500, 0, len(self.dna))
# add attr
dnaAttr.insert(fg_color)
dnaAttr.insert(spacing)
# set attr
layout.set_attributes(dnaAttr)
#set font
font = pango.FontDescription("monospace normal " + "1")
font.set_size(pango.SCALE * self.fontsize)
layout.set_font_description(font)
# font and color are prepared for the DNA
# get selection, if any
start, end, zero = self.get_selection()
if end != -1:
# correct direktion of selection
if start > end:
s = end - 1
e = start
else:
s = start - 1
e = end
# make markup selection
if abs(end - start) >= 0 and zero == -1 and end != -1:
senseText = self.dna[
0:s] + '<span background="#0082ED">' + self.dna[
s:e] + '</span>' + self.dna[e:]
antiText = self.cdna[
0:s] + '<span background="#0082ED">' + self.cdna[
s:e] + '</span>' + self.cdna[e:]
elif abs(end - start) >= 0 and zero == 1 and end != -1:
senseText = '<span background="#0082ED">' + self.dna[
0:s] + '</span>' + self.dna[
s:e] + '<span background="#0082ED">' + self.dna[
e:] + '</span>'
antiText = '<span background="#0082ED">' + self.cdna[
0:s] + '</span>' + self.cdna[
s:e] + '<span background="#0082ED">' + self.cdna[
e:] + '</span>'
else:
senseText = self.dna
antiText = self.cdna
# output dna
self.ctx.move_to(self.dX, self.sY)
layout.set_markup(senseText)
self.pango.update_layout(layout)
self.pango.show_layout(layout)
# copy sense layout
self.senseLayout = layout.copy()
# determine the length and height of a line
self.lineLength = layout.get_line(0).length
x1, y1, w1, h1 = self.senseLayout.index_to_pos(1)
x2, y2, w2, h2 = self.senseLayout.index_to_pos(1 + self.lineLength)
self.lineHeight = abs(y1 - y2) / pango.SCALE
# print anti sense strain
self.ctx.move_to(self.dX, self.sY + self.fontsize + self.lineGap)
layout.set_markup(antiText)
self.pango.update_layout(layout)
self.pango.show_layout(layout)
# update the height of the context, based on the inserted dna
w, h = layout.get_pixel_size()
self.minHeight = h + 2 * self.sY
# resize window
# w,h = self.GetSize() # prevents missfomration on resize
# self.SetSize(wx.Size(w,self.minHeight)) # prevents missfomration on resize
return None
def drawFeatures(self):
features = genbank.gb.get_all_feature_positions()
paths = {} # (color, path)
featureheight = 10
if self.cairoStorage['features'] != features:
# something changed, we have to draw the paths new
self.drawn_fw_locations = []
self.drawn_rv_locations = []
# font settings
# draw the name somewhere at the start
nameheight = 9 # px
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
self.ctx.set_font_size(nameheight)
for feature in features:
featuretype, complement, start, finish, name, index = feature
if featuretype != "source":
# get names
hname = self.hitName(name, index)
name = self.nameBeautiful(name)
#get position
xs, ys, ws, hs = self.senseLayout.index_to_pos(start)
xf, yf, wf, hf = self.senseLayout.index_to_pos(finish + 1)
# linecount:
# if ys and yf are not the same, we have feature over multiple lines!
dy = abs(ys - yf) / pango.SCALE
ySteps = dy / self.lineHeight # number of lines!
xs = xs / pango.SCALE
xf = xf / pango.SCALE
ys = (ys / pango.SCALE) + self.sY
yf = yf / pango.SCALE
# first sense strain over the text
if complement == False:
self.drawn_fw_locations, l = self.find_overlap(
self.drawn_fw_locations, (start, finish))
level = l * (featureheight + 6)
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(
name)
ys = ys - level - 5
self.ctx.move_to(xs + 10, ys)
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# end name
# box for name
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys - featureheight,
TextWidth + 20, nameheight + 5)
# lines above the dna
while ySteps >= 0:
if ySteps == 0:
xE = xf
else:
xE = self.w + 5 # TODO: figure out, why we need to add 5 px, to make it look correct
# make a box-path
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys - 5, xE - xs, 5)
# the second x start is always 8px, or what we will opt for
xs = self.dX
ys = ys + self.lineHeight
ySteps = ySteps - 1
# path
fillpath = self.ctx.copy_path()
self.ctx.new_path()
# get color
color = eval(featuretype)[
'fw'] #get the color of feature (as string)
else:
self.drawn_rv_locations, l = self.find_overlap(
self.drawn_rv_locations, (start, finish))
level = l * (featureheight + 6)
# set y
ys = ys + 2 * self.fontsize + self.lineGap + 9 + level
# lines below the dna
while ySteps >= 0:
if ySteps == 0:
xE = xf
else:
xE = self.w
# make the path
#self.ctx.move_to(xs, ys)
#self.ctx.line_to(xE, ys)
self.ctx.move_to(xs, ys)
self.ctx.rectangle(xs, ys + 5, xE - xs, 5)
xs = self.dX
ys = ys + self.lineHeight
ySteps = ySteps - 1
# change y:
ys = ys - self.lineHeight
# buffer path
bufferPath = self.ctx.copy_path()
self.ctx.new_path()
# name at the end:
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(
name)
self.ctx.move_to(xf - TextWidth - 10, ys + 10)
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# end name
# box for name
self.ctx.append_path(bufferPath)
self.ctx.move_to(xf - TextWidth, ys + featureheight)
self.ctx.rectangle(xf - TextWidth - 20, ys,
TextWidth + 20, nameheight + 5)
# get path
fillpath = self.ctx.copy_path()
self.ctx.new_path()
# get color
color = eval(featuretype)[
'fw'] #get the color of feature (as string)
paths[hname] = (color, fillpath, textpath)
self.ctx.new_path() # clear canvas
# save the paths
self.cairoStorage['fPaths'] = paths
# update storage status
self.cairoStorage['features'] = features
# draw the beautiful features
for a in self.cairoStorage['fPaths']:
color, path, tpath = self.cairoStorage['fPaths'][a]
# get color
assert type(color) == str
r, g, b = colcol.hex_to_rgb(color)
r = float(r) / 255
g = float(g) / 255
b = float(b) / 255
# append and draw path
self.ctx.append_path(path)
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(r, g, b, 1) # Solid color
#self.ctx.stroke_preserve()
self.ctx.fill()
# write text
self.ctx.append_path(tpath)
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(1, 1, 1, 1) # Solid color
self.ctx.fill()
return None
def drawEnzymes(self):
# load enzymes
enzymes = genbank.gb.restrictionEnzymes.selection
# create hash of selection and DNA
hashable = "%s%s" % (frozenset(enzymes), genbank.gb.gbfile['dna'])
e1 = hashlib.md5(hashable).hexdigest()
if e1 != self.cairoStorage['enzymes']:
nameheight = 9 # px
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
self.ctx.set_font_size(nameheight)
dna = self.dna
length = len(dna)
index = 0 # same as in plasmid_GUI.py
enzymesPaths = {}
# loop enzymes ordered dict
for e in enzymes:
for site in enzymes[e].restrictionSites:
name, start, end, cut51, cut52, dnaMatch = site
startRef = start - 1
hitname = self.hitName(name, index)
# get position to draw
xs, ys, ws, hs = self.senseLayout.index_to_pos(startRef)
xs = xs / pango.SCALE + self.dX
ys = ys / pango.SCALE + self.sY
hs = hs / pango.SCALE
# move there, but above the line
y = ys # - hs
self.ctx.move_to(xs, y)
# print text as path
self.ctx.text_path(name)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# make a line, representing the cut
xC51, yC51, wC51, hC51 = self.senseLayout.index_to_pos(
startRef + enzymes[e].c51)
xC31, yC31, wC31, hC31 = self.senseLayout.index_to_pos(
startRef + enzymes[e].c31)
xC51 = xC51 / pango.SCALE + self.dX
yC51 = yC51 / pango.SCALE + self.sY
tHeight = hC51 / pango.SCALE
xC31 = xC31 / pango.SCALE + self.dX
yC31 = yC31 / pango.SCALE + self.sY
if yC51 == yC31:
self.ctx.move_to(xC51, yC51)
self.ctx.line_to(xC51,
yC51 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31,
yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(
xC31, yC31 + 2 * tHeight + 0.5 * self.lineGap)
else:
if yC51 <= yC31:
lineend = self.dX + self.w
linestart = self.dX
else:
# switch
linestart = self.dX + self.w
lineend = self.dX
# split the drawing in two parts
self.ctx.move_to(xC51, yC51)
self.ctx.line_to(xC51,
