[med-svn] [Git][med-team/microbegps][master] More PyQt5 changes
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 6 11:59:58 BST 2019
Andreas Tille pushed to branch master at Debian Med / microbegps
Commits:
2ad53545 by Andreas Tille at 2019-09-06T10:59:31Z
More PyQt5 changes
- - - - -
1 changed file:
- debian/patches/PyQt5.patch
Changes:
=====================================
debian/patches/PyQt5.patch
=====================================
@@ -37,47 +37,144 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
def __init__(self,mainWindow):
super(Pipeline, self).__init__()
self.mainWindow = mainWindow
-@@ -126,13 +126,13 @@ class Pipeline(QtGui.QWidget):
- sublayout = QtGui.QHBoxLayout()
+@@ -101,13 +101,13 @@ class Pipeline(QtGui.QWidget):
+ self.step_visualize]
+ self.currentPipelineThread = None
+
+- recipeLbl = QtGui.QLabel('Pipeline')
+- settingsLbl = QtGui.QLabel('Settings')
++ recipeLbl = QtWidgets.QLabel('Pipeline')
++ settingsLbl = QtWidgets.QLabel('Settings')
+
+- self.recipeList = QtGui.QListWidget()
++ self.recipeList = QtWidgets.QListWidget()
+ itemNames = ['Load Data', 'Raw Filter', 'Calculate Reference Table', 'Quality Filtering', 'Calculate Candidates', 'Visualize Results']
+ for name in itemNames:
+- item = QtGui.QListWidgetItem(self.redIcon,name)
++ item = QtWidgets.QListWidgetItem(self.redIcon,name)
+ item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
+ self.recipeList.addItem(item)
+ self.recipeList.setMinimumWidth(230)
+@@ -116,119 +116,119 @@ class Pipeline(QtGui.QWidget):
+
+
+ # create all settings pages
+- self.settingsBox = QtGui.QStackedWidget()
++ self.settingsBox = QtWidgets.QStackedWidget()
+
+ # page 0: load data
+- self.fileNameEdit = QtGui.QLineEdit()
+- selectButton = QtGui.QPushButton(self.openIcon,'')
++ self.fileNameEdit = QtWidgets.QLineEdit()
++ selectButton = QtWidgets.QPushButton(self.openIcon,'')
+ selectButton.clicked.connect(self.selectDirectory)
+ selectButton.setToolTip('Open directory containing SAM files')
+- sublayout = QtGui.QHBoxLayout()
++ sublayout = QtWidgets.QHBoxLayout()
sublayout.addWidget(self.fileNameEdit,stretch=4)
sublayout.addWidget(selectButton,stretch=1)
- subwidget = QtGui.QWidget()
+ subwidget = QtWidgets.QWidget()
subwidget.setLayout(sublayout)
- layout = QtGui.QGridLayout()
+- layout = QtGui.QGridLayout()
++ layout = QtWidgets.QGridLayout()
layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
- layout.addWidget(QtGui.QLabel('Input Directory'),0,0)
+- layout.addWidget(QtGui.QLabel('Input Directory'),0,0)
++ layout.addWidget(QtWidgets.QLabel('Input Directory'),0,0)
layout.addWidget(subwidget,0,1)
- loadDataWidget = QtGui.QWidget()
+ loadDataWidget = QtWidgets.QWidget()
loadDataWidget.setLayout(layout)
self.settingsBox.addWidget(loadDataWidget)
-@@ -167,7 +167,7 @@ class Pipeline(QtGui.QWidget):
- layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)
- layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)
- layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)
+ # page 1: Raw Filter
+- self.minSupportBox = QtGui.QSpinBox()
++ self.minSupportBox = QtWidgets.QSpinBox()
+ self.minSupportBox.setRange(1,1000000000)
+ self.minSupportBox.setValue(50)
+ self.minSupportBox.setMinimumWidth(100)
+ self.minSupportBox.valueChanged.connect(lambda: self.modifiedSettings(1))
+- self.maxMatchesBox = QtGui.QSpinBox()
++ self.maxMatchesBox = QtWidgets.QSpinBox()
+ self.maxMatchesBox.setRange(2,1000000000)
+ self.maxMatchesBox.setValue(80)
+ self.maxMatchesBox.setMinimumWidth(100)
+ self.maxMatchesBox.valueChanged.connect(lambda: self.modifiedSettings(1))
+- self.maxMappingError = QtGui.QDoubleSpinBox()
++ self.maxMappingError = QtWidgets.QDoubleSpinBox()
+ self.maxMappingError.setDecimals(2)
+ self.maxMappingError.setRange(0,1)
+ self.maxMappingError.setValue(1)
+ self.maxMappingError.setSingleStep(0.05)
+ self.maxMappingError.setMinimumWidth(100)
+ self.maxMappingError.valueChanged.connect(lambda: self.modifiedSettings(1))
+- self.mappingErrorQuantile = QtGui.QDoubleSpinBox()
++ self.mappingErrorQuantile = QtWidgets.QDoubleSpinBox()
+ self.mappingErrorQuantile.setDecimals(2)
+ self.mappingErrorQuantile.setRange(0,1)
+ self.mappingErrorQuantile.setValue(1)
+ self.mappingErrorQuantile.setSingleStep(0.05)
+ self.mappingErrorQuantile.setMinimumWidth(100)
