def initUI(self):
self.setWindowTitle('Import PDB Options')
vertical_layout = QtWidgets.QVBoxLayout()
# Installation options label.
info_text = "Please select the 3D structure import mode:"
self.fetch_info_label = QtWidgets.QLabel(info_text, self)
# self.fetch_info_label.setStyleSheet(label_style_1)
vertical_layout.addWidget(self.fetch_info_label)
vertical_layout.addStretch(1)
# Import options radiobuttons.
horizontal_layout = QtWidgets.QHBoxLayout()
self.import_all_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod the structure of every chain of the PDB files.")
# self.import_all_radiobutton.setChecked(True)
# self.import_all_radiobutton.setStyleSheet(label_font_1)
vertical_layout.addWidget(self.import_all_radiobutton)
self.import_fragment_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod only the structure of the hit sequences fragments."
)
# label_font_1
self.import_fragment_radiobutton.setStyleSheet("margin-bottom: 10px")
vertical_layout.addWidget(self.import_fragment_radiobutton)
# Import fragments button.
self.import_button = QtWidgets.QPushButton("Import 3D Structures",
self)
# self.import_button.setStyleSheet(label_style_2)
self.import_button.clicked.connect(self.on_import_button_click)
horizontal_layout.addWidget(self.import_button)
horizontal_layout.addStretch(1)
# Cancel button.
self.cancel_button = QtWidgets.QPushButton('Cancel', self)
# self.cancel_button.setStyleSheet(label_style_2)
self.cancel_button.clicked.connect(self.on_cancel_button_click)
horizontal_layout.addWidget(self.cancel_button)
vertical_layout.addLayout(horizontal_layout)
self.setLayout(vertical_layout)
def build_protocol_middle_frame(self):
#------------------
# Simple options. -
#------------------
# Let users decide how to import new sequences when the query is a child element (that
# is, it is already present in a cluster).
if self.protocol.blast_query_element.is_child():
self.import_mode_vbox = QtWidgets.QVBoxLayout()
self.import_mode_label = QtWidgets.QLabel("Hit Import Mode")
self.import_mode_vbox.addWidget(self.import_mode_label)
self.import_mode_button_group = QtWidgets.QButtonGroup()
self.middle_formlayout.addRow(self.import_mode_vbox)
# Build new alignment.
new_alignment_radiobutton = QtWidgets.QRadioButton("Build a new alignment with the query and the new hit sequences")
new_alignment_radiobutton._value = "build-new"
new_alignment_radiobutton.setChecked(True)
self.import_mode_vbox.addWidget(new_alignment_radiobutton)
self.import_mode_button_group.addButton(new_alignment_radiobutton)
# Expand alignment.
expand_alignment_radiobutton = QtWidgets.QRadioButton("Expand the existing alignment by appending the new hit sequences")
# "Expand the already existing cluster by appending to it the new hit sequences"
expand_alignment_radiobutton._value = "expand"
self.import_mode_vbox.addWidget(expand_alignment_radiobutton)
self.import_mode_button_group.addButton(expand_alignment_radiobutton)
# Each algorithm will have its own standard widgets.
self.build_algorithm_standard_options_widgets()
# E-value selection.
if self.protocol.protocol_name in hmmer_protocols_names:
e_value_threshold_enf_text = "c-Evalue Threshold"
else:
e_value_threshold_enf_text = "E-value Threshold"
self.e_value_threshold_enf = PyMod_entryfield_qt(label_text=e_value_threshold_enf_text,
value=str(self.protocol.e_value_threshold_default),
validate={'validator': 'real',
'min': 0.0, 'max': 1000.0})
self.middle_formlayout.add_widget_to_align(self.e_value_threshold_enf, validate=True)
# Max hit number selection.
self.max_hits_enf = PyMod_entryfield_qt(label_text="Max Number of Hits",
value=str(self.protocol.default_max_number_of_hits),
validate={'validator': 'integer',
'min': 1, 'max': 5000})
self.middle_formlayout.add_widget_to_align(self.max_hits_enf, validate=True)
# -------------------
# Advanced options. -
# -------------------
self.show_advanced_button()
# Minimum id% on with query.
self.min_id_enf = PyMod_entryfield_qt(label_text="Min Id% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_id_enf, advanced_option=True, validate=True)
# Maximum id% on with query.
self.max_id_enf = PyMod_entryfield_qt(label_text="Max Id% Threshold",
value="100",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.max_id_enf, advanced_option=True, validate=True)
# Minimum coverage on the query.
self.min_coverage_enf = PyMod_entryfield_qt(label_text="Min Coverage% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_coverage_enf, advanced_option=True, validate=True)
# Advanced options for a specific algorithm.
self.build_algorithm_advanced_options_widgets()
self.middle_formlayout.set_input_widgets_width("auto")
def build_strategy_specific_modes_frames(self):
"""
Build components of the GUI to show the alignment options.
