class DisplaySettings(QDialog, Ui_DisplaySettings, object):
updateSig = pyqtSignal(QModelIndex)
def __init__(self, workPath=None, parent=None):
super(DisplaySettings, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.parent = parent
self.workPath = workPath
self.setupUi(self)
# 设置比例
self.splitter.setStretchFactor(1, 7)
# 保存主界面设置
self.data_settings = QSettings(
self.factory.workPlaceSettingPath + os.sep + 'data_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.data_settings.setFallbacksEnabled(False)
# 保存设置
self.display_settings = QSettings(
self.thisPath + '/settings/display_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.display_settings.setFallbacksEnabled(False)
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss',
encoding="utf-8",
errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
# 恢复用户的设置
self.guiRestore()
self.listWidget.installEventFilter(self)
## brief demo
self.label_6.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-4-2-Information-display-and-modification"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
ok
"""
self.saveNewContents()
self.updateSig.emit(QFileSystemModel(self).index(self.workPath))
self.close()
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
Cancel
"""
self.close()
@pyqtSlot()
def on_pushButton_del_clicked(self):
"""
delete
"""
listItems = self.listWidget.selectedItems()
if not listItems:
return
for item in listItems:
if item.text() == "Latest modified":
QMessageBox.information(
self, "PhyloSuite",
"<p style='line-height:25px; height:25px'><span style='font-weight:600; color:#ff0000;'>Latest modified</span> must be maintained!!</p>"
)
continue
self.listWidget.takeItem(self.listWidget.row(item))
def saveNewContents(self):
key = re.sub(r"/|\\", "_", self.workPath) + "_displayedArray"
itemsTextList = [
self.listWidget.item(i).text()
for i in range(self.listWidget.count())
]
arrayManager = ArrayManager(self.array)
new_array = arrayManager.updateArrayByColheader(itemsTextList)
self.data_settings.setValue(key, new_array)
##然后是有新的列就读取对应数据，如果没有新的列就直接展示
def guiSave(self):
# Save geometry
self.display_settings.setValue('size', self.size())
# self.display_settings.setValue('pos', self.pos())
# for name, obj in inspect.getmembers(self):
# # if type(obj) is QComboBox: # this works similar to isinstance, but
# # missed some field... not sure why?
# if isinstance(obj, QlistWidget):
# # save combobox selection to registry
# text = obj.currentText()
# if text:
# allItems = [
# obj.itemText(i) for i in range(obj.count())]
# allItems.remove(text)
# sortItems = [text] + allItems
# self.data_settings.setValue(name, sortItems)
# if isinstance(obj, QCheckBox):
# state = obj.isChecked()
# self.data_settings.setValue(name, state)
# if isinstance(obj, QRadioButton):
# state = obj.isChecked()
# self.data_settings.setValue(name, state)
def guiRestore(self):
# Restore geometry
self.resize(self.display_settings.value('size', QSize(685, 511)))
self.factory.centerWindow(self)
# self.move(self.display_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QListWidget):
key = re.sub(r"/|\\", "_", self.workPath) + "_displayedArray"
self.array = self.data_settings.value(
key, None) #每点一个工作区，就会自动初始化一个，所以一般不会none
if self.array:
displayed_info = self.array[0]
self.updatelistWidget(None, displayed_info)
if isinstance(obj, QTreeView):
self.updateTreee()
# key = re.sub(r"/|\\", "_", self.workPath) + "_availableInfo"
# value = self.data_settings.value(
# key, None) #每点一个工作区，就会自动初始化一个，所以一般不会none
# treeModel = TreeModel(value)
# obj.setModel(treeModel)
# obj.clicked.connect(self.updatelistWidget)
# obj.expandAll()
# lineage_set = CustomTreeIndexWidget("Lineages", parent=self.treeView)
# lineage_set.addBtn("Configure", QIcon(":/picture/resourses/cog.png"))
# lineage_set.toolBtn.clicked.connect(self.popUpSettings)
# self.treeView.setIndexWidget(self.treeView.model().index(1, 0, self.treeView.rootIndex()), lineage_set)
def updateTreee(self):
key = re.sub(r"/|\\", "_", self.workPath) + "_availableInfo"
