def concatenate(self):
'''Sets whether to join modifications at the same position'''
storage = updating.Storage('concatenate_hybrid_modifications')
concatenate = updating.CheckBox("Concatenate", self, storage,
tooltip="Join modifications at the same position.")
self.layout.addWidget(concatenate)
def global_search(self):
'''Sets checkbox to include mixed isotope-labeling populations'''
storage = updating.Storage('quantify_globally')
globally = updating.CheckBox("Search in all Files", self, storage,
tooltip="Extract XICs from identified crosslinks in all files.")
self.layout.addWidget(globally)
def filtering_intensity(self):
'''Sets whether to filter by intensity during export'''
storage = updating.Storage('filter_transitions_byintensity')
filter_ = updating.CheckBox("Filter by Intensity", self, storage,
tooltip="Filter exported XIC ratios by intensity.")
self.layout.addWidget(filter_)
def hierarchical(self):
'''Sets whether to write hierarchical or flattened modifications'''
storage = updating.Storage('write_hierarchical_modifications')
hierarchical = updating.CheckBox("Hierarchical", self, storage,
tooltip="Write Hierarchical (not flattened) modifications.")
self.layout.addWidget(hierarchical)
def isotope_labels(self):
'''Whether to add isotope labels to the crosslinker'''
storage = updating.Storage('add_isotopic_labels')
labels = updating.CheckBox("Crosslinker Isotope Labels",
self, storage, tooltip="Add isotope labels to the crosslinkers.")
self.layout.addWidget(labels)
def __set_conditions(self):
'''Set updating checkboxes describing search parameters'''
storage = updating.Storage('search_case_sensitive')
self.casesensitive = updating.CheckBox(
"Case Sensitive",
self,
storage,
tooltip="Force case matches during search queries")
self.layout.addWidget(self.casesensitive, 6, 0, 6, 3)
storage = updating.Storage('search_in_selection')
self.inselection = updating.CheckBox(
"In Selection",
self,
storage,
tooltip="Search exclusively within the current selection")
self.layout.addWidget(self.inselection, 6, 3, 6, 3)
def expand_charges(self):
'''Sets the checkbox for whether or not to expand the charge range'''
storage = updating.Storage('expand_charges')
expand = updating.CheckBox("Expand Charges", self, storage,
tooltip="Expand the charges included for XIC extraction "
"to the +/- range")
self.layout.addWidget(expand)
def mixed_populations(self):
'''Sets checkbox to include mixed isotope-labeling populations'''
storage = updating.Storage('include_mixed_populations')
mixed = updating.CheckBox("Include Mixed Populations", self, storage,
tooltip="Include crosslinked peptides where each peptide "
"comes from a different isotope-labeled population.")
self.layout.addWidget(mixed)
def antialias(self):
'''Sets checkbox to use antialiasing during visualization'''
storage = updating.Storage('use_antialiasing')
antialias = updating.CheckBox("Use Antialising", self, storage,
tooltip="Use antialiasing during rendering, default True.\n"
"Not available with OpenGL and some hardware")
self.layout.addWidget(antialias)
def opengl(self):
'''Sets checkbox to use OpenGL during visualization'''
storage = updating.Storage('useOpenGL', qt_config.RENDERING)
opengl = updating.CheckBox("Use OpenGL", self, storage,
tooltip="Use OpenGL during rendering. Provides performance\n"
"enhancements, however, is buggy on most systems.")
self.layout.addWidget(opengl)
def launch(self):
'''Sets checkbox to include mixed isotope-labeling populations'''
storage = updating.Storage('launch', qt_config.TRANSITIONS)
launch = updating.CheckBox("Launch Running Window", self, storage,
tooltip="Launch the window to validate during\nCrosslink "
"Discoverer prior to OpenOffice spreadsheet generation.")
self.layout.addWidget(launch)
def filtering_metrics(self):
'''Sets whether to filter by identification score during export'''
storage = updating.Storage(
'filter_transitions_byscore')
metrics = updating.CheckBox("Filter by Score", self, storage,
tooltip="Filter exported XIC ratios by identification score.")
self.layout.addWidget(metrics)
def weighted_ratio(self):
'''Sets whether to use a weighted or unweighted ratio'''
storage = updating.Storage('weighted_comparative_ratio')
weighted = updating.CheckBox("Weighted Ratios", self, storage,
tooltip="Weight quantitative ratios when merging\n"
"cross-linked peptide linkages.")
self.layout.addWidget(weighted)
def verify(self):
'''Sets a checkbox for whether to verify the precursor scan or not'''
storage = updating.Storage('check_precursor')
verify = updating.CheckBox(
"Verify Precursor",
self,
storage,
tooltip="Verify the precursor m/z exists in precursor scan")
self.layout.addWidget(verify)
def active(self):
'''Sets whether product-level quantitation is set active'''
storage = updating.Storage('reporterion_quantitation')
self.quantitation = updating.CheckBox(
"Reporter Ion Quantitation",
self,
storage,
tooltip="Use product scans-level reporter ions for quantitation.")
self.quantitation.clicked.connect(self.toggle)
self.layout.addWidget(self.quantitation)