def __init__(self, data, title, flags="chroma", parent=None, **k):
QWidget.__init__(self, parent)
MSDialogController.__init__(self, 0, parent)
self.model = self.qApp.model
self.view = self.qApp.view
self.data = data
self.title = title
self.flags = flags
if self.flags == 'peak':
if self.acTree not in (self.view.treeView_2, self.view.treeView_3):
print "Unknown Error"
return
idx = self.acTree.selectedIndexes()[0]
s = qApp.instance().dockControl.currentSample[
1 if self.acTree is self.view.treeView_2 else 2]
if s is None:
print "unknow error"
return
values = map(float, idx.data().toString().split('/')[:2])
self.currentPeak = s.peakAt(*values)
#connection to update the selected Peak object
self.connect(self.acTree, SIGNAL("changedLine"),
self.updateCurrentPeak)
self.minX, self.maxX, self.maxY = [0] * 3
#if flags != 'peak':
# self.minX, self.maxX, self.maxY = self.getMax()
self.pw = PlotWidget(self.minX, self.maxX, self.maxY, parent=self,
**k) #parent=self,
#self.pw.setAttribute(Qt.WA_DeleteOnClose)#plotItem.setAttribute(Qt.WA_PaintOnScreen & Qt.WA_PaintUnclipped)
if k.get('antialiased', False):
self.pw.setRenderHint(0x01) #antialiasing i suppose
self.pw.setTitle(title)
self.pw.updateGrid()
self._setupUi()
self.connect(self, SIGNAL('linePlotted'), self.updateContextMenu)
self.connect(self.view.sampleTableView,
SIGNAL("disHighlightRequested(QModelIndex)"),
self.disHighlightOne)
self.connect(self.view.sampleTableView,
SIGNAL("highlightRequested(QModelIndex)"), self.highlight)
self.connect(self.view.sampleTableView,
SIGNAL("noHighlightRequested()"), self.disHighlight)
self.connect(self.view.ppmEditer, SIGNAL('valueChanged(double)'),
self.redrawAll)
self.drawnItems = {}
self.trashItems = [] #why unecessary? nope to collect annotation stuff
self.textLabels = []
self.pixmaps = []
self.dataPoints = None
self._plotting(self.data) #initial plotting
def __init__(self,lspl, win, creation):
MSDialogController.__init__(self, lspl, win, creation)
QObject.connect(self.view.lineEdit, SIGNAL("textChanged(const QString &)"), self.checkLineEdit)
if paramikoSupport:
try:
QObject.connect(self.view.parallel, SIGNAL("clicked()"), self.showSSHConnect)
except AttributeError:
pass
self.checkLineEdit("")
self.view.exec_()
def setModels(self):
"""Add the model to the view when the thread ended"""
if self.showDirectResult:
table = QTableView()
view = MSTableView(table, model=self.buildModel(self.sampleList[0].rawPeaks[0]), selection=True)
self.qApp.view.addMdiSubWindow(view, "identification of mapped peaks of %s"%self.sampleList[0].shortName())
currentSample = self.qApp.dockControl.currentSample[2]
if currentSample is not None:
MSDialogController.actualizeClusterModel(currentSample)
self.qApp.view.showInformationMessage("Job Done", "Identification is done !")