value = self.data_settings.value(key,
None) # 每点一个工作区，就会自动初始化一个，所以一般不会none
treeModel = TreeModel(value)
self.treeView.setModel(treeModel)
self.treeView.clicked.connect(self.updatelistWidget)
self.treeView.expandAll()
lineage_set = CustomTreeIndexWidget("Lineages", parent=self.treeView)
lineage_set.addBtn("Configure", QIcon(":/picture/resourses/cog.png"))
lineage_set.toolBtn.clicked.connect(self.popUpSettings)
self.treeView.setIndexWidget(
self.treeView.model().index(1, 0, self.treeView.rootIndex()),
lineage_set)
def updatelistWidget(self, treeIndex=None, list_infos=None):
infos = [treeIndex.internalPointer().itemData
] if treeIndex else list_infos
itemsTextList = [
self.listWidget.item(i).text()
for i in range(self.listWidget.count())
]
for i in infos:
if i in itemsTextList + [
"Annotations", "Lineages", "Reference", "Sources"
]:
continue
item = QListWidgetItem(i, parent=self.listWidget)
if i in ["ID", "Organism"]:
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
# 背景颜色
if self.listWidget.count() % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
self.listWidget.addItem(item)
def closeEvent(self, event):
self.guiSave()
def popUpSettings(self):
self.setting = Setting(self)
self.setting.taxmyChangeSig.connect(lambda x: [
self.parent.updateTable(x),
self.parent.updateTableWorker.finished.connect(self.updateTreee)
])
self.setting.display_table(self.setting.listWidget.item(0))
self.setting.setWindowFlags(self.setting.windowFlags()
| Qt.WindowMinMaxButtonsHint)
self.setting.exec_()
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
name = obj.objectName()
if isinstance(obj, QListWidget):
if event.type() == QEvent.ChildRemoved:
if name == "listWidget":
if self.listWidget.item(0).text() != "ID":
QMessageBox.critical(
self, "Extract sequence",
"<p style='line-height:25px; height:25px'>\"ID\" must be the first column!</p>",
QMessageBox.Ok)
list_infos = [
self.listWidget.item(row).text()
for row in range(self.listWidget.count())
]
list_infos.remove("ID")
list_infos.insert(0, "ID")
self.refreshListWidget(list_infos)
return super(DisplaySettings, self).eventFilter(obj, event) # 0
def refreshListWidget(self, listInfos):
self.listWidget.clear()
for i in listInfos:
if i in ["Annotations", "Lineages", "Reference", "Sources"]:
continue
item = QListWidgetItem(i, parent=self.listWidget)
if i in ["ID", "Organism"]:
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
# 背景颜色
if self.listWidget.count() % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
self.listWidget.addItem(item)
class ExtractGB(QDialog, Ui_Extractor, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
progressSig = pyqtSignal(int) # 控制进度条
threadFinished = pyqtSignal()
startButtonStatusSig = pyqtSignal(list)
def __init__(
self,
gb_files=None,
list_names=None,
workPath=None,
totleID=None,
clearFolderSig=None,
focusSig=None,
parent=None):
super(ExtractGB, self).__init__(parent)
self.parent = parent
self.setupUi(self)
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.gb_files = gb_files
self.workPath = workPath
self.totleID = totleID
self.clearFolderSig = clearFolderSig
self.list_names = list_names
self.focusSig = focusSig
self.installEventFilter(self)
self.dict_icon = {
"rectangle": ":/itol_domain/resourses/itol/re.png",
"horizontal hexagon": ":/itol_domain/resourses/itol/hh.png",
"vertical hexagon": ":/itol_domain/resourses/itol/hv.png",
"ellipse": ":/itol_domain/resourses/itol/el.png",
"rhombus (diamond)": ":/itol_domain/resourses/itol/di.png",
"right pointing triangle": ":/itol_domain/resourses/itol/tr.png",
"left pointing triangle": ":/itol_domain/resourses/itol/tl.png",
"left pointing pentagram": ":/itol_domain/resourses/itol/pl.png",
"right pointing pentagram": ":/itol_domain/resourses/itol/pr.png",
"up pointing pentagram": ":/itol_domain/resourses/itol/pu.png",
"down pointing pentagram": ":/itol_domain/resourses/itol/pd.png",
"octagon": ":/itol_domain/resourses/itol/oc.png",
"rectangle (gap)": ":/itol_domain/resourses/itol/gp.png"}