+ self.mappingErrorQuantile.valueChanged.connect(lambda: self.modifiedSettings(1))
+- layout = QtGui.QFormLayout()
++ layout = QtWidgets.QFormLayout()
+ layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+- layout.addRow(QtGui.QLabel('Minimum Genome Support'),self.minSupportBox)
+- layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)
+- layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)
+- layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)
- rawFilterWidget = QtGui.QWidget()
++ layout.addRow(QtWidgets.QLabel('Minimum Genome Support'),self.minSupportBox)
++ layout.addRow(QtWidgets.QLabel('Max. Read Matches'),self.maxMatchesBox)
++ layout.addRow(QtWidgets.QLabel('Max. Read Mapping Error'),self.maxMappingError)
++ layout.addRow(QtWidgets.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)
+ rawFilterWidget = QtWidgets.QWidget()
rawFilterWidget.setLayout(layout)
self.settingsBox.addWidget(rawFilterWidget)
-@@ -191,12 +191,12 @@ class Pipeline(QtGui.QWidget):
- sublayout1 = QtGui.QHBoxLayout()
+ # page 2: Calculate Reference Table
+- self.useIdMapping = QtGui.QRadioButton('No Mapping')
++ self.useIdMapping = QtWidgets.QRadioButton('No Mapping')
+ self.useIdMapping.toggled.connect(lambda: self.modifiedSettings(2))
+- self.useMappingFile = QtGui.QRadioButton('Mapping File')
++ self.useMappingFile = QtWidgets.QRadioButton('Mapping File')
+ self.useMappingFile.toggled.connect(lambda: self.modifiedSettings(2))
+- self.mappingFileEdit = QtGui.QLineEdit()
+- self.useNCBIFiles = QtGui.QRadioButton('NCBI catalog')
++ self.mappingFileEdit = QtWidgets.QLineEdit()
++ self.useNCBIFiles = QtWidgets.QRadioButton('NCBI catalog')
+ self.useNCBIFiles.setChecked(True)
+ self.useNCBIFiles.toggled.connect(lambda: self.modifiedSettings(2))
+- self.NCBICatalogPath = QtGui.QLineEdit('<default>')
++ self.NCBICatalogPath = QtWidgets.QLineEdit('<default>')
+ self.NCBICatalogPath.setToolTip('Clear this field to use the default catalog.')
+- selectButton1 = QtGui.QPushButton(self.openIcon,'')
++ selectButton1 = QtWidgets.QPushButton(self.openIcon,'')
+ selectButton1.clicked.connect(self.selectMappingFile)
+ selectButton1.setToolTip('Load Mapping File')
+- selectButton2 = QtGui.QPushButton(self.openIcon,'')
++ selectButton2 = QtWidgets.QPushButton(self.openIcon,'')
+ selectButton2.clicked.connect(self.selectNCBICatalog)
+ selectButton2.setToolTip('Load NCBI catalog file')
+- sublayout1 = QtGui.QHBoxLayout()
++ sublayout1 = QtWidgets.QHBoxLayout()
sublayout1.addWidget(self.mappingFileEdit,stretch=4)
sublayout1.addWidget(selectButton1,stretch=1)
- subwidget1 = QtGui.QWidget()
+ subwidget1 = QtWidgets.QWidget()
subwidget1.setLayout(sublayout1)
- sublayout2 = QtGui.QHBoxLayout()
+- sublayout2 = QtGui.QHBoxLayout()
++ sublayout2 = QtWidgets.QHBoxLayout()
sublayout2.addWidget(self.NCBICatalogPath,stretch=4)
sublayout2.addWidget(selectButton2,stretch=1)
- subwidget2 = QtGui.QWidget()
+ subwidget2 = QtWidgets.QWidget()
subwidget2.setLayout(sublayout2)
- layout = QtGui.QGridLayout()
+- layout = QtGui.QGridLayout()
++ layout = QtWidgets.QGridLayout()
layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
-@@ -205,7 +205,7 @@ class Pipeline(QtGui.QWidget):
+ layout.addWidget(self.useIdMapping,0,0)
+ layout.addWidget(self.useMappingFile,1,0)
layout.addWidget(subwidget1,1,1)
layout.addWidget(self.useNCBIFiles,2,0)
layout.addWidget(subwidget2,2,1)
@@ -86,51 +183,160 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
referenceTableWidget.setLayout(layout)
self.settingsBox.addWidget(referenceTableWidget)
-@@ -228,7 +228,7 @@ class Pipeline(QtGui.QWidget):
- layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)
- layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)
+ # page 3: Quality Filtering
+- self.minAbsoluteUnique = QtGui.QSpinBox()
++ self.minAbsoluteUnique = QtWidgets.QSpinBox()
+ self.minAbsoluteUnique.setRange(0,1000000000)
+ self.minAbsoluteUnique.setValue(20)
+ self.minAbsoluteUnique.setMinimumWidth(100)
+ self.minAbsoluteUnique.valueChanged.connect(lambda: self.modifiedSettings(3))
+- self.maxHomogeneity = QtGui.QDoubleSpinBox()
++ self.maxHomogeneity = QtWidgets.QDoubleSpinBox()
+ self.maxHomogeneity.setDecimals(3)
+ self.maxHomogeneity.setValue(0.6)
+ self.maxHomogeneity.setRange(0.,1.)