yC51 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(lineend,
yC51 + tHeight + 0.25 * self.lineGap)
# part 2
self.ctx.move_to(linestart,
yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31,
yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(xC31,
yC31 + tHeight + 0.25 * self.lineGap)
self.ctx.line_to(
xC31, yC31 + 2 * tHeight + 0.5 * self.lineGap)
linepath = self.ctx.copy_path()
self.ctx.new_path()
enzymesPaths[hitname] = (textpath, linepath)
# raise index
index = index + 1
# update storage
self.cairoStorage['enzymes'] = e1
self.cairoStorage['ePaths'] = enzymesPaths
# draw enzymes:
self.ctx.set_line_width(1)
self.ctx.set_source_rgba(0.6, 0.3, 0.3, 1) # Solid color
for e in self.cairoStorage['ePaths']:
path, pathc = self.cairoStorage['ePaths'][e]
self.ctx.append_path(path)
self.ctx.fill()
self.ctx.append_path(pathc)
self.ctx.stroke()
def drawTicks(self):
''' draw the nice infos about the dna position in each line'''
nameheight = 9 # px
self.ctx.set_font_size(nameheight)
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
# number of lines:
if len(self.dna) != 0 and self.cairoStorage['ticks'] != self.dna:
# count the lines:
nLines = math.ceil((len(self.dna) - 1) / self.lineLength)
# empty paths:
self.cairoStorage['tPaths'] = []
n = 0 # counter
y = self.sY - 2 #- self.fontsize - 2
# clear paths
self.ctx.new_path()
while n <= nLines:
self.ctx.move_to(self.dX + 3, y)
# make the tick
text = "%d" % (n * self.lineLength + 1)
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(
text)
self.ctx.text_path(text)
textpath = self.ctx.copy_path()
self.ctx.new_path()
# make a box
boxPath = self.carioRoundBox(self.dX, y - TextHeight - 2,
TextWidth + 6, TextHeight + 4,
0.6)
self.ctx.new_path()
#save paths
self.cairoStorage['tPaths'].append((textpath, boxPath))
# raise counter
y = y + self.lineHeight
n = n + 1
# set storage:
self.cairoStorage['ticks'] = self.dna
# print the ticks:
self.ctx.set_line_width(0)
for i in self.cairoStorage['tPaths']:
textpath, boxPath = i
# draw box
self.ctx.set_source_rgba(1, 1, 1, 0.6) # white, transparent
self.ctx.append_path(boxPath)
self.ctx.fill()
# draw position
self.ctx.set_source_rgba(0, 0, 0, 1) # dark black
self.ctx.append_path(textpath)
self.ctx.fill()
return None
def carioRoundBox(self, x, y, width=10, height=10, aspect=0.8):
''' draw a box with rounded corners '''
# from http://cairographics.org/samples/rounded_rectangle/
corner_radius = height / 10.0
radius = corner_radius / aspect
degrees = math.pi / 180.0
self.ctx.new_sub_path()
self.ctx.arc(x + width - radius, y + radius, radius, -90 * degrees,
0 * degrees)
self.ctx.arc(x + width - radius, y + height - radius, radius,
0 * degrees, 90 * degrees)
self.ctx.arc(x + radius, y + height - radius, radius, 90 * degrees,
180 * degrees)
self.ctx.arc(x + radius, y + radius, radius, 180 * degrees,
270 * degrees)
self.ctx.close_path()
path = self.ctx.copy_path()
self.ctx.new_path()
return path
def drawCursor(self):
''' draw and display cursor in the textfield'''
indexO = self.cairoStorage['cursor']
index = self.PositionPointer
pos1, pos2, zero = self.get_selection()
if indexO != index and pos2 == -1:
index = index - 1 # we save the genetic curors 1-len(), but mean the cursor 0-len()-1
# turn index to x,y
x, y, w, h = self.senseLayout.index_to_pos(index)
x = x / pango.SCALE + self.dX
y = (y / pango.SCALE) + self.sY
y1 = y
y2 = y + 0.5 * self.lineHeight
# move cursor if its the line end:
if self.PositionPointerEnd == True:
x = x + self.dX
self.ctx.move_to(x, y1)
self.ctx.line_to(x, y2)
self.cairoStorage['cursorPath'] = self.ctx.copy_path()
self.ctx.new_path()
elif pos2 != -1:
# there is a selection, so no cursor:
self.cairoStorage['cursorPath'] = None
if self.cairoStorage['cursorPath'] != None:
# draw cursor:
self.ctx.append_path(self.cairoStorage['cursorPath'])
self.ctx.set_line_width(0.3)
self.ctx.set_source_rgba(0, 0, 0, 1) # Solid color
self.ctx.stroke()
######################################################
def OnLeftDown(self, event):
# remove selection:
self.set_dna_selection()
# get position
x, y = self.ScreenToClient(wx.GetMousePosition())
xp = (x - self.dX) * pango.SCALE
yp = int(y - self.sY - self.fontsize) * pango.SCALE
self.LeftDownIndex = None
index = self.senseLayout.xy_to_index(xp, yp)
if index != False:
# click can be left or right of the center of the char
if index[1] == 0:
self.LeftDownIndex = index[0] + 1
else:
self.LeftDownIndex = index[0] + 2
# update cursor
self.PositionPointer = self.LeftDownIndex
self.set_cursor_position()
event.Skip(
) #very important to make the event propagate and fulfill its original function
def OnLeftUp(self, event):
# get selection
pos1, pos2, zero = self.get_selection()
if pos2 == -1:
# reset selection
#self.set_dna_selection()
# maybe we cliked on a feature, label or a line?
hit = self.HitTest()
if hit != None:
self.hit = hit
# we hit one, so we need to draw the selection!
# wich feature was hit?
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0, len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[
i]
hName = self.hitName(name, index)
if hit == hName:
# a feature with start smaller then finish, is a featur laying over zero
if start > finish:
zero = 1 # 1 --> feature starts left and ends right of +1
# set selection
self.set_dna_selection((start, finish, zero))
self.set_cursor_position(start)
else:
self.hit = None
# update the UI maybe?
self.update_ownUI()
self.update_globalUI()
event.Skip(
) #very important to make the event propagate and fulfill its original function
def OnLeftDouble(self, event):
'''doubleclick aktion'''
# remove selection:
self.set_dna_selection()
# if we hit a feature, wen can open a dialog
hit = self.HitTest()
if hit != None:
# wich feature was hit?
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0, len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[
i]
hName = self.hitName(name, index)
if hit == hName:
genbank.feature_selection = copy.copy(index)
dlg = featureedit_GUI.FeatureEditDialog(
None,
'Edit Feature') # creation of a dialog with a title'''
dlg.ShowModal()
dlg.Center()
# update the UI maybe?
self.update_ownUI()
self.update_globalUI()
def OnMotion(self, event):
if event.Dragging() and event.LeftIsDown():
oldSel = genbank.dna_selection
# get position
x, y = self.ScreenToClient(wx.GetMousePosition())
xp = (x - self.dX) * pango.SCALE
yp = int(y - self.sY - self.fontsize) * pango.SCALE
self.LeftMotionIndex = None
index = self.senseLayout.xy_to_index(xp, yp)
# get motion cursor
if index != False:
if index[1] == 0:
self.LeftMotionIndex = index[0] + 1
else:
self.LeftMotionIndex = index[0] + 2
# update cursor
if self.LeftMotionIndex >= self.LeftDownIndex:
self.PositionPointer = self.LeftMotionIndex + 1
else:
self.PositionPointer = self.LeftMotionIndex
# end of line excepions
if (
self.PositionPointer - 1
) % self.lineLength == 0 and self.PositionPointer >= self.lineLength:
self.PositionPointerEnd = True
self.PositionPointer = self.PositionPointer - 1
else:
self.PositionPointerEnd = False
# get selection
if self.LeftDownIndex <= self.LeftMotionIndex:
selection = (self.LeftDownIndex, self.LeftMotionIndex, -1)
else:
selection = (self.LeftMotionIndex, self.LeftDownIndex, -1)
if oldSel != selection:
self.set_dna_selection(
selection
) #update the varable keeping track of DNA selection
self.update_ownUI()
self.update_globalUI()
event.Skip(
) #very important to make the event propagate and fulfill its original function
# def OnRightUp(self, event):
# event.Skip() #very important to make the event propagate and fulfill its original function
#### rendering
####################################################################
def find_overlap(self, drawn_locations, new_range):
'''
Takes two ranges and determines whether the new range has overlaps with the old one.
