def __init__(self, mode="PF2", parent=None):
self.factory = Factory()
self.thisPath = self.factory.thisPath
super(PartitionEditor, self).__init__(parent)
# 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.resize(400, 600)
self.setWindowFlags(self.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.setupUi(self)
self.header = ["Name", "", "Start", "", "Stop"]
self.pushButton_2.clicked.connect(self.addRow)
self.pushButton.clicked.connect(self.deleteRow)
self.pushButton_recog.clicked.connect(self.recogFromText)
self.pushButton_codon.clicked.connect(self.ToCodonMode)
self.pushButton_nocodon.clicked.connect(self.CancelCodonMode)
self.data_type = "NUC"
self.mode = mode
## brief demo
country = self.factory.path_settings.value("country", "UK")
url = "http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#5-10-2-Brief-tutorial-for-partition-editor" if \
country == "China" else "https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-10-2-Brief-tutorial-for-partition-editor"
self.label_4.clicked.connect(
lambda: QDesktopServices.openUrl(QUrl(url)))
def __init__(self, **kwargs):
self.factory = Factory()
self.dict_args = kwargs
self.outpath = self.dict_args["exportPath"]
self.dict_species = {}
self.dict_statistics = dict(prefix='taxon')
self.partition_style = '***partitionfinder style***\n'
self.partition_codon = "\n***codon style***\n"
self.bayes_style = '\n***bayes style***\n'
self.bayes_codon = "\n***bayes codon style***\n"
self.iqtree_style = '\n***IQ-TREE style***\n#nexus\nbegin sets;\n'
self.iqtree_codon = "\n***IQ-TREE codon style***\n#nexus\nbegin sets;\n"
self.parent = self.dict_args["parent"]
self.partition_name = ''
self.partition_codname = ""
self.gene_index = []
self.dist_warning_message = OrderedDict()
self.error_message = ""
self.parsefmt = Parsefmt(self.error_message)
self.dict_genes_alignments = OrderedDict()
self.unaligned = False
self.unaligns = []
self.exportName = self.dict_args["export_name"]
self.interrupt = False
self.list_empty_files = []
for num, eachFile in enumerate(self.dict_args["files"]):
if self.interrupt:
break
geneName = os.path.splitext(os.path.basename(eachFile))[0]
dict_taxon = self.parsefmt.readfile(eachFile)
set_length = set([len(dict_taxon[i]) for i in dict_taxon])
if set_length == {0}:
self.list_empty_files.append(os.path.basename(eachFile))
continue
self.error_message += self.parsefmt.error_message
if self.factory.is_aligned(dict_taxon):
self.dict_genes_alignments[geneName] = dict_taxon
else:
self.unaligned = True
self.unaligns.append(geneName)
if self.list_empty_files:
if len(self.list_empty_files) == 1:
text = "The empty file \"%s\" will be ignored" % self.list_empty_files[
0]
else:
file_names = "\", \"".join(
self.list_empty_files[:-1]
) + "\" and \"%s\"" % self.list_empty_files[-1]
text = "The empty files \"%s will be ignored" % file_names
QMetaObject.invokeMethod(self.parent, "popupEmptyFileWarning",
Qt.BlockingQueuedConnection,
Q_ARG(str, text))
if self.unaligned:
self.dict_args["unaligned_signal"].emit(self.unaligns)
if self.dict_genes_alignments:
self.supplement()
self.concatenate()
self.ok = True
else:
self.ok = False
def main():
args = parse_args()
set_global_seeds(666)
config = get_config(args.config)
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
runner = PytorchInference(device)
test_loader = make_data(**config['data_params'], mode='test')
weights_paths = collect_weight_paths(args.path, args.fold)
os.makedirs(args.output, exist_ok=True)
predictions = defaultdict(lambda: {'mask': 0, 'empty': 0})
for i, weights_path in enumerate(weights_paths):
torch.cuda.empty_cache()
print(f'weights: {weights_path}')
config['train_params']['weights'] = weights_path
factory = Factory(config['train_params'])
model = factory.make_model(device)
for result in tqdm(iterable=runner.predict(model, test_loader),
total=len(test_loader) *
config['data_params']['batch_size']):
ensemble_mask = (predictions[result['image_id']]['mask'] * i +
result['mask']) / (i + 1)
ensemble_empty = (predictions[result['image_id']]['empty'] * i +
result['empty']) / (i + 1)
predictions[result['image_id']]['mask'] = ensemble_mask
