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 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 set_banner(self):
'''Add a banner to the layout'''
layout = self.add_layout(QtGui.QHBoxLayout, alignment='Center')
banner = widgets.Label("Keyboard Shortcuts")
banner.set_stylesheet('bannerwhite')
layout.addWidget(banner)
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 set_text(self):
'''Create QLabel with text and add to layout'''
self.label = widgets.Label(self._text)
self.label.setAlignment(qt.ALIGNMENT['HCenter'])
self.layout.addWidget(self.label)
self.layout.addSpacing(1)
def __init__(self, shortcut):
super(ShortCutWidget, self).__init__()
self.set_layout(QtGui.QGridLayout, alignment='Left')
icon = IconLabel(KEYICONS[shortcut.key])
self.layout.addWidget(icon, 0, 0, 4, 4)
label = widgets.Label(shortcut.sequence)
label.set_stylesheet('keywhite')
self.layout.addWidget(label, 0, 4, 2, 6)
label = widgets.Label(shortcut.description)
label.set_stylesheet('descriptionwhite')
self.layout.addWidget(label, 2, 4, 2, 6)
self.setMaximumSize(self.size, self.size)
def __init__(self, parent):
super(BaseSection, self).__init__(parent)
layout = getattr(self, "_layout", QtGui.QVBoxLayout)
self.set_layout(layout, alignment='Top')
header = widgets.Label(self._title, font=qt.BOLD_FONT)
self.layout.addWidget(header)
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 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 current(self):
'''Sets the currently active report ions'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
self.reporterlabel = widgets.Label("Current Reporter Ions")
hlayout.addWidget(self.reporterlabel)
self.reporterions = CurrentReporterIonBox(self)
hlayout.addWidget(self.reporterions)
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_widgets(self, text="Don't ask me again"):
'''
Make label above a labelled QCheckbox preventing user
from accidentally quitting while running calculations.
'''
label = widgets.Label(exception.CODES['007'])
self.layout.addWidget(label)
self.checkbox = widgets.ClickCheckBox(text, self.ignore, self.update)
self.layout.addWidget(self.checkbox)
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 __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 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 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 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 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 image(self, regex=r"[0-9a-zA-Z]{2,4}"):
'''Sets the default image extension for XL Discoverer'''
label = widgets.Label("Image")
self.layout.addWidget(label, 3, 0)
storage = updating.Storage('image_extension', qt_config.TRANSITIONS)
validator = QtGui.QRegExpValidator(QtCore.QRegExp(regex))
image = updating.LineEdit(self, storage,
tooltip="Default extension for exported images.",
validator=validator,
width=75,
attr='extension')
self.layout.addWidget(image, 3, 1)
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)
def enzyme(self):
'''Sets the currently active proteolytic enzyme for peptide cleavage'''
label = widgets.Label("Enzyme")
self.layout.addWidget(label, 1, 0, 1, 5)
values = sorted(proteins.ENZYMES)
storage = updating.Storage('current_enzyme')
enzyme = updating.ComboBox(
self,
values,
storage,
tooltip='Proteolytic enzyme used prior to mass spectrometry')
self.layout.addWidget(enzyme, 1, 5, 1, 5)
def document(self, regex=r"[0-9a-zA-Z]{2,4}"):
'''Sets the default document extension for XL Discoverer'''
label = widgets.Label("Document")
self.layout.addWidget(label, 2, 0)
storage = updating.Storage('document_extension', qt_config.TRANSITIONS)
validator = QtGui.QRegExpValidator(QtCore.QRegExp(regex))
document = updating.LineEdit(self, storage,
tooltip="Default extension for the transitions docuyment.",
validator=validator,
width=75,
attr='extension')
self.layout.addWidget(document, 2, 1)
def __set_limiteddatabase(self):
'''Sets the limited database status for the current proteins object'''
layout = self.add_layout(QtGui.QHBoxLayout)
self.add_spacer(layout)
label = widgets.Label("Limited Database: ")
layout.addWidget(label)
self.limited = dbwidgets.LimitedDatabaseComboBox(self,
self.proteins,
tooltip="Select a limited or automatically generated database")
layout.addWidget(self.limited)
self.add_spacer(layout)
def comparative_integration(self):
'''Sets the default inegration mode for the comparative report'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Comparative")
hlayout.addWidget(label)
storage = updating.Storage('ratio_quantitation')
values = ['Area', 'Intensity']
order = updating.ComboBox(self, values, storage,
tooltip="Integration ratios for the quantitative "
"comparative report.")
hlayout.addWidget(order)
def minimum_crosslinker(self):
'''Sets the maximum modifications fragments per peptide'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Modifications")
hlayout.addWidget(label)
storage = updating.Storage('maximum_modifications')
modifications = updating.SpinBox(self, storage,
minimum=0,
maximum=10,
tooltip="Maximum number of modifications per peptide.",
width=75)
hlayout.addWidget(modifications)
def sorting(self):
'''Sets the sorting key for transitions document'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Sorting")
hlayout.addWidget(label)
storage = updating.Storage('transition_sortkey')
values = ['RT', 'Peptide', 'Score', 'EV', 'Mod Count']
sorting = updating.ComboBox(self, values, storage,
tooltip="Default sorting while constructing the "
"transitions document.",
width=75)
hlayout.addWidget(sorting)
def database(self):
'''Sets the current spectral engine for the modification selection'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Database")
hlayout.addWidget(label)
storage = updating.Storage('modification_engine')
values = ['Protein Prospector', 'Mascot', 'Proteome Discoverer']
self.engine = updating.ComboBox(self, values, storage,
tooltip='Current modification database for modification selection')
self.engine.currentIndexChanged.connect(self.reset_database)
hlayout.addWidget(self.engine)
def maximum_crosslinkers(self):
'''Sets the maximum crosslinker fragments per peptide'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Crosslinkers")
hlayout.addWidget(label)
storage = updating.Storage('maximum_crosslinkers')
crosslinkers = updating.SpinBox(self, storage,
minimum=0,
maximum=10,
tooltip="Maximum number of crosslinker fragments per peptide.",
width=75)
hlayout.addWidget(crosslinkers)
def normalization(self):
'''Sets the normalization mode for XIC areas and intensities'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Normalize To")
hlayout.addWidget(label)
storage = updating.Storage('xic_normalization')
values = ["Light", "Medium", "Heavy", "Min", "Max"]
normalization = updating.ComboBox(self, values, storage,
tooltip="How to normalization XICs areas and intensities "
"during ratio reporting.",
width=75)
hlayout.addWidget(normalization)
def filtering_score(self):
'''Sets the minimum scoring threshold for transition exportation'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Minimum Peptide Score")
hlayout.addWidget(label)
storage = updating.Storage('transition_score_threshold')
score = updating.DoubleSpinBox(self, storage,
minimum=0.1,
maximum=100,
tooltip="Minimum peptide score for quantified "
"crosslink exportation.",
width=100)
hlayout.addWidget(score)