self.dict_shape = {
"rectangle": "RE",
"horizontal hexagon": "HH",
"vertical hexagon": "HV",
"ellipse": "EL",
"rhombus (diamond)": "DI",
"right pointing triangle": "TR",
"left pointing triangle": "TL",
"left pointing pentagram": "PL",
"right pointing pentagram": "PR",
"up pointing pentagram": "PU",
"down pointing pentagram": "PD",
"octagon": "OC",
"rectangle (gap)": "GP"}
self.showOn()
self.extractGB_settings = QSettings(
self.thisPath + '/settings/extractGB_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.extractGB_settings.setFallbacksEnabled(False)
self.settings_ini = QSettings(self.thisPath + '/settings/setting_settings.ini', QSettings.IniFormat)
self.settings_ini.setFallbacksEnabled(False)
# 保存主界面设置
self.mainwindow_settings = QSettings(
self.thisPath + '/settings/mainwindow_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.mainwindow_settings.setFallbacksEnabled(False)
# 恢复用户的设置
self.guiRestore()
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss', encoding="utf-8", errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
self.progressSig.connect(self.runProgress)
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.tableWidget_2.installEventFilter(self)
self.table_popMenu = QMenu(self)
self.Copy = QAction("Copy", self,
statusTip="Copy color(s)",
shortcut="Ctrl+C",
triggered=self.copyColor)
self.Cut = QAction("Cut", self,
statusTip="Cut color(s)",
shortcut="Ctrl+X",
triggered=self.cutColor)
self.Paste = QAction("Paste", self,
statusTip="Paste color(s)",
shortcut="Ctrl+V",
triggered=self.pasteColor)
self.remove = QAction("Delete", self,
shortcut=QKeySequence.Delete,
statusTip="Remove color(s)",
triggered=self.on_pushButton_9_clicked)
self.table_popMenu.addAction(self.Copy)
self.table_popMenu.addAction(self.Cut)
self.table_popMenu.addAction(self.Paste)
self.table_popMenu.addAction(self.remove)
self.tableWidget_2.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableWidget_2.customContextMenuRequested.connect(lambda x: self.table_popMenu.exec_(QCursor.pos()))
self.comboBox_6.activated[str].connect(self.switchSeqType)
# self.checkBox.toggled.connect(self.judgeCodonW)
self.switchSeqType(self.comboBox_6.currentText())
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
self.work_action = QAction(QIcon(":/picture/resourses/work.png"), "", menu)
self.work_action.triggered.connect(lambda: self.factory.swithWorkPath(self.work_action, parent=self))
self.dir_action = QAction(QIcon(":/picture/resourses/folder.png"), "Output Dir: ", menu)
self.dir_action.triggered.connect(lambda: self.factory.set_direct_dir(self.dir_action, self))
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton_2.toolButton.setMenu(menu)
self.pushButton_2.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True, parent=self) # 初始化一下
## brief demo
self.label_3.clicked.connect(lambda: QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-1-1-Brief-example")))
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
execute program
"""
self.dict_args = {}
self.dict_args["progressSig"] = self.progressSig
self.dict_args["gb_files"] = self.gb_files
self.dict_args["workPath"] = self.workPath
# 创建输出文件夹
self.output_dir_name = self.factory.fetch_output_dir_name(self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath +
os.sep + "extract_results" + os.sep + self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
self.dict_args["codon"] = str(
self.comboBox_9.currentText()).split(" ")[0]
self.dict_args["Name Type"] = [self.comboBox_4.itemText(i) for i in range(self.comboBox_4.count())
if self.comboBox_4.model().item(i).checkState() == Qt.Checked]
# self.dict_args["Gene Number"] = str(
# self.comboBox_8.currentText())
# bool
self.dict_args["if ignore duplicated"] = True #self.checkBox_2.isChecked()
self.dict_args["if statistics"] = True #self.checkBox_3.isChecked()
self.dict_args["if itol"] = self.groupBox_4.isChecked()
self.dict_args["totleID"] = self.totleID
self.dict_args["seq type"] = str(self.comboBox_6.currentText())