predictions[result['image_id']]['empty'] = ensemble_empty
mmcv.dump(dict(predictions), osp.join(args.output,
f'fold_{args.fold}.pkl'))
def __init__(self, exportPath=None, parent=None):
super(Lg_addFiles, self).__init__(parent)
self.factory = Factory()
self.parent = parent
self.thisPath = self.factory.thisPath
self.exportPath = exportPath
# 保存设置
self.addFiles_settings = QSettings(
self.thisPath +
'/settings/addFiles_settings.ini',
QSettings.IniFormat)
self.closeGUI_signal.connect(self.close)
self.progressDiologSig.connect(self.runProgressDialog)
# self.close() 不能在信号槽里面
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
# 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.setupUi(self)
self.guiRestore()
self.exception_signal.connect(self.popupException)
self.interrupt = False
self.label_3.clicked.connect(lambda : QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-1-1-Brief-example")))
def __init__(self,
workPath=None,
focusSig=None,
autoFiles=None,
parent=None):
super(ConvertFMT, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoFiles = autoFiles
self.setupUi(self)
# 保存设置
self.convertFmt_settings = QSettings(
self.thisPath + '/settings/convertFmt_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.convertFmt_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.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) #自动识别可用的输入
self.unalignedSig.connect(self.popupUnaligns)
# 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.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-8-1-Brief-example"
)))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
def __init__(self,
autoInputs=None,
workPath=None,
focusSig=None,
RscriptPath=None,
parent=None):
super(DrawRSCUfig, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoInputs = autoInputs
self.RscriptPath = RscriptPath
self.setupUi(self)
# 保存设置
self.DrawRSCUfig_settings = QSettings(
self.thisPath + '/settings/DrawRSCUfig_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.DrawRSCUfig_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.exception_signal.connect(self.popupException)
self.warning_signal.connect(self.popupWarning)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.listWidget_3.installEventFilter(self)
# 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.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
country = self.factory.path_settings.value("country", "UK")
url = "http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#5-14-3-1-Brief-example" if \
country == "China" else "https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-14-3-1-Brief-example"
self.label_2.clicked.connect(
lambda: QDesktopServices.openUrl(QUrl(url)))
def main():
args = parse_args()
set_global_seeds(666)
config = get_config(args.config)
pprint(config)
config['train_params'][
'name'] = f'{config["train_params"]["name"]}/fold{args.fold}'
factory = Factory(config['train_params'])
data_factory = DataFactory(config['data_params'], fold=args.fold)
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
callbacks = create_callbacks(config['train_params']['name'],
config['dumps'])
trainer = Runner(stages=config['stages'],
factory=factory,
callbacks=callbacks,
device=device)
trainer.fit(data_factory)
def __init__(self, unRecognisetRNA=None, gbContent=None, predict_signal=None, parent=None):
super(Lg_ReANNT, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.setupUi(self)
self.textBrowser.setText(unRecognisetRNA)
self.gbContent = gbContent
self.predict_signal = predict_signal
self.totaltRNA = unRecognisetRNA.count(">")
# 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)
# 信号和槽
self.progressSig.connect(self.normProgress)
self.close_sig.connect(self.closeWindow)
self.exception_signal.connect(self.popupException)
def __init__(self, nmlgb):
self.dict_args = nmlgb.dict_args
super(GbEditor, self).__init__(self.dict_args["parent"])
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.factory = Factory()
self.thisPath = self.factory.thisPath
# 保存设置
self.gbEditor_settings = QSettings(self.thisPath +
'/settings/gbEditor_settings.ini',
QSettings.IniFormat,
parent=self)
