class MaskDialog(QDialog):
def __init__(self, mask_names):
super().__init__()
self.mask_names = mask_names
completer = QCompleter(list(mask_names))
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.setWindowTitle("Masks name choose")
self.mask1_name = QLineEdit()
self.cancel_btn = QPushButton("Cancel")
self.ok_btn = QPushButton("Ok")
self.mask1_name.setCompleter(completer)
self.mask1_name.textChanged.connect(self.text_changed)
self.cancel_btn.clicked.connect(self.close)
self.ok_btn.clicked.connect(self.accept)
self.ok_btn.setDisabled(True)
layout = QGridLayout()
layout.addWidget(right_label("Mask 1 name:"), 0, 0)
layout.addWidget(self.mask1_name, 0, 1)
layout.addWidget(self.cancel_btn, 2, 0)
layout.addWidget(self.ok_btn, 2, 1)
self.setLayout(layout)
def text_changed(self):
text1 = self.get_result()[0]
if text1 == "" or text1 not in self.mask_names:
self.ok_btn.setDisabled(True)
else:
self.ok_btn.setDisabled(False)
def get_result(self):
text1 = str(self.mask1_name.text()).strip()
return (text1,)
class TwoMaskDialog(QDialog):
def __init__(self, mask_names):
"""
:type mask_names: set
:param mask_names: iterable collection of all available mask names
"""
super().__init__()
self.mask_names = mask_names
completer = QCompleter(list(mask_names))
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.setWindowTitle("Masks name choose")
self.mask1_name = QLineEdit()
self.mask2_name = QLineEdit()
self.cancel_btn = QPushButton("Cancel")
self.ok_btn = QPushButton("Ok")
self.mask1_name.setCompleter(completer)
self.mask1_name.textChanged.connect(self.text_changed)
self.mask2_name.setCompleter(completer)
self.mask2_name.textChanged.connect(self.text_changed)
self.cancel_btn.clicked.connect(self.close)
self.ok_btn.clicked.connect(self.accept)
self.ok_btn.setDisabled(True)
layout = QGridLayout()
layout.addWidget(right_label("Mask 1 name:"), 0, 0)
layout.addWidget(self.mask1_name, 0, 1)
layout.addWidget(right_label("Mask 2 name:"), 1, 0)
layout.addWidget(self.mask2_name, 1, 1)
layout.addWidget(self.cancel_btn, 2, 0)
layout.addWidget(self.ok_btn, 2, 1)
self.setLayout(layout)
def text_changed(self):
text1, text2 = self.get_result()
if text1 == "" or text2 == "" or text1 not in self.mask_names or text2 not in self.mask_names:
self.ok_btn.setDisabled(True)
return
else:
self.ok_btn.setDisabled(text1 == text2)
def get_result(self):
text1 = str(self.mask1_name.text()).strip()
text2 = str(self.mask2_name.text()).strip()
return text1, text2
def add_desired_region(self):
i = self.desired_list.rowCount()
self.desired_list.insertRow(i)
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
item = QLineEdit("1")
self.desired_list.setCellWidget(i, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(i, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(i, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(i, 3, item)
import sys
from qtpy.QtCore import Qt
from qtpy.QtWidgets import QApplication, QCompleter, QLineEdit, QStringListModel
def get_data(model):
model.setStringList(["completion", "data", "goes", "here"])
if __name__ == "__main__":
app = QApplication(sys.argv)
edit = QLineEdit()
completer = QCompleter()
edit.setCompleter(completer)
model = QStringListModel()
completer.setModel(model)
get_data(model)
edit.show()
sys.exit(app.exec_())
class PMGListCtrl(BaseExtendedWidget):
def __init__(self,
layout_dir: str,
title: str,
initial_value: List[List[str]],
new_id_func: Callable = None):
super().__init__(layout_dir)
self.choices = []
self.text_list = []
lab_title = QLabel(text=title)
layout = QHBoxLayout()
self.central_layout.addWidget(lab_title)
self.on_check_callback = None
self.list_widget = QListWidget()