for row, row_text in enumerate(
["atp", "nad", "cytb", "cox", "rRNA", "tRNA", "NCR"]):
for column, column_text in enumerate(
["checked", "colour", "length", "shape"]):
if column == 0:
self.dict_args[row_text + column_text] = True if self.tableWidget.item(
row, column).checkState() == Qt.Checked else False # bool
elif column == 1:
self.dict_args[row_text +
column_text] = self.tableWidget.item(row, column).text()
elif column == 2:
self.dict_args[row_text +
column_text] = self.tableWidget.item(row, column).text()
elif column == 3:
shape_combo = self.tableWidget.cellWidget(row, column)
shape = shape_combo.currentText()
self.dict_args[row_text +
column_text] = self.dict_shape[shape] # 转为缩写形式
self.dict_args["gene interval"] = self.doubleSpinBox.value()
self.dict_args["included_lineages"] = [self.comboBox_7.itemText(i) for i in range(self.comboBox_7.count())
if self.comboBox_7.model().item(i).checkState() == Qt.Checked]
# {"Family":["red", "green", ""]}
dict_color_array = self.getLineageColor()
for i in dict_color_array:
while "" in dict_color_array[i]:
# 删除空行
dict_color_array[i].remove("")
self.dict_args["lineage color"] = dict_color_array
##提取的设置
dict_extract_settings = copy.deepcopy(self.dict_gbExtract_set[self.comboBox_6.currentText()])
#提取所有的话，记得先判断有没有那个键
extract_all_features = dict_extract_settings.pop("extract all features") if "extract all features" \
in dict_extract_settings else False
self.dict_args["extract_intergenic_regions"] = dict_extract_settings.pop("extract intergenic regions") if "extract intergenic regions" \
in dict_extract_settings else True
self.dict_args["extract_overlapping_regions"] = dict_extract_settings.pop("extract overlapping regions") if "extract overlapping regions" \
in dict_extract_settings else True
self.dict_args["intergenic_regions_threshold"] = dict_extract_settings.pop("intergenic regions threshold") if "intergenic regions threshold" \
in dict_extract_settings else 200
self.dict_args["overlapping_regions_threshold"] = dict_extract_settings.pop(
"overlapping regions threshold") if "overlapping regions threshold" \
in dict_extract_settings else 1
self.dict_args["features"] = dict_extract_settings.pop("Features to be extracted") if not extract_all_features else "All"
# self.dict_args["features"] = "All" if self.extract_all_features else self.dict_args["features"]
name_unify = dict_extract_settings.pop("Names unification")
self.dict_args["replace"] = {i[0]: i[1] for i in name_unify}
self.dict_args["extract_list_gene"] = dict_extract_settings.pop("extract listed gene") if "extract listed gene" \
in dict_extract_settings else False
self.dict_args["qualifiers"] = dict_extract_settings ###只剩下qualifier的设置
self.dict_args["extract_entire_seq"] = self.radioButton.isChecked()
self.dict_args["entire_seq_name"] = self.lineEdit.text() if self.lineEdit.text() else "sequence"
ok = self.factory.remove_dir(self.dict_args["exportPath"], parent=self)
if not ok:
# 提醒是否删除旧结果，如果用户取消，就不执行
return
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
def run_command(self):
try:
# 清空文件夹再生成结果,放在这里执行好统一管理报错
# self.clearFolderSig.emit(self.dict_args["exportPath"])
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit(
[self.pushButton_2, self.progressBar, "start", self.dict_args["exportPath"], self.qss_file, self])
if (self.dict_args["seq type"] == "Mitogenome") and (not self.dict_args["extract_entire_seq"]):
# 如果是整个序列提取，也不能用这个
extract = GBextract_MT(**self.dict_args)
extract._exec()
else:
extract = GBextract(**self.dict_args)
extract._exec()
# extract = GBextract(**self.dict_args)
if extract.Error_ID:
stopStatus = extract.Error_ID
elif extract.source_feature_IDs:
stopStatus = "extract_no_feature%s"%", ".join(extract.source_feature_IDs)
else:
stopStatus = "stop"
self.startButtonStatusSig.emit(
[self.pushButton_2, self.progressBar, stopStatus, self.dict_args["exportPath"], self.qss_file, self])
self.focusSig.emit(self.dict_args["exportPath"])
time_end = datetime.datetime.now()