# File only, no fallback to registry or or.
self.gbEditor_settings.setFallbacksEnabled(False)
self.settings_ini = QSettings(
self.thisPath + '/settings/setting_settings.ini',
QSettings.IniFormat)
self.settings_ini.setFallbacksEnabled(False)
self.setupUi(self)
self.allcontent = nmlgb.allContent
self.errors = nmlgb.errors
self.warings = nmlgb.warnings
self.unRecognisetRNA = nmlgb.unRecognisetRNA
self.dict_replace = nmlgb.dict_replace
self.workPath = self.dict_args["outpath"]
self.showOn()
# 信号和槽
self.progressSig.connect(self.normProgress)
self.findSig.connect(self.popupFindOver)
self.predict_signal.connect(self.reANNT_validate)
self.exception_signal.connect(
lambda x: self.factory.popupException(self, x))
# 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.installEventFilter(self)
self.guiRestore()
self.checkBox.toggled.connect(self.askRemoveMisc)
self.removeMISC = False
def __init__(self, parent=None):
super(Launcher, self).__init__(parent)
self.factory = Factory()
self.thisPath = self.factory.thisPath
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.launcher_settings = QSettings(
self.thisPath + '/settings/launcher_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.launcher_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)
self.setupUi(self)
self.guiRestore()
if platform.system().lower() == "darwin":
cursor = self.textEdit.textCursor()
self.textEdit.selectAll()
self.textEdit.setFontPointSize(12)
self.textEdit.setTextCursor(cursor)
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
country = self.factory.path_settings.value("country", "UK")
url = "http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#4-4-2-Information-display-and-modification" if \
country == "China" else "https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-4-2-Information-display-and-modification"
self.label_6.clicked.connect(
lambda: QDesktopServices.openUrl(QUrl(url)))
def __init__(self, workPath=None, parent=None):
super(SerhNCBI, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.setupUi(self)
# 保存设置
self.serhNCBI_settings = QSettings(
self.thisPath + '/settings/serhNCBI_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.serhNCBI_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.exception_signal.connect(self.popupException)
# self.progressSig.connect(self.runProgress)
# self.logGuiSig.connect(self.addText2Log)
self.lineEdit.buttonSearch.clicked.connect(lambda: [
self.startSearch(),
self.sync_completer_texts(self.lineEdit.text())
])
self.lineEdit.buttonStop.clicked.connect(self.stopSearch)
# self.lineEdit.completer().popup().show()
# self.lineEdit.clicked.connect(lambda : self.lineEdit.completer().popup())
self.dict_ncbi_headers = {
"GBSeq_accession-version": "ID",
"GBSeq_definition": "Description",
"GBSeq_organism": "Organism",
"GBSeq_length": "Length",
"GBSeq_update-date": "Update date",
"GBSeq_taxonomy": "Taxonomy",
"GBSeq_create-date": "Create date",
"GBSeq_moltype": "Molecular type",
"GBSeq_topology": "Topology",
"GBSeq_references": "References",
"GBSeq_source": "Source",
"GBSeq_keywords": "Keywords",
"GBSeq_project": "Project",
"GBSeq_other-seqids": "Other IDs",
"GBSeq_strandedness": "Strandedness",
"GBSeq_comment": "Comments"
}
self.init_list()
self.updateSig.connect(self.updateTable)
self.searchSig.connect(self.ctrlSearchState)
self.progressBarSig.connect(self.searchProgress)
self.progressDiologSig.connect(self.runProgressDialog)
self.spinBox.valueChanged.connect(self.sync_display_items)
self.ctrlItemsSig.connect(self.ctrlItems)
# self.downloadFinished.connect(self.downloadDone)
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
self.NCBI_model = MyNCBITableModel([self.list_table_header],
parent=self)
self.tableView.setModel(self.NCBI_model)
header = CheckBoxHeader(parent=self.tableView)
header.clicked.connect(self.check_displayed)
self.tableView.setHorizontalHeader(header)
self.NCBI_model.checkedChanged.connect(self.ctrl_text)
self.interrupt = False
##下载的状态
widget = QWidget(self)
horizBox = QHBoxLayout(widget)
