class RampZMagHintsTheme:
"RampBeadStatusTheme"
name: str = "ramp.zmaghints"
height: int = 80
columns: List[List] = dflt([["val", "Consensus", 160, "0.00"],
["err", "Uncertainty", 160, "0.00"],
["zmag", "Z magnet (mm)", 160, "0.00"]])
units: List[str] = dflt(["(µm)", "(% strand size)"])
rows: List[float] = dflt([50, 66, 80, 95])
@property
def width(self) -> int:
"the width of the widget"
return sum(i[2] for i in self.columns) # pylint: disable=not-an-iterable
class RampZMagResultsTheme:
"RampBeadStatusTheme"
name: str = "ramp.zmageresults"
step: float = .01
value: float = -.4
heights: Tuple[int, ...] = (48, 150)
width: int = 500
title: str = "Loosing {bead:.3f} ± {err:.3f} {unit} with Zmag ="
ranges: List[float] = dflt([.05, .1, .2, .5, 1.])
alpha = .5
color = 'yellow'
units: List[str] = dflt(RampZMagHintsTheme().units)
columns: List[List] = dflt([["closing", "Closing ≥", 40, "0%"],
["count", "Count", 40, "0"],
["percent", "(%)", 40, "0%"],
["beads", "Beads", 180, ""]])
class MessagesListWidgetTheme:
"MessagesListWidgetTheme"
name: str = "qc.messages"
height: int = 150
labels: Dict[str, str] = dflt(NAMES)
columns: List[List] = dflt([
['bead', u'Bead', '0', 65],
['type', u'Type', '', (320-65)//3],
['cycles', u'Cycles', '0', (320-65)//3],
['message', u'Message', '', (320-65)//3]
])
@property
def width(self) -> int:
"return the full width"
return sum([i[-1] for i in self.columns]) # pylint: disable=not-an-iterable
class QCHairpinSizeTheme:
"RampBeadStatusTheme"
name: str = "qc.hairpinsize"
title: str = "Hairpins bin size"
binsize: float = .1
binstart: float = .05
binend: float = 1.
binstep: float = .05
headers: bool = False
tableheight: int = 125
sliderheight: int = 48
columns: List[List] = dflt([
["z", "Δz (µm)", 60, ""],
["count", "Count", 40, "0"],
["percent", "(%)", 40, ""],
["beads", "Beads", 180, ""]
])
@property
def width(self) -> int:
"return the full width"
return sum(i[2] for i in self.columns) # pylint: disable=not-an-iterable
def __post_init__(self):
# pylint: disable=unsubscriptable-object
cols = self.columns
if not self.headers:
cols[2][-1] = cols[0][-1] = ""
else:
if cols[2][-1] == "":
cols[2][-1] = "0"
if cols[0][-1] == "":
cols[2][-1] = "0.00"
class PeakIDPathTheme:
"PeakIDPathTheme"
name: str = "hybridstat.peaks.idpath"
title: str = ""
dialogtitle: str = 'Select an id file path'
placeholder: str = 'Id file path'
filechecks: int = 500
width: int = 225
height: int = 32
tableerror: List[str] = dflt(['File extension must be .xlsx', 'warning'])
class PeaksStatsWidgetTheme:
"PeaksStatsWidgetTheme"
name: str = "hybridstat.peaks.stats"
line: str = _LINE
openhairpin: str = ' & open hairpin'
orientation: str = '-+ '
style: Dict[str, Any] = dflt({})
lines: List[List[str]] = dflt([['Cycles', '.0f'],
['Stretch (base/µm)', '.3f'],
['Bias (µm)', '.4f'], ['σ[HF] (µm)', '.4f'],
['σ[Peaks] (µm)', '.4f'],
['Average Skew ', '.2f'],
['Peak count', '.0f'],
['Baseline (µm)', '.3f'],
['Singlestrand (µm)', '.3f'],
['Events per Cycle', '.1f'],
['Down Time Φ₅ (s)', '.1f'],
['Sites found', ''], ['Silhouette', '.1f'],
['reduced χ²', '.1f']])
height: int = 20 * 14
width: int = 230
class SequenceTickerTheme:
"sequence ticker theme"
name: str = "sequence.ticker"
standoff: int = -2
grid: dict = dflt({
'color': {
'dark': ('lightgray', 'lightgreen'),
'basic': ('gray', 'lightgreen')
},
'width': (1, 1),
'alpha': (.8, .8),
'dash': ('solid', 'solid')
})
class QCBeadStatusTheme:
"RampBeadStatusTheme"
name: str = "qc.status"
status: Dict[str, str] = dflt({i: i for i in ("ok", "fixed", "bad", "missing")})
tableheight: int = 102
headers: bool = False
