class FastTextAreaInput(_BkTextAreaInput):
"""The FastTextAreaInput enables using the `fast-textarea-input` with Bokeh."""
# value is inherited
# placeholder is inherited
# max_length is inherited
# cols is inherited
# rows is inherited
appearance = properties.String(
help=
"""Determines the appearance of the textinput. One of `outline` or `filled`.
Defaults to outlined""", )
autofocus = properties.Bool(
help="""The autofocus attribute. Defaults to `False`""", )
resize = properties.String(help="""The resize attribute. One of
`None`, `both`, `horizontal` or `vertical`. Defaults to `None`.""", )
min_length = properties.Int(
help="""The minimum length of the text string""", )
spellcheck = properties.Bool(
help="""Whether or not the spell check is enabled. Default is False""")
required = properties.Bool(
help=
"""Whether or not the FastTextInput is required. Default is False""")
readonly = properties.Bool(
help=
"""Whether or not the FastTextInput is readonly. Default is False""")
class DpxToolbar(Widget):
"Toolbar model"
__css__ = route("view.css", "icons.css", "toolbar.css")
__implementation__ = 'toolbar.ts'
__javascript__ = route()
frozen = props.Bool(True)
open = props.Int(0)
save = props.Int(0)
doc = props.Int(0)
quit = props.Int(0)
bead = props.Int(-1)
discarded = props.String('')
accepted = props.String('')
currentbead = props.Bool(True)
currentfile = props.Int(-1)
delfile = props.Int(-1)
filelist = props.List(props.String)
seltype = props.Bool(True)
message = props.String('')
helpmessage = props.String('')
hasquit = props.Bool(False)
hasdoc = props.Bool(False)
def __init__(self, **kwa):
super().__init__(name='Main:toolbar', **kwa)
class FastTextInput(_BkTextInput):
# value is inherited
# placeholder is inherited
# list is not supported
appearance = properties.String(
help=
"""Determines the appearance of the textinput. One of `outline` or `filled`.
Defaults to outlined""", )
autofocus = properties.Bool(
help="""The autofocus attribute. Defaults to `False`""", )
type_of_text = properties.String(
help=
"""Determines the type of text accepted. One of `email`, `password`, `tel`, `text` or `url`.
Defaults to text.
""")
max_length = properties.Int(
help="""The maximum length of the text string""", )
min_length = properties.Int(
help="""The minimum length of the text string""", )
pattern = properties.String(
help=
"""A regular expression that the input's value must match in order for the value to pass constraint validation"""
)
size = properties.Int(
help=
"""Valid for email, password, tel, and text input types only. Specifies how much of the input is shown""",
)
spellcheck = properties.Bool(
help="""Whether or not the spell check is enabled. Default is False""")
required = properties.Bool(
help=
"""Whether or not the FastTextInput is required. Default is False""")
readonly = properties.Bool(
help=
"""Whether or not the FastTextInput is readonly. Default is False""")
class DpxFitParams(Widget):
"Interface to filters needed for cleaning"
__css__ = route("peaksplot.css")
__javascript__ = [ROUTE + "/jquery.min.js", ROUTE + "/jquery-ui.min.js"]
__implementation__ = "_widget.ts"
frozen = props.Bool(True)
stretch = props.String("")
bias = props.String("")
locksequence = props.Bool(False)
class DpxDiscardedBeads(Widget):
"Toolbar model"
__css__ = route("groupedbeads.css", "icons.css")
__implementation__ = '_widget.ts'
__javascript__ = route()
frozen = props.Bool(True)
hassequence = props.Bool(False)
discarded = props.String('')
discardedhelp = props.String('')
forced = props.String('')
forcedhelp = props.String('')
class FastButton(_BkButton):
appearance = properties.String(
default="neutral",
help="The appearance attribute",
)
autofocus = properties.Bool(
default=False,
help="The autofocus attribute",
)
class KeyModResponder(LayoutDOM):
"""capture all aspects of keydown/up events"""
#__implementation__ = TypeScript(KEYBOARDRESPONDERCODE_TS)
__implementation__ = "keymodresponder.ts"
# can use # __css__ = '<a css file.css>'
# can use # __javascript__ = 'katex.min.js' # for additional javascript
# this should match with javascript/typescript implementation
key = properties.String(default="")
keyCode = properties.Int(default=0)
altKey = properties.Bool(default=False)
ctrlKey = properties.Bool(default=False)
metaKey = properties.Bool(default=False)
shiftKey = properties.Bool(default=False)
key_num_presses = properties.Int(default=0)
keypress_callback = properties.Instance(bokeh.models.callbacks.Callback,
help=""" A callback to run in the browser whenever a key is pressed
""")
class FastButton(_BkButton):
"""The FastButton enables using the `fast-button` with Bokeh."""
appearance = properties.String(
default="neutral",
help="The appearance attribute",
)
autofocus = properties.Bool(
default=False,
help="The autofocus attribute",
)
class DpxRamp(Widget):
"Interface to filters needed for cleaning"
__css__ = route("ramp.css")
__javascript__ = route()
__implementation__ = "_widget.ts"
frozen = props.Bool(True)
minhfsigma = props.Float(RampStatsTask.hfsigma[0])
maxhfsigma = props.Float(RampStatsTask.hfsigma[1])
minextension = props.Float(RampStatsTask.extension[0])
fixedextension = props.Float(RampStatsTask.extension[1])
maxextension = props.Float(RampStatsTask.extension[2])
displaytype = props.Int(0)
class DpxCleaning(Widget):
"Interface to filters needed for cleaning"
__css__ = route("cleaning.css")
__javascript__ = route()
__implementation__ = "_widget.ts"
frozen = props.Bool(True)
framerate = props.Float(30.)