horizBox.setContentsMargins(0, 0, 0, 0)
spacerItem = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.disp_check_label = QLabel(
"<span style='font-weight:600; color:red;'>Searching...</span>",
self)
self.disp_check_gifLabel = QLabel(self)
movie = QMovie(":/picture/resourses/Spinner-1s-34px.gif")
self.disp_check_gifLabel.setMovie(movie)
self.disp_check_progress = QProgressBar(self)
self.disp_check_progress.setFixedWidth(100)
movie.start()
horizBox.addItem(spacerItem)
horizBox.addWidget(self.disp_check_gifLabel)
horizBox.addWidget(self.disp_check_label)
horizBox.addWidget(self.disp_check_progress)
self.statusbar.addPermanentWidget(widget)
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.installEventFilter(self)
self.spinBox.installEventFilter(self)
table_popMenu = QMenu(self)
table_popMenu.setToolTipsVisible(True)
OpenID = QAction(QIcon(":/seq_Viewer/resourses/field-Display.png"),
"Open in NCBI webpage",
self,
triggered=self.openID)
OpenID.setToolTip("Open sequence in NCBI webpage")
table_popMenu.addAction(OpenID)
def table_popmenu(qpoint):
if self.tableView.indexAt(qpoint).isValid():
table_popMenu.exec_(QCursor.pos())
self.tableView.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableView.customContextMenuRequested.connect(table_popmenu)
# self.tableView.horizontalHeader().resizeSection(1, 300)
# self.tableView.horizontalHeader().resizeSection(2, 80)
# ##增加check按钮
# self.check_all = QCheckBox("Check/Uncheck", self)
# self.check_all.toggled.connect(self.check_displayed)
# self.statusbar.addWidget(self.check_all)
## brief demo
self.label_6.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-3-1-Brief-example"
)))
def __init__(self,
files=None,
workPath=None,
focusSig=None,
workflow=False,
parent=None):
super(Matrix, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
# 保存设置
if not workflow:
self.concatenate_settings = QSettings(
self.thisPath + '/settings/concatenate_settings.ini',
QSettings.IniFormat)
else:
self.concatenate_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.concatenate_settings.beginGroup("Workflow")
self.concatenate_settings.beginGroup("temporary")
self.concatenate_settings.beginGroup('Concatenate Sequence')
# File only, no fallback to registry or or.
self.concatenate_settings.setFallbacksEnabled(False)
self.setupUi(self)
self.files = files
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
# 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.groupBox_top_line.setStyleSheet('''QGroupBox{
border-bottom:none;
border-right:none;
border-left:none;
}
QGroupBox::title{
subcontrol-origin: margin;
subcontrol-position: top left;
}''')
self.unalignedSig.connect(self.unaligned)
self.exception_signal.connect(self.popupException)
# self.warning_signal.connect(self.popupWarning)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) #自动识别可用的输入
##设置拖拽排序
self.comboBox_4.view().setDragEnabled(True)
self.comboBox_4.view().setDragDropMode(QAbstractItemView.InternalMove)
self.comboBox_4.view().setDefaultDropAction(Qt.MoveAction)
# self.comboBox_4.view().setSelectionMode(QAbstractItemView.MultiSelection)
self.comboBox_4.view().installEventFilter(self)
# 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.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-7-1-Brief-example"
)))
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")))
def __init__(self,
autoInputs=None,
workPath=None,
focusSig=None,
gb_exe=None,
workflow=False,
parent=None):
super(Gblocks, self).__init__(parent)
self.parent = parent
self.function_name = "Gblocks"
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
self.gb_exe = '"' + gb_exe + '"'
self.autoInputs = autoInputs
self.interrupt = False
self.setupUi(self)
# 保存设置
if not workflow:
self.gblocks_settings = QSettings(
self.thisPath + '/settings/gblocks_settings.ini',
QSettings.IniFormat)
else:
self.gblocks_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.gblocks_settings.beginGroup("Workflow")
self.gblocks_settings.beginGroup("temporary")
self.gblocks_settings.beginGroup('Gblocks')