"""
#------------------------------------------
# Perform a profile to profile alignment. -
#------------------------------------------
if self.protocol.can_perform_ptp_alignment:
# profile_profile_rb_text = "Profile to profile: perform a profile to profile alignment."
profile_profile_rb_text = "Profile to profile"
self.profile_to_profile_radiobutton = QtWidgets.QRadioButton(profile_profile_rb_text)
self.profile_to_profile_radiobutton.clicked.connect(self.click_on_profile_to_profile_radio)
self.profile_to_profile_radiobutton._value = "profile-to-profile"
self.profile_to_profile_radiobutton.setChecked(True)
self.alignment_mode_vbox.addWidget(self.profile_to_profile_radiobutton)
self.alignment_mode_button_group.addButton(self.profile_to_profile_radiobutton)
#-----------------------------------------
# Perform sequence to profile alignment. -
#-----------------------------------------
sequence_profile_rb_text = None
build_target_profile_frame = False
# Shows a different label for the checkbutton if there is one or more clusters involved.
if len(self.protocol.selected_clusters_list) > 1:
# sequence_profile_rb_text = "Sequence to profile: align to a target profile the rest of the selected sequences."
sequence_profile_rb_text = "Sequence to profile"
build_target_profile_frame = True
elif len(self.protocol.selected_clusters_list) == 1:
profile_cluster_name = self.protocol.involved_clusters_list[0].my_header
# sequence_profile_rb_text = "Sequence to profile: align the selected sequence to the target profile '%s'." % (profile_cluster_name)
sequence_profile_rb_text = "Sequence to profile"
# Radiobutton.
self.sequence_to_profile_radiobutton = QtWidgets.QRadioButton(sequence_profile_rb_text)
self.sequence_to_profile_radiobutton.clicked.connect(self.click_on_sequence_to_profile_radio)
self.sequence_to_profile_radiobutton._value = "sequence-to-profile"
if not self.protocol.can_perform_ptp_alignment:
self.sequence_to_profile_radiobutton.setChecked(True)
self.alignment_mode_vbox.addWidget(self.sequence_to_profile_radiobutton)
self.alignment_mode_button_group.addButton(self.sequence_to_profile_radiobutton)
# If there is more than one selected cluster, then build a frame to let the user choose
# which is going to be the target profile.
if build_target_profile_frame:
# Frame with the options to choose which is going to be the target profile.
self.target_profile_frame = QtWidgets.QFormLayout()
self.alignment_mode_vbox.addLayout(self.target_profile_frame)
# Label.
self.target_alignment_label = QtWidgets.QLabel("Target profile:")
self.target_alignment_label.setStyleSheet("margin-left: 35px")
# Combobox.
self.target_alignment_combobox = QtWidgets.QComboBox()
for cluster in self.protocol.involved_clusters_list:
self.target_alignment_combobox.addItem(cluster.my_header)
self.target_alignment_combobox.setEditable(False)
self.target_profile_frame.addRow(self.target_alignment_label, self.target_alignment_combobox)
self.target_alignment_combobox.setFixedWidth(self.target_alignment_combobox.sizeHint().width())
def build_strategy_specific_modes_frames(self):
#----------------------------
# Rebuild an old alignment. -
#----------------------------
if self.protocol.rebuild_single_alignment_choice:
new_alignment_rb_text = "Rebuild alignment"
new_alignment_rb_help = "Rebuild the alignment with all its sequences."
self.new_alignment_radiobutton = QtWidgets.QRadioButton(new_alignment_rb_text)
self.new_alignment_radiobutton.clicked.connect(self.click_on_build_new_alignment_radio)
self.new_alignment_radiobutton._value = "rebuild-old-alignment"
self.new_alignment_radiobutton.setChecked(True)
self.alignment_mode_vbox.addWidget(self.new_alignment_radiobutton)
self.alignment_mode_button_group.addButton(self.new_alignment_radiobutton)
return None
#------------------------------------------------------
# Build a new alignment using the selected sequences. -
#------------------------------------------------------
new_alignment_rb_text = "Build a new alignment"
new_alignment_rb_help = "Build a new alignment from scratch using the selected sequences."