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (str(time_start), str(time_end),
str(time_end - time_start))
with open(self.dict_args["exportPath"] + os.sep + "summary.txt", "w", encoding="utf-8") as f:
f.write("If you use PhyloSuite, please cite:\nZhang, D., Gao, F., Li, W.X., Jakovlić, I., Zou, H., "
"Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop "
"platform for streamlined molecular sequence data management and evolutionary phylogenetics "
"studies. bioRxiv, doi: 10.1101/489088.\n\n" + self.time_used_des
+ "For the summary of this extraction, please see \"overview.csv\"")
except BaseException:
self.exceptionInfo = ''.join(
traceback.format_exception(
*sys.exc_info())) # 捕获报错内容，只能在这里捕获，没有报错的地方无法捕获
self.exception_signal.emit(self.exceptionInfo) # 激发这个信号
self.startButtonStatusSig.emit(
[self.pushButton_2, self.progressBar, "except", self.dict_args["exportPath"], self.qss_file, self])
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
self.close()
@pyqtSlot()
def on_pushButton_6_clicked(self):
"""
Add row
"""
currentRows = self.tableWidget_2.rowCount()
self.tableWidget_2.setRowCount(currentRows + 1)
for column in range(self.tableWidget_2.columnCount()):
item = QTableWidgetItem("")
item.setToolTip("Double click to set colors")
self.tableWidget_2.setItem(currentRows, column, item)
@pyqtSlot()
def on_pushButton_8_clicked(self):
"""
delete row
"""
selecteditems = self.tableWidget_2.selectedItems()
rows = sorted(set([i.row() for i in selecteditems]), reverse=True)
for row in rows:
self.tableWidget_2.removeRow(row)
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
delete cell
"""
selecteditems = self.tableWidget_2.selectedItems()
if selecteditems:
for i in selecteditems:
i.setText("")
i.setBackground(QColor('transparent'))
@pyqtSlot()
def on_toolButton_3_clicked(self):
"""
GenBank file extract settings
"""
self.extract_setting = ExtractSettings(self)
self.extract_setting.closeSig.connect(self.displaySettings)
# 添加最大化按钮
self.extract_setting.setWindowFlags(self.extract_setting.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.extract_setting.exec_()
@pyqtSlot()
def on_pushButton_10_clicked(self):
"""
GenBank file lineage recognization settings
"""
self.setting = Setting(self)
self.setting.display_table(self.setting.listWidget.item(0))
self.setting.closeSig.connect(self.updateLineageCombo)
self.setting.closeSig.connect(self.updateLineageTable)
self.setting.setWindowFlags(self.setting.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.setting.exec_()
def showOn(self):
list_color = [
"#ffff33",
"#99ffff",
"#ff9999",
"#6699ff",
"#DAA520",
"#ccff00",
"#bfbfbf"]
self.tableWidget.itemClicked.connect(self.handleItemClicked)
for row in range(self.tableWidget.rowCount()):
# 2列颜色 (必须初始化一个item，不然恢复界面设置会出错)
item2 = QTableWidgetItem(list_color[row])
item2.setBackground(QColor(list_color[row]))
self.tableWidget.setItem(row, 1, item2)
model = QStandardItemModel()
for i in self.dict_icon:
item = QStandardItem(i)
item.setIcon(QIcon(self.dict_icon[i]))
font = item.font()
font.setPointSize(13)
item.setFont(font)
model.appendRow(item)
comb_box = MyComboBox(self)
comb_box.setModel(model)
# 改变icon大小
view = comb_box.view()
view.setIconSize(QSize(38, 38))
self.tableWidget.setCellWidget(row, 3, comb_box)
self.tableWidget.resizeColumnsToContents()
self.tableWidget.verticalHeader().setVisible(False)
def handleItemClicked(self, item):
if item.column() == 1:
color = QColorDialog.getColor(QColor(item.text()), self)
if color.isValid():
item.setText(color.name())
item.setBackground(color)
self.tableWidget.clearSelection()
def handleItemClicked_2(self, item):
color = QColorDialog.getColor(QColor(item.text()), self)
if color.isValid():
item.setText(color.name())
item.setBackground(color)
self.tableWidget_2.clearSelection()
def guiSave(self):
# Save geometry
self.extractGB_settings.setValue('size', self.size())
# self.extractGB_settings.setValue('pos', self.pos())
for name, obj in inspect.getmembers(self):