+ self.maxHomogeneity.setSingleStep(0.05)
+ self.maxHomogeneity.setMinimumWidth(100)
+ self.maxHomogeneity.valueChanged.connect(lambda: self.modifiedSettings(3))
+- self.minValidity = QtGui.QDoubleSpinBox()
+- layout = QtGui.QFormLayout()
++ self.minValidity = QtWidgets.QDoubleSpinBox()
++ layout = QtWidgets.QFormLayout()
+ layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+- layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)
+- layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)
++ layout.addRow(QtWidgets.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)
++ layout.addRow(QtWidgets.QLabel('Max. Homogeneity'),self.maxHomogeneity)
- qualFilterWidget = QtGui.QWidget()
+ qualFilterWidget = QtWidgets.QWidget()
qualFilterWidget.setLayout(layout)
self.settingsBox.addWidget(qualFilterWidget)
-@@ -266,7 +266,7 @@ class Pipeline(QtGui.QWidget):
- layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)
- layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)
- layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)
+@@ -239,75 +239,75 @@ class Pipeline(QtGui.QWidget):
+ self.minValidity.setSingleStep(0.05)
+ self.minValidity.setMinimumWidth(100)
+ self.minValidity.valueChanged.connect(lambda: self.modifiedSettings(4))
+- self.coverageSimilarity = QtGui.QDoubleSpinBox()
++ self.coverageSimilarity = QtWidgets.QDoubleSpinBox()
+ self.coverageSimilarity.setDecimals(2)
+ self.coverageSimilarity.setValue(0.2)
+ self.coverageSimilarity.setMinimum(0)
+ self.coverageSimilarity.setSingleStep(0.05)
+ self.coverageSimilarity.setMinimumWidth(100)
+ self.coverageSimilarity.valueChanged.connect(lambda: self.modifiedSettings(4))
+- self.sharedFractionUSR = QtGui.QDoubleSpinBox()
++ self.sharedFractionUSR = QtWidgets.QDoubleSpinBox()
+ self.sharedFractionUSR.setDecimals(2)
+ self.sharedFractionUSR.setValue(0.2)
+ self.sharedFractionUSR.setRange(0.,1.)
+ self.sharedFractionUSR.setSingleStep(0.05)
+ self.sharedFractionUSR.setMinimumWidth(100)
+ self.sharedFractionUSR.valueChanged.connect(lambda: self.modifiedSettings(4))
+- self.sharedFractionAll = QtGui.QDoubleSpinBox()
++ self.sharedFractionAll = QtWidgets.QDoubleSpinBox()
+ self.sharedFractionAll.setDecimals(2)
+ self.sharedFractionAll.setValue(0.6)
+ self.sharedFractionAll.setRange(0.,1.)
+ self.sharedFractionAll.setSingleStep(0.05)
+ self.sharedFractionAll.setMinimumWidth(100)
+ self.sharedFractionAll.valueChanged.connect(lambda: self.modifiedSettings(4))
+- layout = QtGui.QFormLayout()
++ layout = QtWidgets.QFormLayout()
+ layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
+- layout.addRow(QtGui.QLabel('Min. Genome Validity'),self.minValidity)
+- layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)
+- layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)
+- layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)
- extractUSRWidget = QtGui.QWidget()
++ layout.addRow(QtWidgets.QLabel('Min. Genome Validity'),self.minValidity)
++ layout.addRow(QtWidgets.QLabel('Coverage Similarity'),self.coverageSimilarity)
++ layout.addRow(QtWidgets.QLabel('Fraction Shared USR'),self.sharedFractionUSR)
++ layout.addRow(QtWidgets.QLabel('Fraction Shared Reads'),self.sharedFractionAll)
+ extractUSRWidget = QtWidgets.QWidget()
extractUSRWidget.setLayout(layout)
self.settingsBox.addWidget(extractUSRWidget)
-@@ -274,7 +274,7 @@ class Pipeline(QtGui.QWidget):
- self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')
- layout = QtGui.QVBoxLayout()
+ # page 5: Visualize
+- self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')
+- layout = QtGui.QVBoxLayout()
++ self.closeOnFinish = QtWidgets.QCheckBox('Close this window after visualizing results')
++ layout = QtWidgets.QVBoxLayout()
layout.addWidget(self.closeOnFinish)
- visualizeWidget = QtGui.QWidget()
+ visualizeWidget = QtWidgets.QWidget()
visualizeWidget.setLayout(layout)
self.settingsBox.addWidget(visualizeWidget)
-@@ -294,7 +294,7 @@ class Pipeline(QtGui.QWidget):
- consoleLayout = QtGui.QVBoxLayout()
+ # Text boxes
+- self.descriptionText = QtGui.QTextEdit()
++ self.descriptionText = QtWidgets.QTextEdit()
+ self.descriptionText.setReadOnly(True)
+
+- self.consoleText = QtGui.QTextEdit()
++ self.consoleText = QtWidgets.QTextEdit()
+ self.consoleText.setReadOnly(True)
+ consoleFont = self.consoleText.font()
+ consoleFont.setPointSize(self.font().pointSize()-1)
+ self.consoleText.setFont(consoleFont)
+
+ # Progress bar
+- self.progress = QtGui.QProgressBar()
++ self.progress = QtWidgets.QProgressBar()
+
+- consoleLayout = QtGui.QVBoxLayout()
++ consoleLayout = QtWidgets.QVBoxLayout()
consoleLayout.addWidget(self.progress)
consoleLayout.addWidget(self.consoleText)
- consoleWidget = QtGui.QWidget()
+ consoleWidget = QtWidgets.QWidget()
consoleWidget.setLayout(consoleLayout)
- self.runStepBtn = QtGui.QPushButton("Run Step")
-@@ -304,7 +304,7 @@ class Pipeline(QtGui.QWidget):
- buttonLayout = QtGui.QHBoxLayout()
+- self.runStepBtn = QtGui.QPushButton("Run Step")
++ self.runStepBtn = QtWidgets.QPushButton("Run Step")