If there are overlaps the overlap locations are returned.
This is used when drawing features. If two features overlap I want them drawn on different levels.
'''
assert type(drawn_locations) == list
assert type(new_range) == tuple
if drawn_locations == []:
drawn_locations.append([new_range])
return drawn_locations, 0
else:
i = 0
while i < len(drawn_locations):
overlap_found = False
for n in range(0, len(drawn_locations[i])):
if drawn_locations[i][n][0] <= new_range[
0] <= drawn_locations[i][n][1] or drawn_locations[
i][n][0] <= new_range[1] <= drawn_locations[i][
n][1]: #if they overlap
overlap_found = True
elif new_range[0] <= drawn_locations[i][n][0] <= new_range[
1] or new_range[0] <= drawn_locations[i][n][
1] <= new_range[1]: #if they overlap
overlap_found = True
if overlap_found == False:
drawn_locations[i].append(new_range)
return drawn_locations, i
break
elif i + 1 == len(drawn_locations):
drawn_locations.append([new_range])
return drawn_locations, i + 1
break
i += 1
def hitName(self, name, index):
# unique and reproducible id for each feature
name = self.nameBeautiful(name)
seq = "%s%s" % (name, index)
name = ''.join(seq.split())
return name
def HitTest(self):
'''Tests whether the mouse is over any feature or a enzyme'''
hit = None
# get the mouse positions
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x, y)
# list of all the paths:
loop = [
self.cairoStorage['fPaths'], # features
self.cairoStorage['ePaths']
] # enzymes
# loop over all possible paths to find the one we have under the mouse
for paths in loop:
for i in paths:
path = paths[i]
if type(path) == list or type(path) == tuple:
path = path[1]
# load the path
self.ctx.append_path(path)
self.ctx.set_line_width(
0.1
) # reduce linewith, so we can have nice clicking detection
inFill = self.ctx.in_fill(x2, y2)
inStroke = self.ctx.in_stroke(x2, y2)
# check if this path is hit
if inFill == True or inStroke == True:
hit = i
self.ctx.new_path()
return hit
def nameBeautiful(self, name):
# remove any '"' in front or at the end
if name[0:1] == '"':
name = name[1:]
if name[-1:] == '"':
name = name[:-1]
return name
def set_cursor_position(self, pointer=False):
if pointer == False:
pointer = self.PositionPointer
else:
self.PositionPointer = pointer
# set position of cursor for status bar:
genbank.cursor_position = pointer
def set_dna_selection(self, selection=(1, -1, -1)): # standart selection
'''
Updates DNA selection.
'''
##selection = self.get_selection()
a, b, none = selection # new to enable selections over 0
# if start after end, swap them
if a > b and b != -1:
a, b = b, a
selection = (a, b, -1)
genbank.dna_selection = selection
#self.update_globalUI()
#self.update_ownUI()
def moveCursor(self, offset, linejump=False):
### handle cursor movement:
# offset +-int
# linejump False/up/down
index = self.PositionPointer
topology = genbank.gb.gbfile['locus']['topology']
length = len(genbank.gb.GetDNA())
if linejump == False:
# check if we moved to a Line end
# if so, we first do not increase the counter:
if self.PositionPointerEnd == False and index % self.lineLength == 0:
self.PositionPointerEnd = True
elif self.PositionPointerEnd == True and index % self.lineLength == 0:
self.PositionPointerEnd = False
index = index + offset
else:
index = index + offset
elif linejump == "up":
# jump to the last row, but keep index to the left: #TODO, not correctly behaving if jumping between start and end
index = index - self.lineLength
elif linejump == "down":
index = index + self.lineLength
if topology == 'circular':
if index < 1:
index = index + length
elif index > length:
index = index - length
else:
if index < 1:
index = 1
elif index > length - 1:
index = length - 1
self.PositionPointer = index
self.set_cursor_position()
def OnKeyPress(self, evt):
key = evt.GetUniChar()
index = self.PositionPointer
shift = evt.ShiftDown() # is shift down?
if key in [97, 65, 116, 84, 99, 67, 103,
71]: # [a, A, t, T, c, C, g, G']
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it, then paste
genbank.gb.Delete(start + 1, finish, visible=False)
self.PositionPointer = start
if shift == True:
genbank.gb.Paste(index, chr(key).upper())
elif shift == False:
genbank.gb.Paste(index, chr(key).lower())
# move pointer
self.PositionPointer = self.PositionPointer + 1
if finish != -1:
self.set_dna_selection()
self.update_ownUI()
self.update_globalUI()
elif key == 8: #backspace
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it
genbank.gb.Delete(start + 1, finish)
self.set_dna_selection() # remove selection
self.PositionPointer = start
self.update_ownUI()
self.update_globalUI()
else:
genbank.gb.Delete(index - 1, index - 1)
self.PositionPointer = self.PositionPointer - 1 # set pointer back
self.update_ownUI()
self.update_globalUI()
#self.stc.SetSelection(start-1, start-1)
elif key == 127: #delete
start, finish, null = self.get_selection()
if finish != -1: # if a selection, delete it
genbank.gb.Delete(start, finish)
self.PositionPointer = start
else:
genbank.gb.Delete(index, index)
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 314 and shift == False: #left
self.moveCursor(-1)
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 314 and shift == True: #left + select
start, finish, null = self.get_selection()
# start a selection
if finish == -1:
start = self.PositionPointer - 1
finish = self.PositionPointer
if finish == self.PositionPointer:
self.moveCursor(-1)
finish = self.PositionPointer
else:
self.moveCursor(-1)
start = self.PositionPointer
self.set_dna_selection((start, finish, null)) # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 316 and shift == False: #right
self.moveCursor(
1) #self.PositionPointer = self.PositionPointer + 1
self.set_dna_selection() # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 316 and shift == True: #right + select
start, finish, null = self.get_selection()
# start a selection
if finish == -1:
start = self.PositionPointer
finish = self.PositionPointer
if finish == self.PositionPointer:
self.moveCursor(1)
finish = self.PositionPointer
else:
self.moveCursor(1)
start = self.PositionPointer
self.set_dna_selection((start, finish, null)) # remove selection
self.update_ownUI()
self.update_globalUI()
elif key == 315 and shift == False: #up
self.moveCursor(1, "up")
self.update_ownUI()
self.update_globalUI()
elif key == 315 and shift == True: #up + select
print("select with keyboard")
elif key == 317 and shift == False: #down
self.moveCursor(1, "down")
self.update_ownUI()
self.update_globalUI()
elif key == 317 and shift == True: #down + select
print("select with keyboard")
#self.set_dna_selection() #update the varable keeping track of DNA selection
self.set_cursor_position() # udpate cursor position, just in case
##########################
#def make_outputpopup(self):
# '''Creates a popup window in which output can be printed'''
# self.outputframe = wx.Frame(None, title="Output Panel") # creation of a Frame with a title
# self.output = output.create(self.outputframe, style=wx.VSCROLL|wx.HSCROLL) # creation of a richtextctrl in the frame
#########################################
# def dna_output(self, featurelist):
# '''Prints output to the output panel'''
# self.make_outputpopup()
# tabtext = str(self.stc.GetPageText(self.stc.GetSelection()))
# DNA = featurelist[0]
# self.output.write('%s | DNA in clipboard, %d bp' % (tabtext, len(DNA))+'\n', 'File')
# self.output.write(DNA+'\n', 'DNA')
# if len(featurelist) > 1:
# self.output.write('With features: ', 'Text')
# for i in range(1, len(featurelist)):
# feature = featurelist[i]
# self.output.write(('>%s "%s", ' % (feature['key'], feature['qualifiers'][0].split('=')[1])), 'Text')
# self.output.write('\n', 'Text')
# self.outputframe.Show()
################ genbank methods ###############
def select_all(self):
'''Select the entire dna sequence'''
start = 1
finish = len(
genbank.gb.GetDNA()
) + 1 # TODO figure the coorect way to select. Write it in some dokumentation
self.set_dna_selection((start, finish, -1))
#self.set_dna_selection()
self.update_ownUI()
self.update_globalUI()
def get_selection(self):
'''Gets the text editor selection and adjusts it to DNA locations.'''