# if type(obj) is QComboBox: # this works similar to isinstance, but
# missed some field... not sure why?
if isinstance(obj, QComboBox):
# save combobox selection to registry
if name in ["comboBox_7", "comboBox_4"]:
dict_state = {}
for i in range(obj.count()):
text = obj.itemText(i)
state = 2 if obj.model().item(i).checkState() == Qt.Checked else 0
dict_state[text] = state
self.extractGB_settings.setValue(name, dict_state)
elif name != "comboBox_5":
text = obj.currentText()
if text:
allItems = [
obj.itemText(i) for i in range(obj.count())]
allItems.remove(text)
sortItems = [text] + allItems
self.extractGB_settings.setValue(name, sortItems)
if isinstance(obj, QGroupBox):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QRadioButton):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QTableWidget):
if name == "tableWidget":
array = [] # 每一行存：checked, color, length, index_text
for row in range(obj.rowCount()):
checked = "true" if obj.item(
row, 0).checkState() == Qt.Checked else "false"
colour = obj.item(row, 1).text()
length = obj.item(row, 2).text()
shape_combo = obj.cellWidget(row, 3)
shape = shape_combo.currentText()
array.append([checked, colour, length, shape])
self.extractGB_settings.setValue(name, array)
elif name == "tableWidget_2":
dict_color_array = self.getLineageColor()
self.extractGB_settings.setValue(name, dict_color_array)
if isinstance(obj, QTabWidget):
index = obj.currentIndex()
self.extractGB_settings.setValue(name, index)
if isinstance(obj, QDoubleSpinBox):
value = obj.value()
self.extractGB_settings.setValue(name, value)
if isinstance(obj, QLineEdit):
text = obj.text()
self.extractGB_settings.setValue(name, text)
def guiRestore(self):
# Restore geometry
self.resize(self.extractGB_settings.value('size', QSize(571, 680)))
if self.height() < 640:
self.resize(QSize(571, 650))
# self.move(self.extractGB_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox_5":
# 展示输入
model = obj.model()
obj.clear()
for num, i in enumerate(self.list_names):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.changeLable()
elif name == "comboBox_6":
self.displaySettings()
elif name == "comboBox_7":
self.updateLineageCombo()
elif name == "comboBox_4":
key = re.sub(r"/|\\", "_", self.workPath) + "_availableInfo"
value = self.mainwindow_settings.value(
key, None)
if value:
source_keys = value[3][1]
else:
source_keys = None
items = ["Organism", "ID", "Name", "Length", "Description", "Date"] + source_keys \
if source_keys else ["Organism", "ID", "Name", "Length"]
ini_state = {}.fromkeys(items, 0) # 2代表选中
ini_state["Organism"] = 2
ini_state["Name"] = 2
dict_name_state = self.extractGB_settings.value("comboBox_4", ini_state)
if type(dict_name_state) != dict:
dict_name_state = ini_state
self.comboBox_4.sep = "_"
model = self.comboBox_4.model()
self.comboBox_4.clear()
for num, text in enumerate(items):
item = QStandardItem(str(text))
state = dict_name_state[text] if text in dict_name_state else ini_state[text] # 测试一下
item.setCheckState(int(state))
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.comboBox_4.setTopText()
self.comboBox_4.view().pressed.connect(self.judgeName)
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
values = self.extractGB_settings.value(name, allItems)
model = obj.model()
obj.clear()
for num, i in enumerate(values):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
if isinstance(obj, QGroupBox):
# 如果没有name，就设置为True
state = self.extractGB_settings.value(name, "true")
obj.setChecked(self.factory.str2bool(state))
if isinstance(obj, QCheckBox):
value = self.extractGB_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QRadioButton):
value = self.extractGB_settings.value(
name, "first") # get stored value from registry
if value != "first":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QTableWidget):
if name == "tableWidget":
# 每一行存：checked, color, length, index_text
ini_array = [
[
'true', '#ffff33', '25', 'rectangle'], [
'true', '#99ffff', '25', 'rectangle'], [
'true', '#ff9999', '30', 'rectangle'], [
'true', '#6699ff', '25', 'rectangle'], [
'true', '#DAA520', '18', 'rectangle'], [
'true', '#ccff00', '15', 'rectangle'], [
'false', '#bfbfbf', '15', 'ellipse']]
array = self.extractGB_settings.value(name, ini_array)
for row in range(obj.rowCount()):
ifChecked = Qt.Checked if array[row][
0] == "true" else Qt.Unchecked
obj.item(row, 0).setCheckState(ifChecked)
obj.item(row, 1).setText(array[row][1])
obj.item(row, 1).setBackground(QColor(array[row][1]))
obj.item(row, 2).setText(array[row][2])
shape = array[row][3]
shape_combo = obj.cellWidget(row, 3)
shape_combo_index = shape_combo.findText(shape)