self.new_alignment_radiobutton = QtWidgets.QRadioButton(new_alignment_rb_text)
self.new_alignment_radiobutton.clicked.connect(self.click_on_build_new_alignment_radio)
self.new_alignment_radiobutton._value = "build-new-alignment"
self.new_alignment_radiobutton.setChecked(True)
self.alignment_mode_vbox.addWidget(self.new_alignment_radiobutton)
self.alignment_mode_button_group.addButton(self.new_alignment_radiobutton)
#--------------------
# Alignment joiner. -
#--------------------
# This can be performed only if there is one selected child per cluster.
if len(self.protocol.involved_clusters_list) > 1 and self.protocol.check_alignment_joining_selection():
# alignment_joiner_rb_text = "Join the alignments using the selected sequences as bridges (see 'Alignment Joining')."
self.join_alignments_radiobutton = QtWidgets.QRadioButton("Join Alignments")
self.join_alignments_radiobutton.clicked.connect(self.click_on_alignment_joiner_radio)
self.join_alignments_radiobutton._value = "alignment-joining"
self.alignment_mode_vbox.addWidget(self.join_alignments_radiobutton)
self.alignment_mode_button_group.addButton(self.join_alignments_radiobutton)
#---------------------------
# Keep previous alignment. -
#---------------------------
# Right now it can be used only when the user has selected one sequence in a cluster
# and one sequence outside a cluster.
if (# Only one selected cluster.
len(self.protocol.involved_clusters_list) == 1 and
# Only one selected sequence in the selected cluster.
self.protocol.pymod.check_only_one_selected_child_per_cluster(self.protocol.involved_clusters_list[0]) and
# Only one selected sequence outside any cluster.
len(self.protocol.selected_root_sequences_list) == 1):
self.keep_previous_alignment_radiobutton = QtWidgets.QRadioButton("Keep previous alignment")
self.keep_previous_alignment_radiobutton.clicked.connect(self.click_on_keep_previous_alignment_radio)
self.keep_previous_alignment_radiobutton._value = "keep-previous-alignment"
self.alignment_mode_vbox.addWidget(self.keep_previous_alignment_radiobutton)
self.alignment_mode_button_group.addButton(self.keep_previous_alignment_radiobutton)
def __init__(self):
QtWidgets.QWidget.__init__(self, parent, Qt.Window)
self.setMinimumSize(400, 500)
self.setWindowTitle('Register File Extensions')
self.model = QtGui.QStandardItemModel(self)
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
label = QtWidgets.QLabel(
"Select file types to register them with PyMOL", self)
layout.addWidget(label)
alluserslayout = QtWidgets.QHBoxLayout()
alluserslayout.setObjectName("alluserslayout")
layout.addLayout(alluserslayout)
buttonlayout = QtWidgets.QHBoxLayout()
buttonlayout.setObjectName("buttonlayout")
layout.addLayout(buttonlayout)
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.model)
layout.addWidget(self.table)
button = QtWidgets.QPushButton("Register Recommended (*)", self)
buttonlayout.addWidget(button)
button.pressed.connect(self.setRecommended)
button = QtWidgets.QPushButton("Register All", self)
buttonlayout.addWidget(button)
button.pressed.connect(self.setAll)
button = QtWidgets.QPushButton("Clear", self)
button.setToolTip("Clean up Registry")
buttonlayout.addWidget(button)
button.pressed.connect(self.clear)
if isAdmin():
r0 = QtWidgets.QRadioButton("Only for me")
r0.setToolTip("HKEY_CURRENT_USER registry branch")
r0.setChecked(True)
r1 = QtWidgets.QRadioButton("For all users")
r1.setToolTip("HKEY_LOCAL_MACHINE registry branch")
allusersgroup = QtWidgets.QButtonGroup(self)
allusersgroup.addButton(r0)
allusersgroup.addButton(r1)
allusersgroup.buttonClicked.connect(self.populateData)
alluserslayout.addWidget(r0)
alluserslayout.addWidget(r1)
alluserslayout.addStretch()
self.allusersbutton = r1
else:
self.allusersbutton = None
self.finalize_timer = QtCore.QTimer()
self.finalize_timer.setSingleShot(True)
self.finalize_timer.setInterval(500)
self.finalize_timer.timeout.connect(finalize)
self.populateData()
# keep reference to window, otherwise Qt will auto-close it
self._self_ref = self