'''start, finish = self.stc.GetSelection()
if start == finish: #not a selection
finish = 0
elif start > finish: #the selection was made backwards
start, finish = finish, start
selection = (start+1, finish)'''
return genbank.dna_selection
def uppercase(self):
'''Change selection to uppercase'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.Upper(start, finish)
self.update_ownUI()
self.set_dna_selection()
def lowercase(self):
'''Change selection to lowercase'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.Lower(start, finish)
self.update_ownUI()
self.set_dna_selection()
def reverse_complement_selection(self):
'''Reverse-complement current selection'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot modify an empty selection')
else:
genbank.gb.RCselection(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def delete(self):
'''Deletes a selection and updates dna and features'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot delete an empty selection')
else:
genbank.gb.Delete(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def cut(self):
'''Cut DNA and store it in clipboard together with any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot cut an empty selection')
else:
genbank.gb.Cut(start, finish)
self.set_cursor_position(start)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def cut_reverse_complement(self):
'''Cut reverse complement of DNA and store it in clipboard together with any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot cut an empty selection')
else:
genbank.gb.CutRC(start, finish)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection()
def paste(self):
'''Paste DNA and any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
pass
else: #If a selection, remove sequence, reposition pointer
genbank.gb.Delete(start, finish, visible=False)
self.set_cursor_position(start)
genbank.gb.RichPaste(genbank.cursor_position)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection() # reset selection
def paste_reverse_complement(self):
'''Paste reverse complement of DNA and any features present on that DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
pass
else: #If a selection, remove sequence, reposition pointer
genbank.gb.Delete(start, finish, visible=False)
self.set_cursor_position(start)
genbank.gb.PasteRC(genbank.cursor_position)
self.update_ownUI()
self.update_globalUI()
self.set_dna_selection() # reset selection
def copy(self):
'''Copy DNA and features into clipboard'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot copy an empty selection')
else:
#genbank.gb.Copy(start, finish)
# try the new copy:
genbank.gb.RichCopy(start, finish)
def copy_reverse_complement(self):
'''Copy reverse complement of DNA'''
start, finish, zero = self.get_selection()
if finish == -1:
raise ValueError('Cannot copy an empty selection')
else:
genbank.gb.CopyRC(start, finish)
#######################################################
####### Protein functions #######
def translate_output(self, protein, DNA, info):
'''Generate output in the output.panel'''
# tabtext = str(self.stc.GetPageText(self.stc.GetSelection()))
self.make_outputpopup()
self.output.write('Translate %s\n' % (info), 'File')
self.output.write(('%d AA from %d bases, %d bases left untranslated' %
(len(protein), len(DNA), len(DNA) % 3)) + '\n',
'Text')
self.output.write(protein, 'Protein')
self.outputframe.Show()
def translate_selection(self):
'''Translate selected DNA'''
start, finish = self.get_selection()
if finish == -1:
raise ValueError('Cannot translate an empty selection')
else:
DNA = genbank.gb.GetDNA(start, finish)
protein = dna.Translate(DNA)
self.translate_output(protein, DNA, 'leading strand')
def translate_selection_reverse_complement(self):
'''Translate reverse-complement of selected DNA'''
start, finish = self.get_selection()
if finish == -1:
raise ValueError('Cannot translate an empty selection')
else:
DNA = genbank.gb.GetDNA(start, finish)
protein = dna.Translate(dna.RC(DNA))
self.translate_output(protein, DNA, 'complement strand')
#update this one...
def translate_feature(self):
'''Translate specified feature'''
feature = genbank.gb.allgbfeatures[2]
DNA = genbank.gb.getdnaforgbfeature(feature[4])
protein = dna.Translate(DNA)
self.translate_output(protein, DNA, 'feature "%s"' % feature[4][7:])
################ other functions ###############################
def OnCloseWindow(self, e):
self.close_all("")
foo = self.GetSize() ###except for the window size of file
if (self.IsMaximized() == 0):
file = open(files['size'], "w")
file.write(str(foo[0]) + "\n" + str(foo[1]))
file.close()
self.Destroy()
self.update_ownUI() #refresh everything
def mouse_position(self, event):
'''Get which features are at a given position'''
xposition, yposition = self.stc.ScreenToClient(wx.GetMousePosition())
if xposition > 1 and yposition > 1:
mposition = self.stc.CharPositionFromPoint(xposition, yposition)
# #which feature corresponds to this pos?
Feature = genbank.gb.get_featurename_for_pos(mposition)
return mposition, Feature
else:
return None, None
class drawPlasmid(DNApyBaseDrawingClass):
''' This class handle the drawing of a plasmid'''
'''
it should draw:
- Plasmid
- Features
- feature names
- RestriktionSites
- Names of Restriction sites
- Selection
- higlights
It has to Calculate in this order:
- The Size of the Plasmid
- The angular positon of the features
- If the Label of a feature can be drawn inside
- the angular positions of all Restrictionsites
- The arrangements of the labels
- featurelabels
- Restriktionsite Labels
Possible Interactions:
- select dna
- drag and drop select
- click on feature
- zoom in and out
- double click feature
Each cycle must be something like this:
1. Check if we have to calcaulate the length of the features
self.calc.fl = True
if true: check if this changes anything for the other labels (do labels have to be drawn outside or inside compared to before)
2. Check if we have to calcaulate Label Positions again:
self.calc.lp = true
3. If self.calc.lp and fl == False:
Just redraw the previous plasmid
else:
recalculate the desired stuff
x. Highlight and interaction'''
def __init__(self, parent, id):
# object to store our cacluations over time
self.plasmidstore = plasmidstore()
self.radius = 25 # cairo unit
self.radiusI = self.radius - 0.013 * self.radius # cairo unit
self.radiusO = self.radius + 0.013 * self.radius # cairo unit
self.radiusLabels = self.radius + 17 # cairo unit
self.arrowWidth = 1.8 # cairo unit
self.labelHeight = 12 # pixel
self.Highlight = None # store who to highlight
self.enzymeGap = "-|-" # seperator to make unique hitname less unique
#self.EnzymeMonitor = Monitor()
# start the window
DNApyBaseDrawingClass.__init__(self, parent, wx.ID_ANY)
# bind events
self.Bind(wx.EVT_LEFT_UP, self.OnLeftUp)
self.Bind(wx.EVT_LEFT_DOWN, self.OnLeftDown)
self.Bind(wx.EVT_MOTION, self.OnMotion)
self.Bind(wx.EVT_LEFT_DCLICK, self.OnLeftDouble)
return None
def update_globalUI(self):
'''
Method should be modified as to update other panels in response to changes in own panel.
'''
MSG_CHANGE_TEXT = "change.text"
pub.sendMessage(MSG_CHANGE_TEXT, text="Plasmid view says update!")
def update_ownUI(self):
"""
This would get called if the drawing needed to change, for whatever reason.
The idea here is that the drawing is based on some data generated
elsewhere in the system. If that data changes, the drawing needs to
be updated.
This code re-draws the buffer, then calls Update, which forces a paint event.
"""
# update selection from editor
self.updateSelection()
self.updatePosition()
# start the calculations if any.
self.checkFeatureCalculations() # changed features may change labels also
self.checkEnzymeCalculations() # check for restriction enzymes
self.checkLabelCalculations() # changed features may change labels also
# check if we even have to redraw anything:
dc = wx.MemoryDC()
dc.SelectObject(self._Buffer)
dc.SetBackground(wx.Brush("White")) # start the DC and clear it
dc.Clear() # make sure you clear the bitmap!
self.ctx = ContextFromDC(dc) # load it into cairo
# seletion starts here
self.checkSelectionCalculations() # check and make a selection arc
# glyphs
#self.pango = pangocairo.CairoContext(self.ctx)
#self.pango.set_antialias(cairo.ANTIALIAS_SUBPIXEL)
self.draw()
dc.SelectObject(wx.NullBitmap) # need to get rid of the MemoryDC before Update() is called.
self.Refresh()
self.Update()
return None
def set_dna_selection(self, selection):
'''Receives requests for DNA selection and then sends it.'''
