def __init__(self,
top=2.0,
bottom=0.0,
minicolor=color(.8, .8, .8),
maincolor=color(0, 0, 0),
align=None,
text_align="middle",
text_color=color(0, 0, 0),
show=True,
fixed_height=True,
**options):
Track.__init__(self, **options)
self.top = top
self.bottom = bottom
self.minicolor = minicolor
self.maincolor = maincolor
self.text_align = text_align
self.text_color = text_color
self.show = show
self.shown = show
self.fixed_height = fixed_height
if align != None:
self.coords = alignlib.CoordConverter(align)
else:
self.coords = None
self.multiscale = Multiscale(marginx=.5,
marginy=.5,
scalex=10,
scaley=10)
def __init__(self, seqs, **options):
options.setdefault("size", [0.0, 0.5])
Track.__init__(self, **options)
self.seqs = seqs
self.shown = False
self.multiscale = Multiscale(marginx=.5, marginy=.5)
def __init__(self, xdata, ydata, **options):
Track.__init__(self, **options)
self.xdata = xdata
self.ydata = ydata
self.multiscale = Multiscale(marginx=.25,
marginy=.25,
scalex=4.0,
scaley=4.0)
self.shown = False
def __init__(self,
aln,
collapse=None,
cols=None,
color_bases=False,
seqtype=None,
show_color_bases=True,
show_bases=True,
show_labels=True,
rowspacing=None,
**options):
Track.__init__(self, **options)
self.size = [aln.alignlen(), len(aln)]
self.multiscale = Multiscale(marginx=.5, marginy=.5)
self.collapse = collapse
self.show_color_bases = show_color_bases
self.show_bases = show_bases
self.show_labels = show_labels
self.rowspacing = rowspacing
self.always_color = False
self.color_bases_vis = None
if seqtype == None:
self.seqtype = guessAlign(aln)
else:
self.seqtype = seqtype
if color_bases == True:
if self.seqtype == "dna":
self.color_bases = dna_colors
elif self.seqtype == "pep":
self.color_bases = pep_colors
else:
self.color_bases = color_bases
if collapse != None:
assert collapse in aln.keys()
cols = util.findneq('-', aln[collapse])
if cols != None:
self.aln = alignlib.subalign(aln, cols)
else:
self.aln = aln
def __init__(self,
win,
start,
end,
height=20,
bottom=0,
unitstr="",
minicolor=color(.8, .8, .8),
maincolor=color(0, 0, 0),
pos=[0.0, 0.0]):
summon.VisObject.__init__(self)
self.win = win
self.start = start
self.end = end
self.height = height
self.bottom = bottom
self.pos = pos[:]
self.minicolor = minicolor
self.maincolor = maincolor
self.multiscale = Multiscale(marginx=.5,
marginy=.5,
scalex=10,
scaley=10)