if shape_combo_index == -1: # add to list if not found
shape_combo.insertItems(0, [value])
index = shape_combo.findText(value)
shape_combo.setCurrentIndex(index)
else:
# preselect a combobox value by index
shape_combo.setCurrentIndex(shape_combo_index)
elif name == "tableWidget_2":
self.updateLineageTable()
if isinstance(obj, QTabWidget):
index = self.extractGB_settings.value(name, 0)
obj.setCurrentIndex(int(index))
if isinstance(obj, QDoubleSpinBox):
value = self.extractGB_settings.value(name, 1.0)
obj.setValue(float(value))
if isinstance(obj, QLineEdit):
text = self.extractGB_settings.value(name, "first")
if text != "first":
obj.setText(text)
def popupException(self, exception):
rgx = re.compile(r'Permission.+?[\'\"](.+\.csv)[\'\"]')
if rgx.search(exception):
csvfile = rgx.search(exception).group(1)
reply = QMessageBox.critical(
self,
"Extract sequence",
"<p style='line-height:25px; height:25px'>Please close '%s' file first!</p>"%os.path.basename(csvfile),
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Yes and platform.system().lower() == "windows":
os.startfile(csvfile)
elif "Permission" in exception:
reply = QMessageBox.critical(
self,
"Extract sequence",
"<p style='line-height:25px; height:25px'>Error happened, please close the window and try again!</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Yes:
self.close()
else:
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(
'The program encountered an unforeseen problem, please report the bug at <a href="https://github.com/dongzhang0725/PhyloSuite/issues">https://github.com/dongzhang0725/PhyloSuite/issues</a> or send an email with the detailed traceback to [email protected]')
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def closeEvent(self, event):
self.guiSave()
def runProgress(self, num):
oldValue = self.progressBar.value()
done_int = int(num)
if done_int > oldValue:
self.progressBar.setProperty("value", done_int)
QCoreApplication.processEvents()
def eventFilter(self, obj, event):
name = obj.objectName()
if isinstance(obj, QTableWidget):
if event.type() == QEvent.KeyPress: # 首先得判断type
modifiers = QApplication.keyboardModifiers()
if name == "tableWidget_2":
if event.key() == Qt.Key_Delete:
self.on_pushButton_9_clicked()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_C):
self.copyColor()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_X):
self.cutColor()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_V):
self.pasteColor()
return True
if (event.type() == QEvent.Show) and (obj == self.pushButton_2.toolButton.menu()):
if re.search(r"\d+_\d+_\d+\-\d+_\d+_\d+",
self.dir_action.text()) or self.dir_action.text() == "Output Dir: ":
self.factory.sync_dir(self.dir_action) ##同步文件夹名字
menu_x_pos = self.pushButton_2.toolButton.menu().pos().x()
menu_width = self.pushButton_2.toolButton.menu().size().width()
button_width = self.pushButton_2.toolButton.size().width()
pos = QPoint(menu_x_pos - menu_width + button_width,
self.pushButton_2.toolButton.menu().pos().y())
self.pushButton_2.toolButton.menu().move(pos)
return True
return super(ExtractGB, self).eventFilter(obj, event)
def changeLable(self):
count = str(self.comboBox_5.count())
self.label_4.setText("Inputs (" + count + "):")
def getLineageColor(self):
dict_color_array = OrderedDict()
columnNum = self.tableWidget_2.columnCount()
rowNum = self.tableWidget_2.rowCount()
for column in range(columnNum):
headerText = self.tableWidget_2.horizontalHeaderItem(column).text()
list_columnText = []
for row in range(rowNum):
if self.tableWidget_2.item(row, column):
list_columnText.append(
self.tableWidget_2.item(row, column).text())
dict_color_array[headerText] = list_columnText
return dict_color_array
def copyColor(self):
selecteditems = self.tableWidget_2.selectedItems()
if selecteditems:
list_selItem_text = [i.text() for i in selecteditems]
QApplication.clipboard().setText("\t".join(list_selItem_text))
def cutColor(self):
selecteditems = self.tableWidget_2.selectedItems()
list_selItem_text = []
if selecteditems:
for i in selecteditems:
list_selItem_text.append(i.text())
i.setText("")
i.setBackground(QColor('transparent'))
QApplication.clipboard().setText("\t".join(list_selItem_text))
def pasteColor(self):
colors = QApplication.clipboard().text()
list_colors = re.split(r"\s+|,", colors)
while "" in list_colors:
list_colors.remove("")
selecteditems = self.tableWidget_2.selectedItems()
for num, i in enumerate(selecteditems):
if (num+1) <= len(list_colors):
color = list_colors[num]
qcolor = QColor(color)
if not qcolor.isValid():
continue
i.setText(color)
i.setBackground(qcolor)