assert type(selection) == tuple, 'Error, dna selection must be a tuple'
selection = (int(selection[0]), int(selection[1]), int(selection[2]))
genbank.dna_selection = selection
self.plasmidstore.interaction["selection"] = selection
self.update_globalUI()
def set_cursor_position(self, position):
# set position of cursor for status bar:
genbank.cursor_position = position
self.plasmidstore.interaction["position"] = position
def updateSelection(self):
''' get selection from editor and update own store '''
selection = genbank.dna_selection
assert type(selection) == tuple, 'Error, dna selection must be a tuple'
selection = (int(selection[0]), int(selection[1]), int(selection[2]))
self.plasmidstore.interaction["selection"] = selection
def updatePosition(self):
''' get position from editor and update own store '''
position = genbank.cursor_position
self.plasmidstore.interaction["position"] = position
def hitName(self, name, index):
# unique and reproducible id for each feature
name = self.nameBeautiful(name)
seq = "%s%s" % (name, index)
name = ''.join(seq.split())
return name
def HitTest(self):
'''Tests whether the mouse is over any feature or label'''
hit = None
# get the mouse positions
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
# list of all the paths:
loop = [self.plasmidstore.drawnfeatures, # features
self.plasmidstore.drawnlabels, # featurelabes
self.plasmidstore.labelBoxes, # featurelabels
self.plasmidstore.drawnlabelsE, # enzymes
self.plasmidstore.labelBoxesE] # enzymes
# loop over all possible paths to find the one we have under the mouse
for paths in loop:
for i in paths:
path = paths[i]
if type(path) == list:
path = path[0]
# load the path
self.ctx.append_path(path)
self.ctx.set_line_width(0.1) # reduce linewith, so we can have nice clicking detection
inFill = self.ctx.in_fill(x2,y2)
inStroke = self.ctx.in_stroke(x2,y2)
# check if this path is hit
if inFill == True or inStroke == True:
hit = i
self.ctx.new_path()
return hit
def HitTestSelection(self):
'''Check if the selection area (area where selection is possible) was hit'''
# get the mouse position
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
self.ctx.append_path(self.plasmidstore.interaction["markerArea1"])
inFill1 = self.ctx.in_fill(x2,y2)
self.ctx.stroke()
self.ctx.append_path(self.plasmidstore.interaction["markerArea2"])
inFill2 = self.ctx.in_fill(x2,y2)
self.ctx.stroke()
# check if the path is hit for selection
if inFill1 == True and inFill2 == False:
return True
else:
return False
def saveSelection(self, start=0, finish=0, zero=-1, featureHit=False):
# feature to highlight or drag and drop?
if featureHit != False:
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0,len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[i]
hName = self.hitName(name, index)
if featureHit == hName:
# a feature with start smaller then finish, is a featur laying over zero
if start > finish:
zero = 1 # 1 --> feature starts left and ends right of +1
# set selection for real!
self.set_dna_selection((start,finish, zero))
else:
self.set_dna_selection((start,finish, zero))
return None
def nameBeautiful(self, name):
# remove any '"' in front or at the end
if name[0:1] == '"':
name = name[1:]
if name[-1:] == '"':
name = name[:-1]
return name
def find_overlap(self, drawn_locations, new_range):
'''
Takes two ranges and determines whether the new range has overlaps with the old one.
If there are overlaps the overlap locations are returned.
This is used when drawing features. If two features overlap I want them drawn on different levels.
'''
assert type(drawn_locations) == list
assert type(new_range) == tuple
if drawn_locations == []:
drawn_locations.append([new_range])
return drawn_locations, 0
else:
i = 0
while i < len(drawn_locations):
overlap_found = False
for n in range(0,len(drawn_locations[i])):
if drawn_locations[i][n][0]<=new_range[0]<=drawn_locations[i][n][1] or drawn_locations[i][n][0]<=new_range[1]<=drawn_locations[i][n][1]: #if they overlap
overlap_found = True
elif new_range[0]<=drawn_locations[i][n][0]<=new_range[1] or new_range[0]<=drawn_locations[i][n][1]<=new_range[1]: #if they overlap
overlap_found = True
if overlap_found == False:
drawn_locations[i].append(new_range)
return drawn_locations, i
break
elif i+1==len(drawn_locations):
drawn_locations.append([new_range])
return drawn_locations, i+1
break
i += 1
############### Inteaction with mosue and keyboard ################
def OnLeftUp(self, event):
''' handle left ouseclick up'''
# get selection
pos1, pos2, zero = self.plasmidstore.interaction["selection"]
if self.plasmidstore.interaction["leftDown"] == True and pos2 != -1:
# selection is finish
self.plasmidstore.interaction["leftDown"] = False
# save the mouse position
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
pos = self.cartesian2position(x2,y2)
self.plasmidstore.interaction["selection"] = (pos1, pos, zero)
elif pos2 == -1:
# reset selection
self.plasmidstore.interaction["selection"] = (1, -1, -1)
# maybe we cliked on a feature, label or a line?
hit = self.HitTest()
if hit != None:
self.plasmidstore.interaction["hit"] = hit
# we hit one, so we need to draw the selection!
# wich feature was hit?
self.saveSelection(1, -1, -1, hit)
else:
self.plasmidstore.interaction["hit"] = None
# update the UI maybe?
self.update_ownUI()
def OnLeftDown(self, event):
# remove the position cursor:
self.set_cursor_position(0)
selection = self.HitTestSelection()
if selection:
# save the mouse position
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
pos = self.cartesian2position(x2,y2)
self.plasmidstore.interaction["leftDown"] = True
self.plasmidstore.interaction["selection"] = (pos, -1, -1)
else:
# remove selection
self.plasmidstore.interaction["hit"] = None
self.saveSelection(1, -1, -1, False)
return None
def OnLeftDouble(self, event):
'''When left button is double clicked, launch the feature edit dialog.'''
hit = self.HitTest() #this does not get the "true" feature index. Some featues are split and this is an index that accounts for that.
if hit is not False:
# get the index of this feature
featurelist = genbank.gb.get_all_feature_positions()
for i in range(0,len(featurelist)):
# load all the feature infos
featuretype, complement, start, finish, name, index = featurelist[i]
hName = self.hitName(name, index)
if hit == hName:
genbank.feature_selection = copy.copy(index)
dlg = featureedit_GUI.FeatureEditDialog(None, 'Edit Feature') # creation of a dialog with a title
dlg.ShowModal()
dlg.Center()
def OnMotion(self, event):
'''When mouse is moved with the left button down determine the DNA selection from angle generated at mouse down and mouse move event.'''
if event.Dragging() and event.LeftIsDown() and self.plasmidstore.interaction["leftDown"] == True:
# save the mouse position
x, y = self.ScreenToClient(wx.GetMousePosition())
x2, y2 = self.ctx.device_to_user(x,y)
pos = self.cartesian2position(x2,y2)
pos1, pos2, zero = self.plasmidstore.interaction["selection"]
self.plasmidstore.interaction["selection"] = (pos1, pos, zero)
# if we have a sudden increase, we might have moven over zero
if abs(pos2 - pos) > self.dnaLength/2 and pos2 != -1:
zero = zero * -1 # turn zero around
self.plasmidstore.interaction["selection"] = (pos1, pos, zero)
#set genebank selection
self.saveSelection(pos1, pos, zero)
self.update_ownUI()
# check if something is beneath the mousecursor
oldhit = self.Highlight
hit = self.HitTest()
# save the state
self.Highlight = hit
# only update after change
if oldhit != hit:
self.update_ownUI()
#elif len(self.selectionDrawing) < 2: # only hover position, if none is selected --> maybe use two variables to make both possible?
# no feature to highlight, but maybe selection hover?
# self.Highlight = None
# check if we are in the "hover area"
# inArea = self.HitTestMarkerArea()
# if inArea == True:
# # get the mouse position
# x, y = self.ScreenToClient(wx.GetMousePosition())
# x2, y2 = self.ctx.device_to_user(x,y)
# self.selectionDrawing = [] # empty it
# self.selectionDrawing.append(self.cartesian2radial(x2,y2))
# self.update_ownUI()
# elif oldhit != hit:
# self.update_ownUI()
# elif len(self.selectionDrawing) == 1: # TODO
# self.selectionDrawing = [] # empty it so the hover line wont be seen all the time
# self.update_ownUI()
############### Setting methods for converting stuff ##############
def radial2cartesian(self,radius, angle, cx=0,cy=0): # angle in radial!
radius = float(radius)
angle = float(angle)
x = radius * math.cos(angle) + cx
y = radius * math.sin(angle) + cy
return x,y
def cartesian2radial(self,x, y):
x = -x # cairo somehow swaps the x axis
diff = -math.radians(90) # remove some radians, because 0 is on top
r = math.atan2(x,y) + 1 * math.pi + diff
return r
def position2angle(self, position):
radMult = float(2*math.pi/self.dnaLength)
angle = (position - 0.5 * self.dnaLength) * radMult + math.pi/2
return angle
def position2cartesian(self, position, radius):
angle = self.position2angle(position)
x,y = self.radial2cartesian(radius, angle)
return x, y
def cartesian2position(self, x,y):
angle = self.cartesian2radial(x,y)
radMult = float(2*math.pi/self.dnaLength)
pos = 0.5 * self.dnaLength + (angle - math.pi/2)/radMult
pos = int(round(pos, 0))
return pos
def merge_dicts(self, *dict_args):
'''
Given any number of dicts, shallow copy and merge into a new dict,
precedence goes to key value pairs in latter dicts.