# File only, no fallback to registry or or.
self.gblocks_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.log_gui = self.gui4Log()
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.gblocks_exception.connect(self.popup_Gblocks_exception)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
# self.comboBox_4.itemRemovedSig.connect(self.auto_parFromfile)
self.comboBox_2.currentIndexChanged[str].connect(self.comboLink)
reg_ex = QRegExp(".{,5}")
validator = QRegExpValidator(reg_ex, self.lineEdit_3)
self.lineEdit_3.setValidator(validator)
self.auto_parSig.connect(self.auto_parFromfile)
# 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.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-6-1-Brief-example"
)))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
def mining():
factory = Factory(image_shape=(224, 224))
factory.mining('training')
factory.mining('validation')
def __init__(self,
workPath=None,
TApath=None,
autoInputs=None,
focusSig=None,
workflow=None,
parent=None):
super(TrimAl, self).__init__(parent)
self.parent = parent
self.function_name = "trimAl"
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.TApath = TApath
self.autoInputs = autoInputs
self.setupUi(self)
# 保存设置
if not workflow:
self.trimAl_settings = QSettings(
self.thisPath + '/settings/trimAl_settings.ini',
QSettings.IniFormat)
else:
self.trimAl_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.trimAl_settings.beginGroup("Workflow")
self.trimAl_settings.beginGroup("temporary")
self.trimAl_settings.beginGroup('trimAl')
# File only, no fallback to registry or or.
self.trimAl_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.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.trimAl_exception.connect(self.popup_trimAl_exception)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
self.comboBox_4.installEventFilter(self)
self.lineEdit_2.installEventFilter(self)
self.lineEdit_3.installEventFilter(self)
self.log_gui = self.gui4Log()
# stat output file name
self.lineEdit_2.setLineEditNoChange(True)
self.lineEdit_3.setLineEditNoChange(True)
self.lineEdit_2.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
self.lineEdit_3.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
# 选框联动
self.checkBox_2.toggled.connect(self.switchCheckBox1)
self.checkBox_5.toggled.connect(self.switchCheckBox1)
# self.groupBox_5.toggled.connect(lambda bool_: self.groupBox_6.setChecked(not bool_))
# self.groupBox_6.toggled.connect(lambda bool_: self.groupBox_5.setChecked(not bool_))
self.checkBox_3.toggled.connect(self.switchCheckBox2)
self.checkBox_6.toggled.connect(self.switchCheckBox2)
self.checkBox_7.toggled.connect(self.switchCheckBox2)
self.checkBox_8.toggled.connect(self.switchCheckBox2)
self.checkBox_9.toggled.connect(self.judgeInput)
self.radioButton.toggled.connect(self.Un_checkBox_9)
self.comboBox_2.currentTextChanged.connect(self.judgeComboBox_2)
self.comboBox.currentTextChanged.connect(self.judgeFormats)
self.radioButton.toggled.connect(self.controlRefineText)
self.interrupt = False
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
action = QAction(QIcon(":/picture/resourses/terminal-512.png"),
"View | Edit command",
menu,
triggered=self.showCMD)
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(action)
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-4-1-Brief-example"
)))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
def __init__(self,
workPath=None,
HmmCleanerPath=None,
autoInputs=None,
perl=None,
focusSig=None,
workflow=None,
parent=None):
super(HmmCleaner, self).__init__(parent)
self.parent = parent
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoInputs = autoInputs
self.HmmCleanerPath = HmmCleanerPath
self.perl = perl
self.setupUi(self)
# 保存设置
if not workflow:
self.HmmCleaner_settings = QSettings(
self.thisPath + '/settings/HmmCleaner_settings.ini',
QSettings.IniFormat)
else:
self.HmmCleaner_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.HmmCleaner_settings.beginGroup("Workflow")
self.HmmCleaner_settings.beginGroup("temporary")
self.HmmCleaner_settings.beginGroup('HmmCleaner')