+ self.runStepBtn.clicked.connect(self.runOneStep)
+- self.runPipelineBtn = QtGui.QPushButton("Run Pipeline")
++ self.runPipelineBtn = QtWidgets.QPushButton("Run Pipeline")
+ self.runPipelineBtn.clicked.connect(self.runPipeline)
+- buttonLayout = QtGui.QHBoxLayout()
++ buttonLayout = QtWidgets.QHBoxLayout()
buttonLayout.addWidget(self.runStepBtn)
buttonLayout.addWidget(self.runPipelineBtn)
- buttonBar = QtGui.QWidget()
+ buttonBar = QtWidgets.QWidget()
buttonBar.setLayout(buttonLayout)
- gridLayout = QtGui.QGridLayout()
+- gridLayout = QtGui.QGridLayout()
++ gridLayout = QtWidgets.QGridLayout()
+ gridLayout.setColumnStretch(0,2)
+ gridLayout.setColumnStretch(1,2)
+ gridLayout.addWidget(recipeLbl,0,0)
+@@ -805,14 +805,14 @@ class Pipeline(QtGui.QWidget):
+ self.stepsDone = min(step-1,self.stepsDone)
+
+ def selectDirectory(self):
+- fname = str(QtGui.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))
++ fname = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))
+ if len(fname):
+ self.pr("Input directory for SAM files: "+fname)
+ self.fileNameEdit.setText(fname)
+ self.modifiedSettings(0)
+
+ def selectMappingFile(self):
+- fname = str(QtGui.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))
++ fname = str(QtWidgets.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))
+ if len(fname):
+ self.pr("Using ID Mapping File "+fname)
+ self.mappingFileEdit.setText(fname)
+@@ -820,7 +820,7 @@ class Pipeline(QtGui.QWidget):
+ self.useMappingFile.setChecked(True)
+
+ def selectNCBICatalog(self):
+- fname = str(QtGui.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))
++ fname = str(QtWidgets.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))
+ if len(fname):
+ self.pr("Using NCBI catalog "+fname)
+ self.NCBICatalogPath.setText(fname)
@@ -871,7 +871,7 @@ class Pipeline(QtGui.QWidget):
self.sharedFractionAll.setValue(settings.get('fraction_shared_all',0.8))
@@ -140,22 +346,31 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
def __init__(self):
super(GPSAnalyzer, self).__init__()
self.initUI()
-@@ -901,19 +901,19 @@ class GPSAnalyzer(QtGui.QMainWindow):
- self.graphicDock = QtGui.QDockWidget('Graphic',self)
- self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+@@ -898,22 +898,22 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ self.pipelineGui = Pipeline(self)
+
+ # Prepare the Docks on the right hand side
+- self.graphicDock = QtGui.QDockWidget('Graphic',self)
+- self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
++ self.graphicDock = QtWidgets.QDockWidget('Graphic',self)
++ self.graphicDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
self.graphicDock.setMinimumSize(450,300)
- self.graphicDock.setTitleBarWidget(QtGui.QWidget())
+ self.graphicDock.setTitleBarWidget(QtWidgets.QWidget())
- self.toolsDock = QtGui.QDockWidget('Tools',self)
- self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+- self.toolsDock = QtGui.QDockWidget('Tools',self)
+- self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
++ self.toolsDock = QtWidgets.QDockWidget('Tools',self)
++ self.toolsDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
self.toolsDock.setMinimumHeight(150)
self.toolsDock.setMaximumHeight(250)
- self.toolsDock.setTitleBarWidget(QtGui.QWidget())
+ self.toolsDock.setTitleBarWidget(QtWidgets.QWidget())
- self.consoleDock = QtGui.QDockWidget('Console',self)
- self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+- self.consoleDock = QtGui.QDockWidget('Console',self)
+- self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
++ self.consoleDock = QtWidgets.QDockWidget('Console',self)
++ self.consoleDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
self.consoleDock.setMinimumHeight(150)
self.consoleDock.setMaximumHeight(450)
- self.consoleDock.setTitleBarWidget(QtGui.QWidget())
@@ -163,7 +378,60 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.graphicDock)
self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.toolsDock)
-@@ -966,7 +966,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+@@ -924,72 +924,72 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ self.figure = plt.figure()
+ self.canvas = FigureCanvas(self.figure)
+
+- self.phyloTreeWidget = QtGui.QTreeWidget()
++ self.phyloTreeWidget = QtWidgets.QTreeWidget()
+ self.phyloTreeWidget.setHeaderHidden(True)
+ self.phyloTreeWidget.setUniformRowHeights(False)
+ self.phyloTreeWidget.setAutoScrollMargin(50)
+- self.phyloTreeWidget.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
+- self.phyloTreeWidget.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
++ self.phyloTreeWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
++ self.phyloTreeWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
+ self.phyloTreeWidget.setMouseTracking(True)
+ self.phyloTreeWidget.itemClicked.connect(self.view_tree_selection)
+ self.phyloTreeWidget.setColumnCount(2)
+ self.phyloTreeWidget.itemCollapsed.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))