'''
result = {}
for dictionary in dict_args:
result.update(dictionary)
return result
########################################
# caclcualting functions
def checkFeatureCalculations(self):
''' this functions takes the current positions and calcualtions
of the features and checks fast if it has to recalculated anything'''
redrawfeatures = False
# compare the features to the previously calculated ones
featuresOld = self.plasmidstore.features
featuresNew = genbank.gb.get_all_feature_positions()
if featuresNew != None:
# get the length once
self.dnaLength = float(len(genbank.gb.GetDNA()))
else:
self.dnaLength = 1 # or 0 but this might cause problems if there is a division x/length
# compare old and new
if featuresOld != featuresNew:
# print ("DO recalc features")
# we only have to redraw if the length, the color or direction changed
# calculate and save all the features
allFeatures = {} # storing list
# some basic info we have to update:
self.drawn_fw_locations = []
self.drawn_rv_locations = []
labelFeature = [] # labels for features outside of the arrow
# save as [[middle, name, index, hitname, y],[...]]
# loop the features and get the path
for feature in featuresNew:
featuretype, complement, start, finish, name, index = feature
hitname = self.hitName(name, index)
# do not display the annoying source
if featuretype != "source":
# path creation
allFeatures[hitname] = [self.cairoFeature(feature), featuretype]
# label handling
length = self.dnaLength
middle = start + (finish-start)/2 % length
name = self.nameBeautiful(name)
y = None # to be populated
labelFeature.append([middle, name, index, hitname, y])
# save the new paths in the fancy storing class for further processing
self.plasmidstore.drawnfeatures = allFeatures
# save label drawn outside as text
self.plasmidstore.LoF = labelFeature
self.plasmidstore.features = featuresNew # everything is over and the new are the current (old)
return redrawfeatures
def cairoFeature(self, feature):
featurepath = None
featuretype, complement, start, finish, name, index = feature
name = self.nameBeautiful(name)
hname = self.hitName(name, index)
# create the correct path for foreward and reverse
if complement == False:
self.drawn_fw_locations, levelMult = self.find_overlap(self.drawn_fw_locations, (start, finish))
arrowMult = 1 # to account for the different direction of addition
radiusAdd = levelMult * (self.arrowWidth + 0.5) + 0.4
radiusO = self.radiusO + radiusAdd + self.arrowWidth
radiusI = self.radiusO + radiusAdd
else:
self.drawn_rv_locations, levelMult = self.find_overlap(self.drawn_rv_locations, (start, finish))
arrowMult = -1 # to account for the different direction of addition
radiusAdd = levelMult * (self.arrowWidth + 0.5) + 0.4
radiusO = self.radiusI - radiusAdd - self.arrowWidth
radiusI = self.radiusI - radiusAdd
# calculate the radians for end and start
s = self.position2angle(start)
e = self.position2angle(finish)
# large features get a arrow head:
arrowHead = False
if abs(e - s) > math.radians(5): # more then x degrees
arrowHead = True
if arrowHead == True and complement == False:
# arrow head has x radians
r = radiusI + arrowMult * self.arrowWidth/2
xA, yA = self.radial2cartesian(r, e)
e = e - math.radians(2) # new end
self.ctx.new_path()
self.ctx.arc(0,0,radiusI, s,e)
# draw arrow head sometimes:
self.ctx.line_to(xA, yA)
#self.ctx.move_to(cx1, cy1)
self.ctx.arc_negative(0,0,radiusO, e,s)
self.ctx.close_path()
featurepath = self.ctx.copy_path()
self.ctx.new_path() # clear canvas
elif arrowHead == True and complement == True:
# arrow head has x radians
r = radiusI + arrowMult * self.arrowWidth/2
xA, yA = self.radial2cartesian(r, s)
s = s + math.radians(2) # new "start"
self.ctx.new_path()
self.ctx.arc_negative(0,0,radiusI, e,s)
self.ctx.line_to(xA, yA)
self.ctx.arc(0,0,radiusO, s,e)
self.ctx.close_path()
featurepath = self.ctx.copy_path()
self.ctx.new_path() # clear canvas
else:
self.ctx.new_path()
self.ctx.arc(0,0,radiusI, s,e)
self.ctx.arc_negative(0,0,radiusO, e,s)
self.ctx.close_path()
featurepath = self.ctx.copy_path()
self.ctx.new_path() # clear canvas
# save the outer radius to allow draing of the lines:
if complement == False:
self.plasmidstore.radiusOuter[hname] = radiusO
else:
self.plasmidstore.radiusOuter[hname] = radiusI
return featurepath
def caironameLabels(self, labels, site, kind):
''' create paths for labels given'''
if kind == "features":
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_BOLD)
else:
self.ctx.select_font_face('Arial', cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
self.ctx.set_font_size(self.lH)
textPaths = {}
linePaths = {}
underlinePaths = {}
boxPaths = {}
shift = 4 # shift the labels closer to the plasmid, as the have a bigger radius
for l in labels:
name = l[1]
y = l[4]
if kind == "enzymes":
name2 = "%s%s" %(name, self.enzymeGap)
else:
name2 = name
hname = self.hitName(name2, l[2])
xbearing, ybearing, TextWidth, TextHeight, xadvance, yadvance = self.ctx.text_extents(name)
if site == "left":
x = - math.cos(math.asin(y/self.radiusLabels)) * self.radiusLabels - TextWidth + shift
else:
x = math.cos(math.asin(y/self.radiusLabels)) * self.radiusLabels - shift
self.ctx.move_to(x, y);
self.ctx.text_path(name)
# save label:
path = self.ctx.copy_path()
textPaths[hname] = path
self.ctx.new_path() # clear canvas
# make a box behind the text, so we can select more easys:
self.ctx.rectangle(x, y - self.lH, TextWidth, self.lH)
boxPaths[hname] = self.ctx.copy_path()
self.ctx.new_path()
# featurs have a underline:
if kind == "features":
self.ctx.move_to(x, y)
self.ctx.line_to(x + TextWidth, y)
path = self.ctx.copy_path()
underlinePaths[hname] = path
self.ctx.new_path() # clear canvas
# make a line from text to plasmid:
if site == "left":
x = x + TextWidth
else:
x = x
# get the radius to where the line should lead:
try:
r = self.plasmidstore.radiusOuter[hname]
except:
r = self.radiusI
y1 = y - self.lH/2 + 0.3
self.ctx.move_to(x, y1)
x2, y2 = self.position2cartesian(l[0], self.radiusO + 7)
x3, y3 = self.position2cartesian(l[0], r)
self.ctx.line_to(x2,y2)
self.ctx.line_to(x3,y3)
linePaths[hname] = self.ctx.copy_path() # save line path
self.ctx.new_path() # clear canvas
return textPaths, linePaths, boxPaths, underlinePaths
def checkLabelCalculations(self):
''' this functions takes the current positions and calcualtions
of the labels and checks fast if it has to recalculated anything'''
# labels to handle:
LoF = self.plasmidstore.LoF
LoE = self.plasmidstore.LoE
# check if the labels changed, onyl recalculate everything, if they did
if LoF != self.plasmidstore.LoFold or LoE != self.plasmidstore.LoEold:
# print("DO recalculate label")
# sort labels for their middle position:
LoF = sorted(LoF, key=lambda x: x[0])
LoE = sorted(LoE, key=lambda x: x[0])
# group the labels
# TODO, should be interactive anyway
# now split in two sites:
half = self.dnaLength/2
# Features
LoF1 = [] # first half
LoF2 = [] # second half
LoF1I = [] # indexing
LoF2I = [] # indexing
for l in LoF:
if l[0] < half:
LoF1.append(l)
LoF1I.append(l[3])
else:
LoF2.append(l)
LoF2I.append(l[3])
# Enzymes
LoE1 = [] # first half
LoE2 = [] # second half
LoE1I = [] # indexing
LoE2I = [] # indexing
for l in LoE:
if l[0] < half:
LoE1.append(l)
LoE1I.append(l[3])
else:
LoE2.append(l)
LoE2I.append(l[3])
# then check the numbers
LoF1, LoE1 = self.checkNumberOfLabels(LoF1, LoE1)
# arrange and draw labels:
Labels1 = self.arrangeLabels(LoF1, LoE1, -1)
Labels2 = self.arrangeLabels(LoF2, LoE2, +1)