def startTask(self):
"""
Main Function
"""
MSDialogController.startTask(self)
self.task= MSIdThread(self.sampleList, **self.parameters)
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'), self.task.begin)
QObject.connect(self.task, SIGNAL("started()"),self.qApp.view.to_indetermined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.qApp.view.to_determined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
self.view.close()
def __init__(self, lspl, win, creation):
MSDialogController.__init__(self, lspl, win, creation)
QObject.connect(self.view.lineEdit,
SIGNAL("textChanged(const QString &)"),
self.checkLineEdit)
if paramikoSupport:
try:
QObject.connect(self.view.parallel, SIGNAL("clicked()"),
self.showSSHConnect)
except AttributeError:
pass
self.checkLineEdit("")
self.view.exec_()
def __init__(self, data, title, flags="chroma", parent=None, **k):
QWidget.__init__(self, parent)
MSDialogController.__init__(self, 0, parent)
self.model = self.qApp.model
self.view = self.qApp.view
self.data=data
self.title=title
self.flags=flags
if self.flags == 'peak':
if self.acTree not in (self.view.treeView_2, self.view.treeView_3):
print "Unknown Error"
return
idx=self.acTree.selectedIndexes()[0]
s = qApp.instance().dockControl.currentSample[1 if self.acTree is self.view.treeView_2 else 2]
if s is None:
print "unknow error"
return
values = map(float, idx.data().toString().split('/')[:2])
self.currentPeak = s.peakAt(*values)
#connection to update the selected Peak object
self.connect(self.acTree, SIGNAL("changedLine"), self.updateCurrentPeak)
self.minX, self.maxX, self.maxY = [0] * 3
#if flags != 'peak':
# self.minX, self.maxX, self.maxY = self.getMax()
self.pw = PlotWidget(self.minX, self.maxX, self.maxY, parent=self, **k)#parent=self,
#self.pw.setAttribute(Qt.WA_DeleteOnClose)#plotItem.setAttribute(Qt.WA_PaintOnScreen & Qt.WA_PaintUnclipped)
if k.get('antialiased', False):
self.pw.setRenderHint(0x01)#antialiasing i suppose
self.pw.setTitle(title)
self.pw.updateGrid()
self._setupUi()
self.connect(self, SIGNAL('linePlotted'), self.updateContextMenu)
self.connect(self.view.sampleTableView, SIGNAL("disHighlightRequested(QModelIndex)"), self.disHighlightOne)
self.connect(self.view.sampleTableView, SIGNAL("highlightRequested(QModelIndex)"), self.highlight)
self.connect(self.view.sampleTableView, SIGNAL("noHighlightRequested()"), self.disHighlight)
self.connect(self.view.ppmEditer, SIGNAL('valueChanged(double)'), self.redrawAll)
self.drawnItems = {}
self.trashItems=[]#why unecessary? nope to collect annotation stuff
self.textLabels = []
self.pixmaps = []
self.dataPoints = None
self._plotting(self.data)#initial plotting
def __init__(self, lspl, visu, creation, showDirectResult=False):
"""
constructor
"""
#data needed to process
MSDialogController.__init__(self, lspl, visu, creation)
self.databases ={"KEGG":None,
"METJP":None,
"BIOCYC":None,
"METEXPLORE":None}
QObject.connect(self.view.checkBox_8, SIGNAL('toggled(bool)'), self._update)
self._update(True)#initializing to metexplore so we keep enabled
self.showDirectResult = showDirectResult
self.view.exec_()
def showClusterTable(self):
if not self.view.sampleTableView.selectedIndexes(
): #not self.acTree.selectedIndexes():
s, b = QInputDialog.getItem(
self.view, "Select one sample", "Select one sample :",
[spl.shortName() for spl in self.model])
if not b:
return
sample = self.model.sample(str(s), fullNameEntry=False)
else:
idx = self.view.sampleTableView.selectedIndexes()[0]
sample = self.model.sample(idx.data().toString(),
fullNameEntry=False)
if sample is None:
print("sample not found...")
return
if not sample.mappedPeaks:
self.view.showErrorMessage(
"No peaks found",
"This sample does not have peaks, please do peak picking before"
)
view = QTableView()
view.setSortingEnabled(True)
view.horizontalHeader().setStretchLastSection(True)
view.setModel(
MSDialogController.getSampleModel(sample, flags='cluster'))
self.view.addMdiSubWindow(view,
"ClusterList of%s" % str(sample.shortName()))
def showPeakTable(self):
"""
TODO: write little function to check if sample is None or good
or write exception with good code
"""
if not self.view.sampleTableView.selectedIndexes(
): #not self.acTree.selectedIndexes():
s, b = QInputDialog.getItem(
self.view, "Select one sample", "Select one sample :",
[spl.shortName() for spl in self.model])
if not b:
return
sample = self.model.sample(str(s), fullNameEntry=False)
else:
idx = self.view.sampleTableView.selectedIndexes()[0]
sample = self.model.sample(idx.data().toString(),
fullNameEntry=False)
if sample is None:
print("sample not found...")