+ self.phyloTreeWidget.itemExpanded.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))
+
+- self.graphicsTab = QtGui.QTabWidget()
+- self.graphicsTab.setTabPosition(QtGui.QTabWidget.South)
++ self.graphicsTab = QtWidgets.QTabWidget()
++ self.graphicsTab.setTabPosition(QtWidgets.QTabWidget.South)
+ self.graphicsTab.addTab(self.canvas,"Figure")
+ self.graphicsTab.addTab(self.phyloTreeWidget,"Tree")
+
+ self.graphicDock.setWidget(self.graphicsTab)
+
+ # Fill the Tools Dock
+- self.enablePlottingBox = QtGui.QCheckBox('Draw Graphics')
++ self.enablePlottingBox = QtWidgets.QCheckBox('Draw Graphics')
+ self.enablePlottingBox.setChecked(True)
+- self.enableTaxonomyTree = QtGui.QCheckBox('Interactive Tree')
++ self.enableTaxonomyTree = QtWidgets.QCheckBox('Interactive Tree')
+ self.enableTaxonomyTree.setChecked(True)
+
+- exportFigureQualityLabel = QtGui.QLabel('Image export quality (DPI)')
+- self.exportFigureQuality = QtGui.QSpinBox()
++ exportFigureQualityLabel = QtWidgets.QLabel('Image export quality (DPI)')
++ self.exportFigureQuality = QtWidgets.QSpinBox()
+ self.exportFigureQuality.setMinimum(10)
+ self.exportFigureQuality.setMaximum(1200)
+ self.exportFigureQuality.setValue(150)
+ self.exportFigureQuality.setSingleStep(10)
+
+- showPipelineBtn = QtGui.QPushButton('Show GPS Pipeline')
++ showPipelineBtn = QtWidgets.QPushButton('Show GPS Pipeline')
+ showPipelineBtn.clicked.connect(self.pipelineGui.show)
+
+- toolsGrid = QtGui.QGridLayout()
++ toolsGrid = QtWidgets.QGridLayout()
+ toolsGrid.addWidget(self.enablePlottingBox,0,0)
+ toolsGrid.addWidget(self.enableTaxonomyTree,0,1)
+ toolsGrid.addWidget(exportFigureQualityLabel,1,0)
toolsGrid.addWidget(self.exportFigureQuality,1,1)
toolsGrid.addWidget(showPipelineBtn,2,0)
@@ -171,7 +439,301 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
+ toolsWidget = QtWidgets.QWidget()
toolsWidget.setLayout(toolsGrid)
- self.toolsTab = QtGui.QTabWidget()
+- self.toolsTab = QtGui.QTabWidget()
++ self.toolsTab = QtWidgets.QTabWidget()
+ self.toolsTab.currentChanged.connect(self.show_module_help)
+- self.toolsTab.setTabPosition(QtGui.QTabWidget.South)
++ self.toolsTab.setTabPosition(QtWidgets.QTabWidget.South)
+ self.toolsTab.addTab(toolsWidget,"Settings")
+
+ self.toolsDock.setWidget(self.toolsTab)
+
+ # Fill the Console Dock
+- self.helpText = QtGui.QTextEdit()
++ self.helpText = QtWidgets.QTextEdit()
+ self.helpText.setReadOnly(True)
+- self.consoleText = QtGui.QTextBrowser()
++ self.consoleText = QtWidgets.QTextBrowser()
+ self.consoleText.setReadOnly(True)
+
+- self.textTabs = QtGui.QTabWidget()
+- self.textTabs.setTabPosition(QtGui.QTabWidget.South)
++ self.textTabs = QtWidgets.QTabWidget()
++ self.textTabs.setTabPosition(QtWidgets.QTabWidget.South)
+ self.textTabs.addTab(self.helpText,"Help")
+ self.textTabs.addTab(self.consoleText,"Console")
+ self.consoleDock.setWidget(self.textTabs)
+
+ # Insert the main Tree Widget
+- self.treeView = QtGui.QTreeWidget()
++ self.treeView = QtWidgets.QTreeWidget()
+ self.treeView.setColumnCount(7)
+ self.treeView.setColumnWidth(0,300)
+ self.treeView.setHeaderLabels(['Name','Reads','Unique','Coverage','Validity','Homogeneity','Mapping Error'])
+@@ -998,8 +998,8 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ self.treeView.itemSelectionChanged.connect(self.selection_changed_handler)
+ self.treeView.setUniformRowHeights(False)
+ self.treeView.setAutoScrollMargin(50)
+- self.treeView.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
+- self.treeView.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
++ self.treeView.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
++ self.treeView.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
+ self.treeView.setMinimumWidth(400)
+ self.treeView.setMouseTracking(True)
+ self.treeView.header().setClickable(True)
+@@ -1007,43 +1007,43 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ self.setCentralWidget(self.treeView)
+
+ # New Analysis action
+- new_analysis = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)
++ new_analysis = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)
+ new_analysis.triggered.connect(self.new_analysis)
+
+ # Load Data action
+- load_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)
++ load_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)
+ load_data.triggered.connect(self.load_data)
+
+ # Save Data action
+- save_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)
++ save_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)
+ save_data.triggered.connect(self.save_data)
+
+ # Exit Program action
+- exit_program = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)
++ exit_program = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)
+ exit_program.triggered.connect(self.close)
+
+ # Export iTOL tree
+- export_iTOL_tree = QtGui.QAction('Export Tree to iTOL', self)
++ export_iTOL_tree = QtWidgets.QAction('Export Tree to iTOL', self)
+ export_iTOL_tree.setToolTip('Export a set of files that can be loaded with the online tree visualizer iTOL.')