# File only, no fallback to registry or or.
self.HmmCleaner_settings.setFallbacksEnabled(False)
# print(self.HmmCleaner_settings.childGroups())
# self.factory.settingsGroup2Group(self.HmmCleaner_settings, "PCGs", "temporary")
# 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.interrupt = False
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
self.log_gui = self.gui4Log()
self.HmmCleaner_exception.connect(self.popup_HmmCleaner_exception)
self.checkBox_4.toggled.connect(self.popupAliWarning)
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
action = QAction(QIcon(":/picture/resourses/terminal-512.png"),
"View | Edit command",
menu,
triggered=self.showCMD)
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(action)
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-5-1-Brief-example"
)))
def __init__(
self,
parent=None):
super(ExtractSettings, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.setupUi(self)
# # 设置比例
# self.splitter.setStretchFactor(1, 7)
# 保存主界面设置
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)
# 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.tableView.installEventFilter(self)
self.tableView.horizontalHeader().setStretchLastSection(True)
self.listWidget.installEventFilter(self)
self.listWidget_2.installEventFilter(self)
tableView_popMenu = QMenu(self)
edit = QAction("Edit", self,
statusTip="Edit select item",
triggered=lambda: self.tableView.edit(self.tableView.currentIndex()))
delete = QAction("Delete", self,
shortcut=QKeySequence.Delete,
statusTip="Remove select rows",
triggered=self.on_toolButton_4_clicked)
add = QAction("Add row", self,
statusTip="Add row",
triggered=self.on_toolButton_3_clicked)
export = QAction("Export", self,
statusTip="Export table",
triggered=self.on_toolButton_5_clicked)
import_ = QAction("Import", self,
statusTip="Import table",
triggered=self.on_toolButton_6_clicked)
tableView_popMenu.addAction(edit)
tableView_popMenu.addAction(delete)
tableView_popMenu.addAction(add)
tableView_popMenu.addAction(export)
tableView_popMenu.addAction(import_)
self.tableView.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableView.customContextMenuRequested.connect(lambda : tableView_popMenu.exec_(QCursor.pos()))
self.listWidget.itemRemoveSig.connect(self.depositeData)
self.listWidget.itemChanged.connect(self.keepMitoFeature)
self.listWidget.itemSelectionChanged.connect(self.keepMitoFeature)
self.listWidget_2.itemRemoveSig.connect(self.depositeData)
self.listWidget_2.model().layoutChanged.connect(self.depositeData)
self.listWidget_2.model().layoutChanged.connect(self.listWidget_2.refreshBackColors) ##拖拽以后刷新颜色
# 恢复用户的设置
self.checkBox_2.stateChanged.connect(self.change_label3)
self.checkBox_2.toggled.connect(lambda bool_: self.changeCheckboxSettings("extract all features", bool_))
self.checkBox.toggled.connect(lambda bool_: self.changeCheckboxSettings("extract listed gene", bool_))
self.checkBox_3.toggled.connect(lambda bool_: self.changeCheckboxSettings("extract intergenic regions", bool_))
self.checkBox_4.toggled.connect(lambda bool_: self.changeCheckboxSettings("extract overlapping regions", bool_))
self.spinBox.valueChanged[int].connect(lambda value: self.changeCheckboxSettings("intergenic regions threshold", value))
self.spinBox_2.valueChanged[int].connect(
lambda value: self.changeCheckboxSettings("overlapping regions threshold", value))
self.guiRestore()
## brief demo
country = self.factory.path_settings.value("country", "UK")
url = "http://phylosuite.jushengwu.com/dongzhang0725.github.io/PhyloSuite-demo/customize_extraction/" if \
country == "China" else "https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/customize_extraction/"
self.label_6.clicked.connect(lambda: QDesktopServices.openUrl(QUrl(url)))
def start():
app = QSingleApplication(sys.argv)
splash = QSplashScreen(
QPixmap(":/picture/resourses/start.jpg"))