return
if not sample.rawPeaks:
self.view.showErrorMessage(
"No peaks found",
"This sample does not have peaks, please do peak picking before"
)
view = QTableView()
view.horizontalHeader().setStretchLastSection(True)
view.setSortingEnabled(True)
model = MSDialogController.getSampleModel(sample, flags='peak')
view.setModel(model)
self.view.addMdiSubWindow(
view, " ".join(["PeakList of",
str(sample.shortName())]))
def startTask(self):
MSDialogController.startTask(self)
self.task = MSIntegrationThread(self.sampleList, **self.parameters)
def begin():
self.view=None
self.task.start()
self.task.exec_()
self.task.begin = begin
#to avoid QObject::killTimers error, wait for the dialog to be deleted
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'), self.task.begin)
QObject.connect(self.task, SIGNAL("started()"),qApp.instance().view.to_indetermined_mode)
QObject.connect(self.task, SIGNAL("finished()"),self.setModels)
QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
self.view.close()
def __init__(self, lspl, visu, creation):
MSDialogController.__init__(self, lspl, visu, creation)
self.polarity=1 #initialisation
if not self.model:
self.goodIdx = 0
else:
self.goodIdx = 0 if self.model[0].kind == 'HighRes' else 1
self.populateTableViews(self.polarity)
self.allAddsChecked = False
self.allFragsChecked = False
QObject.connect(self.view.posmode, SIGNAL('toggled(bool)'), self.updatePolarity)
QObject.connect(self.view.checkAllAdds, SIGNAL('clicked()'), self.checkAdds)
QObject.connect(self.view.checkAllFrags, SIGNAL('clicked()'), self.checkFrags)
self.view.exec_()
def showPeakTable(self):
"""
TODO: write little function to check if sample is None or good
or write exception with good code
"""
if not self.view.sampleTableView.selectedIndexes():#not self.acTree.selectedIndexes():
s, b = QInputDialog.getItem(self.view, "Select one sample", "Select one sample :",
[spl.shortName() for spl in self.model])
if not b:
return
sample = self.model.sample(str(s), fullNameEntry=False)
else:
idx = self.view.sampleTableView.selectedIndexes()[0]
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
print ("sample not found...")
return
if not sample.rawPeaks:
self.view.showErrorMessage("No peaks found",
"This sample does not have peaks, please do peak picking before")
view=QTableView()
view.horizontalHeader().setStretchLastSection(True)
view.setSortingEnabled(True)
model=MSDialogController.getSampleModel(sample, flags='peak')
view.setModel(model)
self.view.addMdiSubWindow(view, " ".join(["PeakList of", str(sample.shortName())]))
def startTask(self):
"""
Main Function (model function) Clustering
"""
MSDialogController.startTask(self)
#qApp.instance().view.showInStatusBar("Clustering Step...Please Wait..", 5000)
self.task = MSClusterThread(self.sampleList, **self.parameters)
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'), self.task.begin)
#self.connect(self.view, SIGNAL('destroyed(QObject *)'), self.setViewToNone)
QObject.connect(self.task, SIGNAL("started()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL('update_pb'), qApp.instance().view.updateProgressBar)
#QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
#print "about to close"
self.view.close()
def setModels(self):
"""
end processing
"""
qApp.instance().view.comparativeTableView.setModel(MSDialogController.actualizePeakModelComparative())
qApp.instance().view.showInformationMessage("Integration Done", "Integration process finished...")
qApp.instance().view.tabWidget.setCurrentIndex(1)
def startTask(self):
"""
Main Function (model function) Clustering
"""
MSDialogController.startTask(self)
#qApp.instance().view.showInStatusBar("Clustering Step...Please Wait..", 5000)
self.task = MSClusterThread(self.sampleList, **self.parameters)
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'),
self.task.begin)
#self.connect(self.view, SIGNAL('destroyed(QObject *)'), self.setViewToNone)
QObject.connect(self.task, SIGNAL("started()"),
qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL('update_pb'),
qApp.instance().view.updateProgressBar)
#QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
#print "about to close"
self.view.close()
def __init__(self, lspl, visu, creation):
MSDialogController.__init__(self, lspl, visu, creation)
self.polarity = 1 #initialisation
if not self.model:
self.goodIdx = 0
else:
self.goodIdx = 0 if self.model[0].kind == 'HighRes' else 1
self.populateTableViews(self.polarity)
self.allAddsChecked = False
self.allFragsChecked = False
QObject.connect(self.view.posmode, SIGNAL('toggled(bool)'),
self.updatePolarity)
QObject.connect(self.view.checkAllAdds, SIGNAL('clicked()'),
self.checkAdds)
QObject.connect(self.view.checkAllFrags, SIGNAL('clicked()'),
self.checkFrags)
self.view.exec_()
def setModels(self):
"""
end processing
"""
qApp.instance().view.comparativeTableView.setModel(
MSDialogController.actualizePeakModelComparative())
qApp.instance().view.showInformationMessage(
"Integration Done", "Integration process finished...")