+ export_iTOL_tree.triggered.connect(self.export_iTOL)
+
+ # Export current graphic
+- export_graphic = QtGui.QAction('Export Figure', self)
++ export_graphic = QtWidgets.QAction('Export Figure', self)
+ export_graphic.setToolTip('Export the figure currently shown in the graphics panel to file.')
+ export_graphic.triggered.connect(self.export_graphic)
+
+ # Show the program information on the console
+- show_program_info = QtGui.QAction('About MicrobeGPS', self)
++ show_program_info = QtWidgets.QAction('About MicrobeGPS', self)
+ show_program_info.setToolTip('Show the program information on the console.')
+ show_program_info.triggered.connect(self.show_program_info)
+
+ # Load online help
+- show_online_help = QtGui.QAction('Online help', self)
++ show_online_help = QtWidgets.QAction('Online help', self)
+ show_online_help.setToolTip('Redirect to the online help of MicrobeGPS.')
+ show_online_help.triggered.connect(self.show_online_help)
+
+ # Show the license on the console
+- show_license = QtGui.QAction('Show License', self)
++ show_license = QtWidgets.QAction('Show License', self)
+ show_license.setToolTip('Show the licensing information on the console.')
+ show_license.triggered.connect(self.show_license)
+
+@@ -1079,18 +1079,18 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ def closeEvent(self, event):
+ if self.saving:
+ quit_msg = "Data saving in progress. Are you sure you want to exit the program? Unsaved data will be lost!"
+- reply = QtGui.QMessageBox.question(self, 'Message',
+- quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
+- if reply == QtGui.QMessageBox.Yes:
++ reply = QtWidgets.QMessageBox.question(self, 'Message',
++ quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
++ if reply == QtWidgets.QMessageBox.Yes:
+ event.accept()
+ self.pipelineGui.close()
+ else:
+ event.ignore()
+ else:
+ quit_msg = "Are you sure you want to exit the program?"
+- reply = QtGui.QMessageBox.question(self, 'Message',
+- quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
+- if reply == QtGui.QMessageBox.Yes:
++ reply = QtWidgets.QMessageBox.question(self, 'Message',
++ quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
++ if reply == QtWidgets.QMessageBox.Yes:
+ event.accept()
+ self.pipelineGui.close()
+ else:
+@@ -1129,7 +1129,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ # find member with most unique reads -> use as representative
+ most_unique = max([(m,grp.members[m].unique) for m in grp.members],key=lambda x:x[1])
+ cand_name = most_unique[0]
+- gr_item = QtGui.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),
++ gr_item = QtWidgets.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),
+ '%i'%grp.reads,'%i'%grp.unique, '%f'%grp.cov, '%f'%grp.max_val,
+ '%f'%grp.cov_homog, '%f'%grp.map_qual],QtCore.Qt.AlignHCenter)
+ gr_item.setIcon(0,candidateIcon)
+@@ -1153,7 +1153,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ for m in sorted_members:
+ mbr = grp.members[m]
+ self.mapq = [min(self.mapq[0],mbr.map_qual),max(self.mapq[1],mbr.map_qual)]
+- m_item = QtGui.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,
++ m_item = QtWidgets.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,
+ '%i'%mbr.unique, '%f'%mbr.coverage, '%f'%mbr.validity,
+ '%f'%mbr.cov_homog, '%f'%mbr.map_qual])
+ m_item.setIcon(0,sequenceIcon)
+@@ -1168,13 +1168,13 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ for i in range(1,m_item.columnCount()):
+ m_item.setTextColor(i,QtCore.Qt.black)
+ # Sub-Item: all reads
+- ar_item = QtGui.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])
++ ar_item = QtWidgets.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])
+ ar_item.i_type = "all reads"
+ # Sub-Item: unique reads
+- ur_item = QtGui.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])
++ ur_item = QtWidgets.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])
+ ur_item.i_type = "unique reads"
+ # Sub-Item: Top Shared Genomes
+- rg_item = QtGui.QTreeWidgetItem(m_item,['Related genomes'])
++ rg_item = QtWidgets.QTreeWidgetItem(m_item,['Related genomes'])
+ rg_item.i_type = "related"
+
+ # Iterate over all items and colorize the fields
+@@ -1182,19 +1182,19 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ for g in range(root.childCount()):
+ group = root.child(g)
+ frac = int(255*(1.-group.unique/float(group.reads)))
+- group.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
++ group.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
+ for m in range(group.childCount()):
+ m_item = group.child(m)
+ frac = 255-int(m_item.unique/float(m_item.reads)*255)
+- m_item.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
++ m_item.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
+ frac = int(255*(1-m_item.validity))
+- m_item.setBackground(4,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
++ m_item.setBackground(4,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
+ frac = int(128.*(m_item.map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
+- m_item.setBackground(6,QtGui.QBrush(QtGui.QColor(127+frac,255-frac,0)))
++ m_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(127+frac,255-frac,0)))
+
+ d_max = math.sqrt(math.log(2/0.05))/math.sqrt(2*m_item.reads)
+ if m_item.cov_homog < d_max:
+- m_item.setBackground(5,QtGui.QBrush(QtGui.QColor(0,0,255)))
++ m_item.setBackground(5,QtWidgets.QBrush(QtWidgets.QColor(0,0,255)))