def displaySettings(self):
###提取的设置
self.GenBankExtract_settings = QSettings(
self.thisPath + '/settings/GenBankExtract_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.GenBankExtract_settings.setFallbacksEnabled(False)
self.dict_gbExtract_set = self.GenBankExtract_settings.value("set_version")
# self.extract_list_gene = self.factory.str2bool(self.GenBankExtract_settings.value("extract listed gene",
# "false"))
# self.extract_all_features = self.factory.str2bool(self.GenBankExtract_settings.value("extract all features",
#
# "false"))
if self.dict_gbExtract_set:
self.allVersions = list(self.dict_gbExtract_set.keys())
model = self.comboBox_6.model()
self.comboBox_6.clear()
for num, i in enumerate(self.allVersions + [">>>More<<<"]):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.switchSeqType(self.comboBox_6.currentText())
def switchSeqType(self, text):
###保存version顺序
if text == ">>>More<<<":
QDesktopServices.openUrl(QUrl("https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/customize_extraction/"))
self.comboBox_6.setCurrentIndex(0)
return
if text != self.allVersions[0]:
if text in self.allVersions:
list_now_versions = copy.deepcopy(self.allVersions)
list_now_versions.remove(text)
reorder_list = [text] + list_now_versions
self.dict_gbExtract_set = OrderedDict((i, self.dict_gbExtract_set[i]) for i in reorder_list)
self.GenBankExtract_settings.setValue('set_version', self.dict_gbExtract_set)
###控制itol
if text != "Mitogenome":
targetIndex = "null"
for index in range(self.tabWidget.count()):
if self.tabWidget.tabText(index) == "Gene order display":
targetIndex = index
if targetIndex != "null":
self.hiddenIndex = targetIndex
self.hiddenWidget = self.tabWidget.widget(self.hiddenIndex)
self.hiddenTabText = self.tabWidget.tabText(self.hiddenIndex)
self.tabWidget.removeTab(self.hiddenIndex)
self.hiddenFlag = True
else:
if hasattr(self, "hiddenFlag") and self.hiddenFlag:
self.tabWidget.insertTab(self.hiddenIndex, self.hiddenWidget, self.hiddenTabText)
self.hiddenFlag = False
self.tabWidget.setCurrentIndex(0)
def updateLineageTable(self):
# tableWidget_2
self.tableWidget_2.itemDoubleClicked.connect(self.handleItemClicked_2)
ini_data = [['Class', 'Order', 'Superfamily', 'Family', 'Subfamily', 'Genus'],
[['', '*tera', '*dea', '*dae', '*nae', ''],
['', '', '*ida', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', '']]]
header, array = self.settings_ini.value("Taxonomy Recognition", ini_data)
countColumn = len(header)
self.tableWidget_2.setColumnCount(countColumn)
ini_dict_array = OrderedDict()
for i in header:
ini_dict_array[i] = [""] * 6
familyColor = [
"#81C7D6", "#FF0033", "#6A00D1", "#49BF4E", "#AA538B", "#FF99CC"]
ini_dict_array[
"Family"] = familyColor if "Family" in ini_dict_array else ini_dict_array["Family"]
self.tableWidget_2.setHorizontalHeaderLabels(
header)
dict_array = self.extractGB_settings.value(
"tableWidget_2", ini_dict_array)
maxRow = len(max(list(dict_array.values()), key=len))
self.tableWidget_2.setRowCount(maxRow)
if len(ini_dict_array) > len(dict_array):
# 如果用户添加了lineage
list_differ = list(
set(ini_dict_array.keys()).difference(set(dict_array.keys())))
for i in list_differ:
# 加上这个lineage
dict_array[i] = [""] * maxRow
for column, columnText in enumerate(header):
for row, rowText in enumerate(dict_array[columnText]):
item = QTableWidgetItem(rowText)
item.setToolTip("Double click to set colors")
color = QColor(rowText)
if color.isValid():
item.setBackground(color)
self.tableWidget_2.setItem(row, column, item)
def updateLineageCombo(self):
ini_data = [['Class', 'Order', 'Superfamily', 'Family', 'Subfamily', 'Genus'],
[['', '*tera', '*dea', '*dae', '*nae', ''],
['', '', '*ida', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', '']]]
header, array = self.settings_ini.value("Taxonomy Recognition", ini_data)
ini_state = {}.fromkeys(header, 2) # 2代表选中
dict_lng_state = self.extractGB_settings.value("comboBox_7", ini_state)
model = self.comboBox_7.model()
self.comboBox_7.clear()
for num, text in enumerate(header):
item = QStandardItem(text)
state = dict_lng_state[text] if text in dict_lng_state else ini_state[text] # 测试一下
item.setCheckState(int(state))
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.comboBox_7.setTopText()
def judgeName(self):
if not set(["Organism", "ID", "Name"]).intersection(set(self.comboBox_4.topText.split("_"))):
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>At least one of the following should be retained: \"Organism\", \"ID\", \"Name\"</p>")
self.comboBox_4.item.setCheckState(Qt.Checked)
self.comboBox_4.setTopText()
def judgeCodonW(self, bool_):
if bool_:
pass