# sperate into features and enzymes...
# this must be, so we can order them together, but color them
# different
LabelsFeatures1 = []
LabelsFeatures2 = []
LabelsEnzymes1 = []
LabelsEnzymes2 = []
for label in Labels1:
hit = label[3]
if hit in LoF1I:
LabelsFeatures1.append(label)
if hit in LoE1I:
LabelsEnzymes1.append(label)
for label in Labels2:
hit = label[3]
if hit in LoF2I:
LabelsFeatures2.append(label)
if hit in LoE2I:
LabelsEnzymes2.append(label)
# done serperating the labels agai
# FEATURES: make the paths for features
laP1, liP1, bP1, UlP1 = self.caironameLabels(LabelsFeatures1, "right", "features")
laP2, liP2, bP2, UlP2 = self.caironameLabels(LabelsFeatures2, "left", "features")
# FEATURES: save paths for displaying
self.plasmidstore.drawnlabels = self.merge_dicts(laP1, laP2)
self.plasmidstore.drawnLLines = self.merge_dicts(liP1, liP2)
self.plasmidstore.labelBoxes = self.merge_dicts(bP1, bP2)
self.plasmidstore.labelULine = self.merge_dicts(UlP1, UlP2)
# ENZYMES: make the paths for enzymes
laP1, liP1, bP1, UlP1 = self.caironameLabels(LabelsEnzymes1, "right", "enzymes")
laP2, liP2, bP2, UlP2 = self.caironameLabels(LabelsEnzymes2, "left", "enzymes")
# ENZYMES: save paths for displaying
self.plasmidstore.drawnlabelsE = self.merge_dicts(laP1, laP2)
self.plasmidstore.drawnLLinesE = self.merge_dicts(liP1, liP2)
self.plasmidstore.labelBoxesE = self.merge_dicts(bP1, bP2)
# save the new status quo of the labels
self.plasmidstore.LoFold = self.plasmidstore.LoF
self.plasmidstore.LoEold = self.plasmidstore.LoE
return None
else:
# print("NOT recalculate label")
return None
def checkNumberOfLabels(self, LoF=None, LoE=None):
''' this function is called before label sorting'''
# determine height of label displaying area
height = self.radius * 2.2
# divide by the height of each label
lH = self.ctx.device_to_user_distance(self.labelHeight,0)[0] # label height
lH = round(lH, 3)
self.lH = lH # for other functions to use
# round down, to make it work
nL = math.trunc(height/lH)
# number of labels to handle
nFL = len(LoF)
nEL = len(LoE)
if nFL + nEL <= nL:
# no problem here
return LoF, LoE # return feature Label and Text Label
elif nFL <= nL:
# reduce the nTL so, that it may work.
# reduce most populated areas
# print("group some Restrictionsite labels agressivly")
# call function and check again if we can fit everything in
# if it did work--> fine
# else show it anyway --> or figure something out
return LoF, LoE # return feature Label and Text Label
elif nFL > nL:
# we have to many feature labels.
# so we hide all TL and remove the labels of the smallest features!
# print("delete some Restrictionsite labels")
return LoF, LoE # return feature Label and Text Label
else:
# print("check Number of labels: undefined")
return LoF, LoE # return feature Label and Text Label
#def groupLabels(self, labels):
# ''' restrictionenzymelabels can be grouped
# as they somtimes occure at the very same place '''
# lastPos = None
# i = 0
# for l in labels:
# pos = l[0]
#
# if pos == lastPos:
# # two labels at the very same position
# # we merge the names
# cname = l[1]
# oname = labels[i][1]
# name = "%s, %s"
# i = i + 1
# # we can group labels of same type and same position
# return None
def groupAgressivly(self):
# we can group some close restrictionlabels
# and only show the position indicating by a number
return None
def arrangeLabels(self, F, E, index):
''' this function does the actual positioning of all labels'''
# now they are equal
# enzymes, features etc: merge
Labels = F + E
Labels = sorted(Labels, key=lambda x: x[0])
# find the most horiziontal one
horzI = None
horzN = self.dnaLength
if index == -1:
target = self.dnaLength / 4 * 1
else:
target = self.dnaLength / 4 * 3
i = 0
# start by putting the initial position
for l in Labels:
# append a new entry with the current y coordinate:
x,y = self.position2cartesian(l[0], self.radiusLabels - 2)
l[4] = round(y, 3)
# most horizontal one:
if abs(l[0] - target) < horzN:
horzN = abs(l[0] - target) # save new differenze
horzI = i # save index
i = i + 1
# create series for loop for better positioning
# this way we start positioning in the hotizontal position and
# arrange the labels in both directions more accurate
h = 1
loop = [horzI]
newI = horzI
switch = 1
both = True
while h < len(Labels):
if newI > 0 and newI < len(Labels)- 1 and both == True:
newI = newI + switch * h
switch = -1 * switch
elif newI == 0:
switch = 1
newI = newI + switch * h
both = False
elif newI == len(Labels) - 1:
switch = -1
newI = newI + switch * h
both = False
else:
newI = newI + switch * 1
loop.append(newI)
h = h + 1
# now iterate n times and check if x[i] overlaps with either x[i+1] or x[i-1]
# this is the key element of the label positioning algorythm
# n is critical for performance, higher n = more steps
# dy is the step size in px
dy = self.ctx.device_to_user_distance(5,0)[0] # amount of movement in pixel
i = 0 # just a counter
n = 100 # n of steps
overlapp = 1 # initial overlap, so it is not 0
while i < n and overlapp > 0:
overlapp = 0
#for l in Labels:
for a in loop:
l = Labels[a]
# for those labels with one upper and lower label
y = l[4] # y
U = y + self.lH # upper border
L = y # lower border
# get the correct upper and lower bound of the adjacend features or the end of the radius
if index > 0:
if a == 0:
# next label
nL = +self.radiusLabels
else:
# next label
nextLabel = Labels[a - 1]
nL = nextLabel[4] # next lower
if a == len(Labels)-1:
lU = -self.radiusLabels
else:
# previous label
prevLabel = Labels[a + 1]
lU = prevLabel[4] + self.lH # last upper
else:
if a == len(Labels)-1:
# next label
nL = self.radiusLabels
else:
# next label
nextLabel = Labels[a + 1]
nL = nextLabel[4] # next lower
if a == 0:
lU = -self.radiusLabels
else:
# previous label
prevLabel = Labels[a - 1]
lU = prevLabel[4] + self.lH # last upper
# check upper bound
dU = U - nL
# check lower bound
dL = lU - L
# move the item up or down, according to its overlapping
if dU > 0 or dL > 0:
# we need to move somewhere
if dU > 0 and dL <= 0:
# move down
y = y - dy
# raise the overlap
overlapp = overlapp + dU
elif dU <= 0 and dL > 0:
# we need to move up
y = y + dy
# raise the overlap
overlapp = overlapp + dL
elif dU > 0 and dL > 0:
# we need to make them even
y = y + (dU - (dU + dL)/2)
# raise the overlap
overlapp = overlapp + dU + dL
# prevent to large y
if y > self.radiusLabels:
y = self.radiusLabels
elif y < -self.radiusLabels:
y = - self.radiusLabels
# save y:
l[4] = y
# print("DO reposition labels, Round: ", i)
i = i + 1
# after n cycles stop calculations and return the positions
return Labels
def checkEnzymeCalculations(self):
# load enzymes
enzymes = genbank.gb.restrictionEnzymes.selection
# create hash of selection and DNA
hashable = "%s%s" % (frozenset(enzymes), genbank.gb.gbfile['dna'])
e1 = hashlib.md5(hashable).hexdigest()
labels = []
if e1 !=self.plasmidstore.enzymes:
# we have new enzymes
index = 0
for e in enzymes:
for site in enzymes[e].restrictionSites:
name, start, end, cut51, cut52, dnaMatch = site
length = self.dnaLength
middle = start + (end-start)/2 % length
name = self.nameBeautiful(name)