+ m_item.setTextColor(5,QtCore.Qt.white)
+
+ # Build the taxonomy tree for all observed genomes
+@@ -1216,7 +1216,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ continue
+ if not tid in self.taxid_to_item:
+ # add item to tree if not already found
+- self.taxid_to_item[tid] = QtGui.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])
++ self.taxid_to_item[tid] = QtWidgets.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])
+ par = self.taxid_to_item[tid]
+
+
+@@ -1235,10 +1235,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ for rd in reads:
+ map_qual = reads[rd]
+ num_matches = len(self.reads[rd].matches)
+- rd_item = QtGui.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])
++ rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])
+ rd_item.i_type = "read"
+ frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
+- rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
++ rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+ if item.i_type == "unique reads":
+ ref_name = str(item.parent().text(0))
+ self.pr("Collecting all unique reads for "+ref_name,False)
+@@ -1250,10 +1250,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ reads[rd] = trg.reads[rd][2]
+ for rd in reads:
+ map_qual = reads[rd]
+- rd_item = QtGui.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])
++ rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])
+ rd_item.i_type = "unique read"
+ frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
+- rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
++ rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+ if item.i_type == "read":
+ rd_name = str(item.text(0))
+ self.pr("Collecting all matches of read "+rd_name,False)
+@@ -1263,10 +1263,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ if rd_name in trg.reads:
+ map_qual = trg.reads[rd_name][2]
+ break
+- mt_item = QtGui.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])
++ mt_item = QtWidgets.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])
+ mt_item.i_type = "match"
+ frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
+- mt_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
++ mt_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+ if item.i_type == "match":
+ match_name = str(item.text(0))
+ group_id = self.ref2group[match_name]
+@@ -1292,10 +1292,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ # Sort by size, descending
+ sorted_names = sorted([(d,related[d]) for d in related],key=lambda x:-x[1])
+ for name,shared in sorted_names:
+- mt_item = QtGui.QTreeWidgetItem(item,[name,'%i'%shared])
++ mt_item = QtWidgets.QTreeWidgetItem(item,[name,'%i'%shared])
+ mt_item.i_type = "match"
+ frac = int(255*(1-shared/float(self.references[ref_name].reads)))
+- mt_item.setBackground(1,QtGui.QBrush(QtGui.QColor(255,frac,frac)))
++ mt_item.setBackground(1,QtWidgets.QBrush(QtWidgets.QColor(255,frac,frac)))
+
+
+ def tree_item_clicked_handler(self,item,column):
+@@ -1492,7 +1492,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ # now color the tree
+ for taxid,item in self.taxid_to_item.items():
+ if not taxid == 1:
+- item.setBackground(0,QtGui.QBrush(QtGui.QColor(255,255,255)))
++ item.setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(255,255,255)))
+ item.setText(1,'')
+ if 1 in reads:
+ total_reads = float(len(reads[1]))
+@@ -1501,7 +1501,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ N_reads = len(reads.get(taxid,set()))
+ frac =100+ int((1.-N_reads/total_reads)*155)
+ if taxid in self.taxid_to_item:
+- self.taxid_to_item[taxid].setBackground(0,QtGui.QBrush(QtGui.QColor(frac,frac,255)))
++ self.taxid_to_item[taxid].setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(frac,frac,255)))
+ self.phyloTreeWidget.expandItem(self.taxid_to_item[taxid])
+ self.taxid_to_item[taxid].setText(1,'%i'%N_reads)
+ self.phyloTreeWidget.resizeColumnToContents(0)
+@@ -1613,7 +1613,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ self.pipelineGui.show()
+
+ def save_data(self):
+- fname = str(QtGui.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
++ fname = str(QtWidgets.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
+ if len(fname):
+ if not fname.endswith('.gpsa'):
+ if not '.' in fname:
+@@ -1641,7 +1641,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+
+
+ def load_data(self):
+- dialog = QtGui.QFileDialog(self,'Load Data')
++ dialog = QtWidgets.QFileDialog(self,'Load Data')
+ fname = str(dialog.getOpenFileName(caption='Load Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
+ if len(fname):
+ self.pr("Loading data from file "+fname)
+@@ -1676,7 +1676,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ """ Export the whole tree to files that can be loaded with iTOL.
+ http://itol.embl.de/upload.cgi"""
+ try:
+- outdir = str(QtGui.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))
++ outdir = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))
+ taxonomy.candidates_to_LCA_tree(self.sgroups,self.taxonomy_nodes,self.taxonomy_names,outdir)
+ except Exception as e:
+ self.pr('Error while saving iTOL files: '+e.message)
+@@ -1686,7 +1686,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ def export_graphic(self):
+ """ export the current content of the figure to file. Use the DPI
+ quality specified in exportFigureQuality """
+- dialog = QtGui.QFileDialog(self,'Save Graphic as ...')