self.list_widget.mouseDoubleClickEvent = self.on_listwidget_double_cicked
self.set_value(initial_value)
layout_tools = QVBoxLayout()
self.button_add_item = QPushButton('+')
self.button_delete_item = QPushButton('-')
self.button_delete_item.clicked.connect(self.delete_row)
self.button_add_item.clicked.connect(self.add_row)
self.button_add_item.setMaximumWidth(20)
self.button_delete_item.setMaximumWidth(20)
layout_tools.addWidget(self.button_add_item)
layout_tools.addWidget(self.button_delete_item)
layout.addLayout(layout_tools)
layout.addWidget(self.list_widget)
self.central_layout.addLayout(layout)
self.data = initial_value
self.new_id_func = new_id_func
self.text_edit = QLineEdit(parent=self.list_widget)
self.text_edit.setWindowFlags(self.text_edit.windowFlags() | Qt.Dialog
| Qt.FramelessWindowHint)
self.text_edit.hide()
self.completer = QCompleter()
self.text_edit.setCompleter(self.completer)
self.completer.setCompletionMode(QCompleter.UnfilteredPopupCompletion)
def set_completions(self, completions: List[str]):
"""
设置补全内容
Args:
completions:
Returns:
"""
self.completer.setModel(QStringListModel(completions))
def new_id(self):
if callable(self.new_id_func):
return self.new_id_func()
else:
return None
def add_row(self):
self.data = self.get_value()
self.data[0].append(self.new_id())
self.data[1].append('Unnamed')
self.list_widget.addItem(QListWidgetItem('Unnamed'))
def delete_row(self):
index = self.list_widget.currentIndex().row()
self.data[0].pop(index)
self.data[1].pop(index)
self.list_widget.takeItem(index)
def on_listwidget_double_cicked(self, evt: QMouseEvent):
print('edit', evt)
pos = evt.globalPos()
current_item: QListWidgetItem = self.list_widget.currentItem()
def set_value():
current_item.setText(self.text_edit.text())
self.text_edit.hide()
self.text_edit.returnPressed.disconnect(set_value)
item: QListWidgetItem = self.list_widget.currentItem()
self.text_edit.setGeometry(pos.x(), pos.y(), 200, 20)
self.text_edit.returnPressed.connect(set_value)
self.text_edit.show()
# self.list_widget.editItem(item)
def get_value(self):
text = []
for i in range(self.list_widget.count()):
text.append(self.list_widget.item(i).text())
self.data[1] = text
assert len(self.data[1]) == len(self.data[0]), repr(self.data)
return self.data
def set_value(self, data: List[List[str]]):
self.list_widget.clear()
self.list_widget.addItems(data[1])
self.data = data
for index in range(self.list_widget.count()):
item: QListWidgetItem = self.list_widget.item(index)
def __init__(self, appdata: CnaData, centralwidget):
QDialog.__init__(self)
self.setWindowTitle("Minimal Cut Sets Computation")
self.appdata = appdata
self.centralwidget = centralwidget
self.eng = appdata.engine
self.out = io.StringIO()
self.err = io.StringIO()
self.layout = QVBoxLayout()
l1 = QLabel("Target Region(s)")
self.layout.addWidget(l1)
s1 = QHBoxLayout()
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.target_list = QTableWidget(1, 4)
self.target_list.setHorizontalHeaderLabels(
["region no", "T", "≥/≤", "t"])
self.target_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.target_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(0, 100)
self.target_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.target_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.target_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.target_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.target_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.target_list.setCellWidget(0, 3, item)
s1.addWidget(self.target_list)
s11 = QVBoxLayout()
self.add_target = QPushButton("+")
self.add_target.clicked.connect(self.add_target_region)
self.rem_target = QPushButton("-")