with open(thisPath + os.sep + 'style.qss', encoding="utf-8", errors='ignore') as f:
qss_file = f.read()
splash.setWindowFlags(Qt.Window)
font_size = 13 if platform.system().lower() == "windows" else 15
splash.setFont(QFont('Arial', font_size))
splash.setStyleSheet(qss_file)
icon = QIcon(":/picture/resourses/windowIcon.png")
splash.setWindowIcon(icon)
splash.show()
app.processEvents()
splash.showMessage("Checking if the program is already running...", Qt.AlignBottom, Qt.black)
if platform.system().lower() == "windows":
multiprocessing.freeze_support() # windows必须调用这个，不然会出错
# 异常调试
import cgitb
sys.excepthook = cgitb.Hook(1, None, 5, sys.stderr, 'text')
##为了存路径到系统
QApplication.setApplicationName("PhyloSuite_settings")
QApplication.setOrganizationName("PhyloSuite")
QSettings.setDefaultFormat(QSettings.IniFormat)
path_settings = QSettings()
path_settings.setValue("thisPath", thisPath)
os.chdir(thisPath)
dialog = QDialog()
dialog.setStyleSheet(qss_file)
# 异常处理
def handle_exception(exc_type, exc_value, exc_traceback):
rgx = re.compile(r'PermissionError.+?[\'\"](.+\.csv)[\'\"]')
if issubclass(exc_type, KeyboardInterrupt):
return sys.__excepthook__(exc_type, exc_value, exc_traceback)
exception = str("".join(traceback.format_exception(
exc_type, exc_value, exc_traceback)))
print(exception)
if rgx.search(exception):
#忽略csv未关闭的报错
return
msg = QMessageBox(dialog)
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_()
sys.excepthook = handle_exception
# 避免重复运行程序
if app.isRunning():
QMessageBox.information(
dialog,
"PhyloSuite",
"<p style='line-height:25px; height:25px'>App is running!</p>")
sys.exit(0)
# 界面运行选择
splash.showMessage("Choosing workplace...", Qt.AlignBottom, Qt.black)
launcher_settings = QSettings(
thisPath + '/settings/launcher_settings.ini', QSettings.IniFormat)
launcher_settings.setFallbacksEnabled(False)
not_exe_lunch = launcher_settings.value("ifLaunch", "false")
workPlace = launcher_settings.value(
"workPlace", [thisPath + os.sep + "myWorkPlace"])
# 删除无效的路径
workPlace_copy = deepcopy(workPlace)
for num,i in enumerate(workPlace_copy):
if not os.path.exists(i):
workPlace.remove(i)
else:
##替换带.的路径
if re.search(r"^\.", i):
workPlace[num] = os.path.abspath(i)
# 如果workPlace被删干净了
if not workPlace:
workPlace = [thisPath + os.sep + "myWorkPlace"]
# 重新保存下路径
if len(workPlace) > 15:
workPlace = workPlace[:15] # 只保留15个工作区
launcher_settings.setValue(
"workPlace", workPlace)
if not_exe_lunch == "true":
splash.showMessage("Starting PhyloSuite...", Qt.AlignBottom, Qt.black)
myMainWindow = MyMainWindow(workPlace)
Factory().centerWindow(myMainWindow)
myMainWindow.show()
splash.finish(myMainWindow)
sys.exit(app.exec_())
else:
launcher = Launcher()
if launcher.exec_() == QDialog.Accepted:
splash.showMessage("Starting PhyloSuite...", Qt.AlignBottom, Qt.black)
workPlace = launcher.WorkPlace
myMainWindow = MyMainWindow(workPlace)
Factory().centerWindow(myMainWindow)
myMainWindow.show()
splash.finish(myMainWindow)
sys.exit(app.exec_())
def __init__(
self,
autoMFPath=None,
partFile=None,
workPath=None,
focusSig=None,
IQ_exe=None,
workflow=False,
parent=None):
super(ModelFinder, self).__init__(parent)
self.parent = parent
self.function_name = "ModelFinder"
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
self.modelfinder_exe = '"' + IQ_exe + '"'
self.autoMFPath = autoMFPath[0] if type(autoMFPath) == list else autoMFPath
self.partFile = partFile
self.interrupt = False
self.setupUi(self)
# 保存设置
if not workflow:
self.modelfinder_settings = QSettings(
self.thisPath + '/settings/modelfinder_settings.ini', QSettings.IniFormat)
else:
self.modelfinder_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini', QSettings.IniFormat)
self.modelfinder_settings.beginGroup("Workflow")
self.modelfinder_settings.beginGroup("temporary")
self.modelfinder_settings.beginGroup('ModelFinder')