++ dialog = QtWidgets.QFileDialog(self,'Save Graphic as ...')
+ fname = str(dialog.getSaveFileName(caption='Save Graphic as ...',filter="Raster Images (*.png *.tiff *.jpg);;Vector Images (*.pdf *.eps)",parent=self))
+ if len(fname) > 0:
+ self.figure.savefig(fname,dpi=self.exportFigureQuality.value())
@@ -1734,7 +1734,7 @@ the LICENSE file shipped with this softw
self.treeView.scrollToItem(sel)
@@ -189,6 +751,29 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
import matplotlib.pyplot as plt
class GPSModule:
+@@ -23,18 +23,18 @@ class GPSModule:
+ self.selectedTaxa = []
+ self.selectedParent = ''
+
+- self.initialAnalysisLabel = QtGui.QLabel('Initial setup')
++ self.initialAnalysisLabel = QtWidgets.QLabel('Initial setup')
+ self.initialAnalysis = QtGui.QPushButton('Scan GPS results')
+ self.initialAnalysis.setToolTip('Run the initial analysis required for the following steps. This may take some time depending on the amount of data.')
+ self.initialAnalysis.clicked.connect(self.initial_analysis)
+
+- self.taxRankBoxLabel = QtGui.QLabel('Select a Taxonomic rank')
++ self.taxRankBoxLabel = QtWidgets.QLabel('Select a Taxonomic rank')
+ self.taxRankBox = QtGui.QComboBox()
+ self.taxRankBox.currentIndexChanged.connect(self.select_tax_rank)
+- self.taxGroupBoxLabel = QtGui.QLabel('Select group')
++ self.taxGroupBoxLabel = QtWidgets.QLabel('Select group')
+ self.taxGroupBox = QtGui.QComboBox()
+ self.taxGroupBox.currentIndexChanged.connect(self.select_taxon)
+- self.taxSelectedText = QtGui.QLabel('Found 0 [Not found]')
++ self.taxSelectedText = QtWidgets.QLabel('Found 0 [Not found]')
+ self.getFromTree = QtGui.QPushButton('Get from tree')
+ self.getFromTree.setToolTip('Use the currently selected taxon from the tree.')
+ self.getFromTree.clicked.connect(self.select_taxon_from_tree)
@@ -56,7 +56,7 @@ class GPSModule:
tabGrid.addWidget(self.getFromTree, 3,1)
tabGrid.addWidget(self.taxSelectedText,4,0)
@@ -206,6 +791,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
from os import linesep
from microbegps import taxonomy
+@@ -21,7 +21,7 @@ class GPSModule:
+ self.exportSupporting.setToolTip('Also export the supporting genomes of each candidate.')
+ self.exportSupporting.setChecked(False)
+
+- columnsLabel = QtGui.QLabel('Columns:')
++ columnsLabel = QtWidgets.QLabel('Columns:')
+
+ self.numReads = QtGui.QCheckBox('Number of Reads')
+ self.numReads.setToolTip('The total number of reads mapped to the candidate/genome.')
@@ -57,7 +57,7 @@ class GPSModule:
tabGrid.addWidget(self.genomeValidity,4,1)
tabGrid.addWidget(self.homogeneity,5,0)
@@ -224,6 +818,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
class GPSModule:
""" This GPS Module implements a search tab, that allows the user to
+@@ -15,7 +15,7 @@ class GPSModule:
+ self.searchText.returnPressed.connect(self.find_reference)
+ self.searchBtn = QtGui.QPushButton('Find Reference')
+ self.searchBtn.clicked.connect(self.find_reference)
+- self.searchRes = QtGui.QListWidget()
++ self.searchRes = QtWidgets.QListWidget()
+ self.searchRes.setMinimumHeight(150)
+ self.searchRes.itemClicked.connect(self.view_search_result)
+
@@ -24,7 +24,7 @@ class GPSModule:
searchGrid.addWidget(self.searchBtn, 0,1)
searchGrid.addWidget(self.searchRes, 1,0,1,2)
@@ -233,6 +836,18 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
searchWidget.setLayout(searchGrid)
GPS.toolsTab.addTab(searchWidget,"Search")
+@@ -38,9 +38,9 @@ class GPSModule:
+ self.searchRes.clear()
+ if len(search_results) > 0:
+ for ref in sorted(search_results):
+- self.searchRes.addItem(QtGui.QListWidgetItem(ref))
++ self.searchRes.addItem(QtWidgets.QListWidgetItem(ref))
+ else:
+- self.searchRes.addItem(QtGui.QListWidgetItem('No matching references found.'))
++ self.searchRes.addItem(QtWidgets.QListWidgetItem('No matching references found.'))
+
+ def view_search_result(self, item):
+ # View the item selected in the search results in the main window
@@ -54,4 +54,4 @@ class GPSModule:
self.GPS.treeView.setCurrentItem(sel)
self.GPS.treeView.expand(self.GPS.treeView.currentIndex())
View it on GitLab: https://salsa.debian.org/med-team/microbegps/commit/2ad535451c262c6835929a5cd5da65e6597992b7
--
View it on GitLab: https://salsa.debian.org/med-team/microbegps/commit/2ad535451c262c6835929a5cd5da65e6597992b7
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