name2 = "%s%s" %(name, self.enzymeGap)
hitname = self.hitName(name2, index)
y = None # to be populated
labels.append([middle, name, index, hitname, y])
index = index + 1
self.plasmidstore.enzymes= e1
self.plasmidstore.LoE = labels
return None
def checkSelectionCalculations(self):
''' only chnage the arc if we changed something '''
# selection
selOld = self.plasmidstore.interaction["selectionOld"]
sel = self.plasmidstore.interaction["selection"]
if sel != selOld:
if sel[1] == -1:
# remove selection arc
self.plasmidstore.drawnSelection = None
else:
# draw selection arc
pos1, pos2, zero = sel
a1 = self.position2angle(pos1)
a2 = self.position2angle(pos2)
if (pos1 < pos2 and zero == -1) or (pos2 < pos1 and zero == 1):
self.ctx.arc(0,0,self.radius,a1,a2)
else :
self.ctx.arc_negative(0,0,self.radius,a1,a2)
path = self.ctx.copy_path() # save line path
self.ctx.new_path() # clear canvas
self.plasmidstore.drawnSelection = path
self.plasmidstore.interaction["selectionOld"] = sel
# draw the line for indicating the position
position = self.plasmidstore.interaction["position"]
positionOld = self.plasmidstore.interaction["positionOld"]
if position != positionOld:
if position < self.dnaLength and position > 0:
# get the coordinates for the line
x1, y1 = self.position2cartesian(position, self.radiusI - 1)
x2, y2 = self.position2cartesian(position, self.radiusO + 1)
# draw the actual line
self.ctx.move_to(x1,y1)
self.ctx.line_to(x2,y2)
# copy, save and delete
path = self.ctx.copy_path()
self.plasmidstore.drawnPosition = path
self.ctx.new_path()
# save settings
else:
self.plasmidstore.drawnPosition = None
self.plasmidstore.interaction["positionOld"] = position
return None
############################################
# drawing functions
def draw(self):
''' # print the stored elements on th canvas'''
# prepare the canvas
width, height = self.GetVirtualSize()
if width < height:
ratio = float(width)/float(height)
# only resize the canvas if software is loaded. This prevents error messages
if width != 0 and height != 0 and width > 100 and height > 100:
self.ctx.scale(width, height*ratio) # Normalizing the canvas
self.ctx.scale(0.01, 0.01) # make it 100*ratiox100
self.ctx.translate (50,50/ratio) # set center to 0,0
if width >= height:
ratio = float(height)/float(width)
# only resize the canvas if software is loaded. This prevents error messages
if width != 0 and height != 0 and width > 100 and height > 100:
self.ctx.scale(width*ratio, height) # Normalizing the canvas
self.ctx.scale(0.01, 0.01) # make it 100*ratiox100
self.ctx.translate (50/ratio,50) # set center to 0,0
self.drawFeatures()
self.drawLabels()
self.drawSelection()
return None
def drawFeatures(self):
# print("DO output path feature")
# only resize the canvas if software is loaded. This prevents error messages
# draw the helper plain white circle to make selection possible:
self.ctx.arc(0,0,self.radiusO+1,0,2*math.pi) # outer circle
self.ctx.set_source_rgb (1, 1, 1) # white
self.ctx.set_line_width (0) # no line
self.plasmidstore.interaction["markerArea1"] = self.ctx.copy_path() # copy for later
self.ctx.new_path() # remove
self.ctx.arc(0,0,self.radiusI-1,0,2*math.pi) # inner circle
self.ctx.set_source_rgb (1,1,1) # Solid white
self.ctx.set_line_width (0) # no line
self.plasmidstore.interaction["markerArea2"] = self.ctx.copy_path() # copy for later
self.ctx.new_path() # remove
# draw the plasmid (two circles with different radius)
radius=10
self.ctx.arc(0,0,self.radiusO,0, 2*math.pi) # circle
self.ctx.set_source_rgb (0, 0, 0) # Solid color
self.ctx.set_line_width (0.24) # line width
self.ctx.stroke() # stroke only no fill!
# inner plasmid
self.ctx.arc(0,0,self.radiusI,0,2*math.pi) # inner circle
self.ctx.stroke() # stroke the same color and settings
# draw the buffered featrues:
i = 0
for a in self.plasmidstore.drawnfeatures:
path = self.plasmidstore.drawnfeatures[a][0]
# get color
featuretype = self.plasmidstore.drawnfeatures[a][1]
color = eval(featuretype)['fw'] #get the color of feature (as string)
assert type(color) == str
r,g,b = colcol.hex_to_rgb(color)
r = float(r)/255
g = float(g)/255
b = float(b)/255
# put the path on the canvas and fill
#self.ctx.new_path()
self.ctx.append_path(path)
self.ctx.set_source_rgba (r,g,b,1.0) # Solid color
self.ctx.fill_preserve()
# outline for the feature that is beneeth the mouse:
if a == self.Highlight:
#self.ctx.set_source_rgb (1, 0, 0)
self.ctx.set_line_width(0.3)
self.ctx.stroke()
else:
# remove path
self.ctx.new_path()
i = i + 1
return None
def drawLabels(self):
''' function to put the labels on the canvas'''
# FEATURES
self.ctx.set_source_rgb (0, 0, 0) # Solid color
self.ctx.set_line_width(0.1)
# draw feature label names
for a in self.plasmidstore.drawnlabels:
path = self.plasmidstore.drawnlabels[a]
self.ctx.append_path(path)
# darker color for the feature that is beneeth the mouse:
if a == self.Highlight:
self.ctx.set_source_rgba (0, 0, 0, 1)
else:
self.ctx.set_source_rgba (0, 0, 0, 0.7)
self.ctx.fill()
# draw the lines
for a in self.plasmidstore.drawnLLines:
path = self.plasmidstore.drawnLLines[a]
self.ctx.append_path(path)
# darker color for the feature that is beneeth the mouse:
if a == self.Highlight:
self.ctx.set_source_rgba (0, 0, 0, 1)
else:
self.ctx.set_source_rgba (0, 0, 0, 0.3)
self.ctx.stroke()
# draw the underlines
#for a in self.plasmidstore.labelULine:
# path = self.plasmidstore.labelULine[a]
# self.ctx.append_path(path)
# self.ctx.set_line_width(2)
#
# # darker color for the feature that is beneeth the mouse:
# if a == self.Highlight:
## self.ctx.set_source_rgba (0, 0, 0, 1)
# else:
# self.ctx.set_source_rgba (0, 0, 0, 0.3)
# self.ctx.stroke()
# ENZYMES
self.ctx.set_source_rgb (0, 0, 0) # Solid color
self.ctx.set_line_width(0.1)
# draw feature label names
for a in self.plasmidstore.drawnlabelsE:
path = self.plasmidstore.drawnlabelsE[a]
self.ctx.append_path(path)
# darker color for the feature that is beneeth the mouse:
if self.Highlight != None and a.split(self.enzymeGap)[0] == self.Highlight.split(self.enzymeGap)[0]:
self.ctx.set_source_rgba (0, 0, 0, 1)
else:
self.ctx.set_source_rgba (0, 0, 0, 0.7)
self.ctx.fill()
# draw the lines
for a in self.plasmidstore.drawnLLinesE:
path = self.plasmidstore.drawnLLinesE[a]
self.ctx.append_path(path)
# darker color for the feature that is beneeth the mouse:
if self.Highlight != None and a.split(self.enzymeGap)[0] == self.Highlight.split(self.enzymeGap)[0]:
self.ctx.set_source_rgba (0, 0, 0, 1)
else:
self.ctx.set_source_rgba (0, 0, 0, 0.3)
self.ctx.stroke()
def drawSelection(self):
''' draw arc for selection '''
if self.plasmidstore.drawnSelection != None:
#0082ED
r,g,b = colcol.hex_to_rgb('#0082ED')
r = float(r)/255
g = float(g) /255
b = float(b) /255
self.ctx.set_source_rgba (r,g,b, 0.6) # Solid color
self.ctx.set_line_width(3)
path = self.plasmidstore.drawnSelection
self.ctx.append_path(path)
self.ctx.stroke()
if self.plasmidstore.drawnSelection == None and self.plasmidstore.drawnPosition != None:
self.ctx.set_source_rgba (0,0,0) # Solid color
self.ctx.set_line_width(0.2)
path = self.plasmidstore.drawnPosition
self.ctx.append_path(path)
self.ctx.stroke()