self.rem_target.clicked.connect(self.rem_target_region)
s11.addWidget(self.add_target)
s11.addWidget(self.rem_target)
s1.addItem(s11)
self.layout.addItem(s1)
l2 = QLabel("Desired Region(s)")
self.layout.addWidget(l2)
s2 = QHBoxLayout()
self.desired_list = QTableWidget(1, 4)
self.desired_list.setHorizontalHeaderLabels(
["region no", "D", "≥/≤", "d"])
self.desired_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.desired_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(0, 100)
self.desired_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.desired_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(0, 3, item)
s2.addWidget(self.desired_list)
s21 = QVBoxLayout()
self.add_desire = QPushButton("+")
self.add_desire.clicked.connect(self.add_desired_region)
self.rem_desire = QPushButton("-")
self.rem_desire.clicked.connect(self.rem_desired_region)
s21.addWidget(self.add_desire)
s21.addWidget(self.rem_desire)
s2.addItem(s21)
self.layout.addItem(s2)
s3 = QHBoxLayout()
sgx = QVBoxLayout()
self.gen_kos = QCheckBox("Gene KOs")
self.exclude_boundary = QCheckBox(
"Exclude boundary\nreactions as cuts")
sg1 = QHBoxLayout()
s31 = QVBoxLayout()
l = QLabel("Max. Solutions")
s31.addWidget(l)
l = QLabel("Max. Size")
s31.addWidget(l)
l = QLabel("Time Limit [sec]")
s31.addWidget(l)
sg1.addItem(s31)
s32 = QVBoxLayout()
self.max_solu = QLineEdit("inf")
self.max_solu.setMaximumWidth(50)
s32.addWidget(self.max_solu)
self.max_size = QLineEdit("7")
self.max_size.setMaximumWidth(50)
s32.addWidget(self.max_size)
self.time_limit = QLineEdit("inf")
self.time_limit.setMaximumWidth(50)
s32.addWidget(self.time_limit)
sg1.addItem(s32)
sgx.addWidget(self.gen_kos)
sgx.addWidget(self.exclude_boundary)
sgx.addItem(sg1)
s3.addItem(sgx)
g3 = QGroupBox("Solver")
s33 = QVBoxLayout()
self.bg1 = QButtonGroup()
optlang_solver_name = interface_to_str(
appdata.project.cobra_py_model.problem)
self.solver_optlang = QRadioButton(f"{optlang_solver_name} (optlang)")
self.solver_optlang.setToolTip(
"Uses the solver specified by the current model.")
s33.addWidget(self.solver_optlang)
self.bg1.addButton(self.solver_optlang)
self.solver_cplex_matlab = QRadioButton("CPLEX (MATLAB)")
self.solver_cplex_matlab.setToolTip(
"Only enabled with MATLAB and CPLEX")
s33.addWidget(self.solver_cplex_matlab)
self.bg1.addButton(self.solver_cplex_matlab)
self.solver_cplex_java = QRadioButton("CPLEX (Octave)")
self.solver_cplex_java.setToolTip("Only enabled with Octave and CPLEX")
s33.addWidget(self.solver_cplex_java)
self.bg1.addButton(self.solver_cplex_java)
self.solver_intlinprog = QRadioButton("intlinprog (MATLAB)")
self.solver_intlinprog.setToolTip("Only enabled with MATLAB")
s33.addWidget(self.solver_intlinprog)
self.bg1.addButton(self.solver_intlinprog)
self.solver_glpk = QRadioButton("GLPK (Octave/MATLAB)")
s33.addWidget(self.solver_glpk)
self.bg1.addButton(self.solver_glpk)
self.bg1.buttonClicked.connect(self.configure_solver_options)
g3.setLayout(s33)
s3.addWidget(g3)
g4 = QGroupBox("MCS search")
s34 = QVBoxLayout()
self.bg2 = QButtonGroup()
self.any_mcs = QRadioButton("any MCS (fast)")
self.any_mcs.setChecked(True)
s34.addWidget(self.any_mcs)
self.bg2.addButton(self.any_mcs)
# Search type: by cardinality only with CPLEX possible
self.mcs_by_cardinality = QRadioButton("by cardinality")
s34.addWidget(self.mcs_by_cardinality)
self.bg2.addButton(self.mcs_by_cardinality)
self.smalles_mcs_first = QRadioButton("smallest MCS first")
s34.addWidget(self.smalles_mcs_first)
self.bg2.addButton(self.smalles_mcs_first)
g4.setLayout(s34)
s3.addWidget(g4)
self.layout.addItem(s3)
# Disable incompatible combinations
if appdata.selected_engine == 'None':
self.solver_optlang.setChecked(True)