columns: List[List] = dflt([["status", "Status", 60, ""],
["count", "Count", 40, "0"],
["percent", "(%)", 40, ""],
["beads", "Beads", 180, ""]])
@property
def width(self) -> int:
"return the full width"
return sum(i[2] for i in self.columns) # pylint: disable=not-an-iterable
def __post_init__(self):
cols = self.columns[2] # pylint: disable=unsubscriptable-object
if not self.headers:
cols[-1] = ""
elif cols[-1] == "":
cols[-1] = "0"
class PeakListTheme:
"PeakListTheme"
name: str = "hybridstat.peaks.list"
height: int = 400
colwidth: int = 60
refid: str = '0.0000'
columns: List[List[str]] = dflt(
[['z', 'Z (µm)', '0.0000'], ['bases', 'Z (base)', '0.0'],
['id', 'Hairpin', '0'], ['orient', 'Strand', ''],
['distance', 'Distance', '0.0'],
['count', PeaksPlotTheme.xlabel, '0.0'],
['duration', PeaksPlotTheme.xtoplabel, '0.000'],
['sigma', 'σ (µm)', '0.0000'], ['skew', 'skew', '0.00']])
@property
def width(self) -> int:
"the table width"
return self.colwidth * len(self.columns)
class TaskDescriptor:
"Access to a task"
_LABEL = '%({self.attrname}){self.fmt}'
__NONE = type('_None', (), {})
label: str = ""
fmt: str = ""
keys: List[str] = dflt([])
attrname: str = ""
def __post_init__(self):
if not self.fmt:
ix1, ix2 = self.label.rfind("%("), self.label.rfind(")")
self.fmt = self.label[ix2 + 1:]
self.keys = self.label[ix1 + 2:ix2].split(".")
self.label = self.label[:ix1].strip()
if isinstance(self.keys, str):
self.keys = self.keys.split('.')
if self.keys[0] == 'task':
self.keys = self.keys[1:]
if len(self.keys) == 2 and self.keys[-1] == 'disabled':
self.keys = self.keys[:1]
if len(self.keys) == 1:
self.fmt = 'b'
assert len(self.keys) >= 1
assert len(self.fmt)
assert len(self.label)
def __set_name__(self, _, name):
self.attrname = name
def __model(self, obj):
return getattr(getattr(obj, '_model'), self.keys[0])
def get(self, obj, wherefrom="default"):
"""
Gets the attribute in the task.
Use config = True to access the default value
"""
mdl = self.__model(obj)
mdl = (
getattr(mdl, 'task', mdl) if wherefrom == "model" else
mdl.configtask if wherefrom == "config" else mdl.defaultconfigtask)
if len(self.keys) == 1:
return False if mdl is None else not mdl.disabled
if '|' not in self.fmt and 'o' in self.fmt:
for key in self.keys[1:]:
mdl = getattr(mdl, key, None)
else:
for key in self.keys[1:]:
mdl = getattr(mdl, key)
if self.fmt == 'b' and not isinstance(mdl, bool):
return mdl is not None
return mdl
def getdefault(self, obj):
"""
Gets the attribute in the task.
Use config = True to access the default value
"""
return self.get(obj)
def __get__(self, obj, tpe):
if obj is None:
return self
return self.get(
obj, 'config' if self.__model(obj).task is None else 'model')
def __set__(self, obj, val):
outp = getattr(obj, '_get_output')()
if len(self.keys) == 1:
outp.setdefault(self.keys[0], {})['disabled'] = not val
return
tsk = self.__model(obj).tasktype
if len(self.keys) == 2:
mdl = getattr(tsk, self.keys[1])
if self.fmt == "b" and not isinstance(mdl, bool):
val = deepcopy(mdl) if val else None
outp.setdefault(self.keys[0], {})[self.keys[1]] = val
return
mdl = outp.setdefault(self.keys[0], {}).get(self.keys[1], self.__NONE)
if mdl is self.__NONE:
mdl = deepcopy(getattr(tsk, self.keys[1]))
outp[self.keys[0]][self.keys[1]] = mdl
for key in self.keys[2:-1]:
mdl = getattr(mdl, key)
attr = getattr(type(mdl)(), self.keys[-1])
if self.fmt == "b" and not isinstance(attr, bool):
val = deepcopy(attr) if val else None
setattr(mdl, self.keys[-1], val)
def line(self) -> Tuple[str, str]:
"return the line for this descriptor"
return self.label, self._LABEL.format(self=self)