def peptide_length(self):
'''Sets the minimum peptide length for spectral searching'''
label = widgets.Label("Peptide Length Range")
self.layout.addWidget(label, 3, 0, 1, 5)
storage = updating.Storage('minimum_peptide_length')
minimum = updating.SpinBox(
self,
storage,
minimum=3,
maximum=10,
tooltip="Minimum peptide length included during spectral searches",
width=50)
self.layout.addWidget(minimum, 3, 8, 1, 1)
storage = updating.Storage('maximum_peptide_length')
maximum = updating.SpinBox(
self,
storage,
minimum=20,
maximum=70,
tooltip="Maximum peptide length included during spectral searches",
width=50)
self.layout.addWidget(maximum, 3, 9, 1, 1)
def charge_range(self):
'''Sets the charges to consider above the identified charge'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Charge Range")
hlayout.addWidget(label)
storage = updating.Storage('minus_charge_range')
minus = updating.SpinBox(self, storage,
minimum=0,
maximum=5,
tooltip="Number of charges below the identified charge to "
"include during XIC extraction.",
width=50,
prefix='-')
hlayout.addWidget(minus)
storage = updating.Storage('plus_charge_charge')
plus = updating.SpinBox(self, storage,
minimum=0,
maximum=5,
tooltip="Number of charges above the identified charge to "
"include during XIC extraction.",
width=50,
prefix='+')
hlayout.addWidget(plus)
def missed_cleavages(self):
'''Sets the minimum missed cleavages during spectral searching'''
label = widgets.Label("Missed Cleavage Range")
self.layout.addWidget(label, 4, 0, 1, 5)
storage = updating.Storage('minimum_missed_cleavages')
minimum = updating.SpinBox(
self,
storage,
minimum=0,
maximum=5,
tooltip="Minimum number of missed cleavages from "
"proteolytic digestion",
width=50)
self.layout.addWidget(minimum, 4, 8, 1, 1)
storage = updating.Storage('maximum_missed_cleavages')
maximum = updating.SpinBox(
self,
storage,
minimum=0,
maximum=10,
tooltip="Maximum number of missed cleavages from "
"proteolytic digestion",
width=50)
self.layout.addWidget(maximum, 4, 9, 1, 1)
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 __init__(self, parent):
store = updating.Storage('current_reporterions')
values = sorted(chemical_defs.REPORTER_IONS)
self.names = {}
super(CurrentReporterIonBox, self).__init__(parent, values, store)
self.setToolTip('Current reporter ions used for quantitation')
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 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 variable_modifications(self):
'''Creates a QListWidget to select variable modifications'''
header = widgets.Label("Variable", font=qt.BOLD_FONT)
self.layout.addWidget(header)
storage = updating.Storage('variable_modifications')
self.variable = ModificationView(self, storage, self.engine)
self.layout.addWidget(self.variable)
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 __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 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 constant_modifications(self):
'''Creates a QListWidget to select constant modifications'''
header = widgets.Label("Constant", font=qt.BOLD_FONT)
self.layout.addWidget(header)
storage = updating.Storage('constant_modifications')
self.constant = ModificationView(self, storage, self.engine)
self.layout.addWidget(self.constant)
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 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 __init__(self, parent, spinbox):
storage = updating.Storage('reporterion_error_mode')
values = ['PPM', 'Da']
super(ErrorComboBox, self).__init__(
parent,
values,
storage,
tooltip="Maximum mass error for reporter ion identification.")
self.spinbox = spinbox
def set_filtering(self):
'''Adds a line edit for a search query filter from the taxonomy'''
label = widgets.Label("Filter Query: ")
self.layout.addWidget(label, 2, 0, 1, 3)
storage = updating.Storage('taxonomy_filter')
searchquery = updating.LineEdit(
self, storage, tooltip="String filter for download queries.")
self.layout.addWidget(searchquery, 2, 3, 1, 7)
def __set_replace(self):
'''Set replace bar and QLineEdit form'''
label = widgets.Label("Replace With:")
self.layout.addWidget(label, 12, 0, 6, 2)
storage = updating.Storage('replace_form')
self.replaceform = updating.LineEdit(self,
storage,
tooltip="Search query.")
self.layout.addWidget(self.replaceform, 12, 2, 6, 4)
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 __set_search(self):
'''Set search bar and QLineEdit form'''
label = widgets.Label("Search For:")
self.layout.addWidget(label, 0, 0, 6, 2)
storage = updating.Storage('search_form')
self.searchform = updating.LineEdit(self,
storage,
tooltip="Search query.")
self.layout.addWidget(self.searchform, 0, 2, 6, 4)
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)
def default_label(self):
'''Whether to add isotope labels to the crosslinker'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Default Isotope Label")
hlayout.addWidget(label)
storage = updating.Storage('default_isotopic_label')
default = updating.LineEdit(self, storage,
tooltip="Default isotope label for the crosslinker (if no "
"isotope-labeled modifications exist on the peptide).")
hlayout.addWidget(default)
def comparative_order(self):
'''Sets the default order for the comparative report'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Comparative")
hlayout.addWidget(label)
storage = updating.Storage('order', self.comparative.other)
values = ['File', 'Crosslinker']
order = updating.ComboBox(self, values, storage,
tooltip="Hierarchical header order for the comparative report.")
hlayout.addWidget(order)
def named_comparative_counts(self):
'''Sets the default counts for the named comparative report'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Named Comparative")
hlayout.addWidget(label)
storage = updating.Storage('counts', self.named_comparative.other)
values = ['Unique', 'Redundant']
order = updating.ComboBox(self, values, storage,
tooltip="Counts format for the named comparative report.")
hlayout.addWidget(order)
def set_taxon(self):
'''Adds a line edit for the taxonomy download'''
label = widgets.Label("Taxonomy: ")
self.layout.addWidget(label, 0, 0, 1, 3)
storage = updating.Storage('taxonomy')
taxonomy = updating.LineEdit(
self,
storage,
tooltip="Taxonomy ID for the UniProt KB database query.",
validator=QtGui.QIntValidator())
self.layout.addWidget(taxonomy, 0, 3, 1, 7)
def non_specific(self):
'''Sets the default non-specific cleavage sites for the experiment'''
label = widgets.Label("Non-Specific")
self.layout.addWidget(label, 2, 0, 1, 5)
values = ['0', 'N', 'C', '1', '2']
storage = updating.Storage('nonspecific_cleavage')
nonspecific = updating.ComboBox(
self,
values,
storage,
tooltip='Non-specific cleavage sites during proteolytic cleavage')
self.layout.addWidget(nonspecific, 2, 5, 1, 5)