self.solver_cplex_matlab.setEnabled(False)
self.solver_cplex_java.setEnabled(False)
self.solver_glpk.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
if optlang_solver_name != 'cplex':
self.mcs_by_cardinality.setEnabled(False)
else:
self.solver_glpk.setChecked(True)
if not self.eng.is_cplex_matlab_ready():
self.solver_cplex_matlab.setEnabled(False)
if not self.eng.is_cplex_java_ready():
self.solver_cplex_java.setEnabled(False)
if self.appdata.is_matlab_set():
self.solver_cplex_java.setEnabled(False)
if not self.appdata.is_matlab_set():
self.solver_cplex_matlab.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
self.configure_solver_options()
s4 = QVBoxLayout()
self.consider_scenario = QCheckBox(
"Consider constraint given by scenario")
s4.addWidget(self.consider_scenario)
self.advanced = QCheckBox(
"Advanced: Define knockout/addition costs for genes/reactions")
self.advanced.setEnabled(False)
s4.addWidget(self.advanced)
self.layout.addItem(s4)
buttons = QHBoxLayout()
# self.save = QPushButton("save")
# buttons.addWidget(self.save)
# self.load = QPushButton("load")
# buttons.addWidget(self.load)
self.compute_mcs = QPushButton("Compute MCS")
buttons.addWidget(self.compute_mcs)
# self.compute_mcs2 = QPushButton("Compute MCS2")
# buttons.addWidget(self.compute_mcs2)
self.cancel = QPushButton("Close")
buttons.addWidget(self.cancel)
self.layout.addItem(buttons)
# max width for buttons
self.add_target.setMaximumWidth(20)
self.rem_target.setMaximumWidth(20)
self.add_desire.setMaximumWidth(20)
self.rem_desire.setMaximumWidth(20)
self.setLayout(self.layout)
# Connecting the signal
self.cancel.clicked.connect(self.reject)
self.compute_mcs.clicked.connect(self.compute)
class PhasePlaneDialog(QDialog):
"""A dialog to create phase plane plots"""
def __init__(self, appdata):
QDialog.__init__(self)
self.setWindowTitle("Phase plane plotting")
self.appdata = appdata
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"),
self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.layout = QVBoxLayout()
l1 = QHBoxLayout()
t1 = QLabel("Reaction (x-axis):")
l1.addWidget(t1)
self.x_axis = CompleterLineEdit(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), "")
self.x_axis.setPlaceholderText("Enter reaction Id")
l1.addWidget(self.x_axis)
l2 = QHBoxLayout()
t2 = QLabel("Reaction (y-axis):")
l2.addWidget(t2)
self.y_axis = QLineEdit("")
self.y_axis.setPlaceholderText("Enter reaction Id")
self.y_axis.setCompleter(completer)
l2.addWidget(self.y_axis)
self.layout.addItem(l1)
self.layout.addItem(l2)
l3 = QHBoxLayout()
self.button = QPushButton("Plot")
self.cancel = QPushButton("Close")
l3.addWidget(self.button)
l3.addWidget(self.cancel)
self.layout.addItem(l3)
self.setLayout(self.layout)
# Connecting the signal
self.cancel.clicked.connect(self.reject)
self.button.clicked.connect(self.compute)
def compute(self):
self.setCursor(Qt.BusyCursor)
with self.appdata.project.cobra_py_model as model:
self.appdata.project.load_scenario_into_model(model)
x_axis = self.x_axis.text()
y_axis = self.y_axis.text()
try:
x_reac_idx = model.reactions.index(x_axis)
y_reac_idx = model.reactions.index(y_axis)
except KeyError:
return
points = 100
with model as ppmodel:
ppmodel.objective = ppmodel.reactions[x_reac_idx]
ppmodel.objective.direction = 'min'
x_lb = ppmodel.slim_optimize()
ppmodel.objective.direction = 'max'
x_ub = ppmodel.slim_optimize()
result2 = numpy.zeros((points, 3))
result2[:, 0] = numpy.linspace(x_lb, x_ub, num=points)
var = numpy.linspace(x_lb, x_ub, num=points)
lb = numpy.full(points, numpy.nan)
ub = numpy.full(points, numpy.nan)
with model as ppmodel:
ppmodel.objective = ppmodel.reactions[y_reac_idx]
for i in range(points):