figure = props.Instance(Figure)
fixedbeads = props.String("")
subtracted = props.String("")
subtractcurrent = props.Int(0)
maxabsvalue = props.Float(getattr(DataCleaningTask, 'maxabsvalue'))
maxderivate = props.Float(getattr(DataCleaningTask, 'maxderivate'))
minpopulation = props.Float(getattr(DataCleaningTask, 'minpopulation'))
minhfsigma = props.Float(getattr(DataCleaningTask, 'minhfsigma'))
maxhfsigma = props.Float(getattr(DataCleaningTask, 'maxhfsigma'))
minextent = props.Float(getattr(DataCleaningTask, 'minextent'))
maxextent = props.Float(getattr(DataCleaningTask, 'maxextent'))
maxsaturation = props.Float(getattr(DataCleaningTask, 'maxsaturation'))
super().validate(value, detail)
if isinstance(value, param.Parameterized):
return
msg = "" if not detail else f"expected param.Parameterized, got {value!r}"
raise ValueError(msg)
_DATA_MODELS = weakref.WeakKeyDictionary()
PARAM_MAPPING = {
pm.Array:
lambda p, kwargs: bp.Array(bp.Any, **kwargs),
pm.Boolean:
lambda p, kwargs: bp.Bool(**kwargs),
pm.CalendarDate:
lambda p, kwargs: bp.Date(**kwargs),
pm.CalendarDateRange:
lambda p, kwargs: bp.Tuple(bp.Date, bp.Date, **kwargs),
pm.ClassSelector:
lambda p, kwargs: ((bp.Instance(DataModel, **kwargs), [
(Parameterized, create_linked_datamodel)
]) if isinstance(p.class_, type) and issubclass(
p.class_, param.Parameterized) else bp.Any(**kwargs)),
pm.Color:
lambda p, kwargs: bp.Color(**kwargs),
pm.DataFrame:
lambda p, kwargs: (bp.ColumnData(bp.Any, bp.Seq(bp.Any), **kwargs), [(
bp.PandasDataFrame, lambda x: ColumnDataSource._data_from_df(x))]),
pm.DateRange:
class SequenceTicker(BasicTicker): # pylint: disable=too-many-ancestors
"Generate ticks at fixed, explicitly supplied locations."
major = props.Dict(props.String, props.Seq(props.Float), default={'': []})
minor = props.Dict(props.String, props.Seq(props.Float), default={'': []})
key = props.String(default='')
usedefault = props.Bool(default=True)
__defaults: dict
__withbase: list
__model: Any
__theme: SequenceTickerTheme
__fig: Figure
__axis: 'SequenceTicker'
__implementation__ = "sequenceticker.ts"
def __init__( # pylint: disable=too-many-arguments
self,
ctrl=None,
fig=None,
mdl=None,
axlabel=None,
loc='right',
**kwa):
"Sets the ticks according to the configuration"
super().__init__(**kwa)
self.__defaults = dict()
self.__withbase = []
if ctrl:
self.__theme = ctrl.theme.add(SequenceTickerTheme(), False)
else:
self.__theme = SequenceTickerTheme()
if mdl is None:
return
self.__model = mdl
self.__fig = fig
self.__axis = type(self)(ctrl)
if 'bases' not in fig.extra_y_ranges:
fig.extra_y_ranges = dict(fig.extra_y_ranges,
bases=Range1d(start=0., end=0.))
fig.add_layout(
LinearAxis(y_range_name="bases",
axis_label=axlabel,
ticker=self.__axis), loc)
# bokehjs will never draw minor lines unless the color is
# is set at startup
fig.ygrid[0].update(minor_grid_line_color='navy',
minor_grid_line_alpha=0.,
ticker=self,
y_range_name='bases')
order = tuple('grid_line_' + i
for i in ('color', 'width', 'dash', 'alpha'))
order += tuple('minor_' + i for i in order) # type: ignore
self.__defaults = {i: getattr(fig.ygrid[0], i) for i in order}
self.__withbase = dict()
theme = self.__model.themename
for name in ('color', 'dash', 'width', 'alpha'):
gridprops = themed(theme, self.__theme.grid[name])
self.__withbase['grid_line_' + name] = gridprops[0]
self.__withbase['minor_grid_line_' + name] = gridprops[1]
@staticmethod
def init(ctrl):
"init private fields"
ctrl.theme.add(SequenceTickerTheme(), False)
@property
def axis(self):
u"returns the fixed axis"
return self.__axis
def reset(self, resets):
"Updates the ticks according to the configuration"
mdl = self.__model
fig = self.__fig
key = (mdl.sequencemodel.currentkey
if mdl.sequencemodel.currentkey is not None and len(mdl.oligos)
else 'NONE')
majors = {}
minors = {}
axis = next(i for i in fig.right if isinstance(i, LinearAxis))
resets[axis].update(axis_label_standoff=self.__theme.standoff)
if key == 'NONE':
resets[fig.ygrid[0]].update(self.__defaults)
else:
resets[fig.ygrid[0]].update(self.__withbase)
for name, peaks in self.__model.hybridisations(...).items():
majors[name] = tuple(peaks['position'][peaks['orientation']])
minors[name] = tuple(peaks['position'][~peaks['orientation']])
resets[self].update(major=majors, minor=minors, key=key)
minor = dict.fromkeys(majors.keys(), tuple()) # type:ignore
major = {i: majors[i] + minors[i] for i in majors}
resets[self.__axis].update(major=major, minor=minor, key=key)
