def __call__(self, a, b):
if isinstance(a, basestring):
a = normalize_composition(a)
b = normalize_composition(b)
keys = self.key_order(sorted(set(a) | set(b), key=self.sorter))
for key in keys:
if a[key] < b[key]:
return -1
elif a[key] > b[key]:
return 1
else:
continue
return 0
def __call__(self, a, b):
if isinstance(a, basestring):
a = normalize_composition(a)
b = normalize_composition(b)
keys = self.key_order(sorted(set(a) | set(b), key=self.sorter))
for key in keys:
if a[key] < b[key]:
return -1
elif a[key] > b[key]:
return 1
else:
continue
return 0
def __call__(self, obj):
obj = normalize_composition(obj)
for rule, color in self.rule_color_map.items():
if rule(obj):
return color
if self.default:
return self.default
raise ValueError("Could not classify %r" % obj)
def __call__(self, obj):
obj = normalize_composition(obj)
for rule, color in self.rule_color_map.items():
if rule(obj):
return color
if self.default:
return self.default
raise ValueError("Could not classify %r" % obj)
def _infer_compositions(self):
residues = set()
for item in self._input_series:
if isinstance(item, basestring):
item = normalize_composition(item)
residues.update(item)
residues = sorted(residues, key=_degree_monosaccharide_alteration)
self.residues = self.order_chooser.key_order(residues)
def _infer_compositions(self):
residues = set()
for item in self._input_series:
if isinstance(item, basestring):
item = normalize_composition(item)
residues.update(item)
residues = sorted(residues, key=_degree_monosaccharide_alteration)
self.residues = self.order_chooser.key_order(residues)
def details_for(analysis_uuid, chromatogram_id):
view = get_view(analysis_uuid)
with view:
snapshot = view.get_items_for_display()
with snapshot.bind(view.session):
model = view.analysis.parameters.get('scoring_model')
chroma = snapshot[chromatogram_id].convert(chromatogram_scoring_model=model)
plot = SmoothingChromatogramArtist(
[chroma], colorizer=lambda *a, **k: 'green', ax=figax()).draw(
label_function=lambda *a, **k: "", legend=False).ax
plot.set_title("Aggregated\nExtracted Ion Chromatogram", fontsize=24)
chroma_svg = report.svguri_plot(
plot, bbox_inches='tight', height=5, width=9, svg_width="100%")
glycan_composition = normalize_composition(chroma.glycan_composition)
membership = [neigh.name for neigh in view.neighborhoods if neigh(glycan_composition)]
mass_shift_separation = ""
if len(chroma.mass_shifts) > 1:
mass_shifts = list(chroma.mass_shifts)
labels = {}
rest = chroma
for mass_shift in mass_shifts:
with_mass_shift, rest = rest.bisect_mass_shift(mass_shift)
labels[mass_shift] = with_mass_shift
mass_shift_plot = SmoothingChromatogramArtist(
labels.values(),
colorizer=lambda *a, **k: 'green', ax=figax()).draw(
label_function=lambda *a, **k: tuple(a[0].mass_shifts)[0].name,
legend=False).ax
mass_shift_plot.set_title(
"Adduct-Separated\nExtracted Ion Chromatogram", fontsize=24)
mass_shift_separation = report.svguri_plot(
mass_shift_plot, bbox_inches='tight', height=5, width=9, svg_width="100%")
charge_separation = ""
if len(chroma.charge_states) > 1:
charge_separating_plot = ChargeSeparatingSmoothingChromatogramArtist(
[chroma], ax=figax()).draw(
label_function=lambda x, *a, **kw: str(tuple(x.charge_states)[0]), legend=False).ax
charge_separating_plot.set_title("Charge-Separated\nExtracted Ion Chromatogram", fontsize=24)
charge_separation = report.svguri_plot(
charge_separating_plot, bbox_inches='tight', height=5, width=9,
svg_width="100%")
return render_template(
"/view_glycan_search/detail_modal.templ", chromatogram=chroma,
chromatogram_svg=chroma_svg, mass_shift_separation_svg=mass_shift_separation,
charge_chromatogram_svg=charge_separation,
logitscore=logitsum(chroma.score_components()),
membership=membership)
def transform(self):
for item in self._input_series:
if isinstance(item, basestring):
item = normalize_composition(item)
counts = [str(item[r]) for r in self.residues]
yield '[%s]' % '; '.join(counts)
def transform(self):
for item in self._input_series:
if isinstance(item, basestring):
item = normalize_composition(item)
counts = [str(item[r]) for r in self.residues]
yield '[%s]' % '; '.join(counts)