# without second context the original reaction bounds are not restored (?)
with ppmodel as ppmodel2:
ppmodel2.reactions[x_reac_idx].lower_bound = result2[i,
0]
ppmodel2.reactions[x_reac_idx].upper_bound = result2[i,
0]
ppmodel2.objective.direction = 'min'
lb[i] = result2[i, 1] = ppmodel2.slim_optimize()
ppmodel2.objective.direction = 'max'
ub[i] = result2[i, 2] = ppmodel2.slim_optimize()
_fig, axes = plt.subplots()
axes.set_xlabel(model.reactions[x_reac_idx].id)
axes.set_ylabel(model.reactions[y_reac_idx].id)
x = [v for v in var] + [v for v in reversed(var)]
y = [v for v in lb] + [v for v in reversed(ub)]
if lb[0] != ub[0]:
x.extend([var[0], var[0]])
y.extend([lb[0], ub[0]])
plt.plot(x, y)
plt.show()
self.appdata.window.centralWidget().show_bottom_of_console()
self.setCursor(Qt.ArrowCursor)
class LabelDialog(QDialog):
def __init__(self, text="Enter object label", parent=None, listItem=None):
super(LabelDialog, self).__init__(parent)
self.edit = QLineEdit()
self.edit.setText(text)
self.edit.setValidator(self.label_validator())
self.edit.editingFinished.connect(self.post_process)
model = QStringListModel()
model.setStringList(listItem)
completer = QCompleter()
completer.setModel(model)
self.edit.setCompleter(completer)
layout = QVBoxLayout()
layout.addWidget(self.edit)
self.buttonBox = bb = BB(BB.Ok | BB.Cancel, Qt.Horizontal, self)
bb.button(BB.Ok).setIcon(QIcon('icons/done.png'))
bb.button(BB.Cancel).setIcon(QIcon('icons/undo.png'))
bb.accepted.connect(self.validate)
bb.rejected.connect(self.reject)
layout.addWidget(bb)
if listItem is not None and len(listItem) > 0:
self.listWidget = QListWidget(self)
for item in listItem:
self.listWidget.addItem(item)
self.listWidget.itemClicked.connect(self.listItemClick)
self.listWidget.itemDoubleClicked.connect(self.listItemDoubleClick)
layout.addWidget(self.listWidget)
self.setLayout(layout)
def label_validator(self):
return QRegExpValidator(QRegExp(r'^[^ \t].+'), None)
def validate(self):
try:
if self.edit.text().trimmed():
self.accept()
except AttributeError:
if self.edit.text().strip():
self.accept()
def post_process(self):
try:
self.edit.setText(self.edit.text().trimmed())
except AttributeError:
self.edit.setText(self.edit.text())
def pop_up(self, text='', move=True):
self.edit.setText(text)
self.edit.setSelection(0, len(text))
self.edit.setFocus(Qt.PopupFocusReason)
if move:
self.move(QCursor.pos())
return self.edit.text() if self.exec_() else None
def listItemClick(self, tQListWidgetItem):
try:
text = tQListWidgetItem.text().trimmed()
except AttributeError:
# PyQt5: AttributeError: 'str' object has no attribute 'trimmed'
text = tQListWidgetItem.text().strip()
self.edit.setText(text)
def listItemDoubleClick(self, tQListWidgetItem):
self.listItemClick(tQListWidgetItem)
self.validate()