# File only, no fallback to registry or or.
self.modelfinder_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.exception_signal.connect(self.popupException)
self.iq_tree_exception.connect(self.popup_IQTREE_exception)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.log_gui = self.gui4Log()
self.lineEdit.installEventFilter(self)
self.lineEdit.autoDetectSig.connect(self.popupAutoDec)
self.lineEdit_2.installEventFilter(self)
self.lineEdit_3.installEventFilter(self)
self.comboBox_3.activated[str].connect(self.controlCodonTable)
self.comboBox_5.activated[str].connect(self.ctrl_ratehet)
self.ctrl_ratehet(self.comboBox_5.currentText())
self.lineEdit_2.setLineEditNoChange(True)
self.lineEdit_3.setLineEditNoChange(True)
self.lineEdit.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
self.lineEdit_2.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
self.lineEdit_3.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
# 初始化codon table的选择
self.controlCodonTable(self.comboBox_3.currentText())
self.checkBox.stateChanged.connect(self.switchPart)
self.switchPart(self.checkBox.isChecked())
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
action = QAction(QIcon(":/picture/resourses/terminal-512.png"), "View | Edit command", menu,
triggered=self.showCMD)
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(action)
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True, parent=self) # 初始化一下
## brief demo
self.label_2.clicked.connect(lambda: QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-9-1-Brief-example")))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
def __init__(self, parent=None):
super(UpdateAPP, self).__init__(parent)
self.factory = Factory()
self.rootPath = self.factory.thisPath
def __init__(self,
workPath=None,
focusSig=None,
workflow=False,
java=None,
macseEXE=None,
autoMFPath=None,
parent=None):
super(MACSE, self).__init__(parent)
self.parent = parent
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.java = java
self.macseEXE = macseEXE
self.autoMFPath = autoMFPath
self.setupUi(self)
# 保存设置
if not workflow:
self.MACSE_settings = QSettings(
self.thisPath + '/settings/MACSE_settings.ini',
QSettings.IniFormat)
else:
self.MACSE_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.MACSE_settings.beginGroup("Workflow")
self.MACSE_settings.beginGroup("temporary")
self.MACSE_settings.beginGroup('MACSE')
# File only, no fallback to registry or or.
self.MACSE_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.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
self.comboBox_5.installEventFilter(self)
self.comboBox_7.installEventFilter(self)
self.log_gui = self.gui4Log()
# self.pushButton_2.clicked.connect(print)
self.doubleSpinBox_5.valueChanged.connect(self.judgeStopCost)
self.doubleSpinBox.valueChanged.connect(self.judgeStopCost)
self.doubleSpinBox_2.valueChanged.connect(self.judgeStoplrCost)
self.doubleSpinBox_6.valueChanged.connect(self.judgeStoplrCost)
self.comboBox_5.itemRemovedSig.connect(self.judgeCombobox5)
self.checkBox_2.toggled.connect(self.controlRefineText)
self.emptySig.connect(self.popup_MACSE_exception)
self.interrupt = False
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
action = QAction(QIcon(":/picture/resourses/terminal-512.png"),
"View | Edit command",
menu,
triggered=self.showCMD)
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(action)
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-3-1-Brief-example"
)))