qApp.instance().view.tabWidget.setCurrentIndex(1)
def startTask(self):
MSDialogController.startTask(self)
self.task = MSIntegrationThread(self.sampleList, **self.parameters)
def begin():
self.view = None
self.task.start()
self.task.exec_()
self.task.begin = begin
#to avoid QObject::killTimers error, wait for the dialog to be deleted
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'),
self.task.begin)
QObject.connect(self.task, SIGNAL("started()"),
qApp.instance().view.to_indetermined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
QObject.connect(self.task, SIGNAL("finished()"),
qApp.instance().view.to_determined_mode)
self.view.close()
def resize():
s = str(d.comboBox.currentText())
min_, max_ = map(float, str(d.lineEdit.text()).split('-'))
d.close()
if s == 'All':
if any([spl.rawPeaks for spl in self.model]):
self.view.showErrorMessage("Error",
"Can not resize sample when peak picking has already been done")
for sample in self.model:
print "Resize %s"%sample.shortName()
sample.resizeSpectraLength(min_, max_)
else:
sample = self.model.sample(s, fullNameEntry=False)
if sample.rawPeaks:
self.view.showErrorMessage("Error",
"Can not resize sample when peak picking has already been done")
sample.resizeSpectraLength(min_, max_)
for tree in (self.view.treeView, self.view.treeView_2, self.view.treeView_3):
tree.removeAll()
for spl in self.model:
MSDialogController.actualizeSpectraModel(spl)
self.view.showInformationMessage("Done", "Resizing has been done !")
def redo(self):
m = QApplication.instance().model
if self.rawData:
m.alignRawData(m)
else:
m.alignPeaksInRTDimension(m, self.polyDegree, self.errorRt)
for tree in (qApp.instance().view.treeView, qApp.instance().view.treeView_2, qApp.instance().view.treeView_3):
tree.removeAll()
for spl in qApp.instance().model:
MSDialogController.actualizeSpectraModel(spl)
if spl.rawPeaks:
MSDialogController.actualizePeakModel(spl)
if spl.mappedPeaks:
MSDialogController.actualizeClusterModel(spl)
qApp.instance().view.showInformationMessage('Alignment calculation done', "Alignment done")
def showClusterTable(self):
if not self.view.sampleTableView.selectedIndexes():#not self.acTree.selectedIndexes():
s, b = QInputDialog.getItem(self.view, "Select one sample", "Select one sample :",
[spl.shortName() for spl in self.model])
if not b:
return
sample = self.model.sample(str(s), fullNameEntry=False)
else:
idx = self.view.sampleTableView.selectedIndexes()[0]
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
print ("sample not found...")
return
if not sample.mappedPeaks:
self.view.showErrorMessage("No peaks found",
"This sample does not have peaks, please do peak picking before")
view= QTableView()
view.setSortingEnabled(True)
view.horizontalHeader().setStretchLastSection(True)
view.setModel(MSDialogController.getSampleModel(sample, flags='cluster'))
self.view.addMdiSubWindow(view, "ClusterList of%s"%str(sample.shortName()))
def actualizeModels(self, idx):
"""
will update several models to fit with the selected
sample
"""
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
self.qApp.view.sampleDockWidget.cursor().setShape(Qt.WaitCursor)
MSDialogController.actualizeSpectraModel(sample)
self.setCurrentSample(sample, 1)
if sample.rawPeaks:
MSDialogController.actualizePeakModel(sample)
self.setCurrentSample(sample, 2)
if sample.mappedPeaks:
MSDialogController.actualizeClusterModel(sample)
self.setCurrentSample(sample, 3)
self.qApp.view.sampleDockWidget.cursor().setShape(Qt.ArrowCursor)
def actualizeModels(self, idx):
"""
will update several models to fit with the selected
sample
"""
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
self.qApp.view.sampleDockWidget.cursor().setShape(Qt.WaitCursor)
MSDialogController.actualizeSpectraModel(sample)
self.setCurrentSample(sample, 1)
if sample.rawPeaks:
MSDialogController.actualizePeakModel(sample)
self.setCurrentSample(sample, 2)
if sample.mappedPeaks:
MSDialogController.actualizeClusterModel(sample)
self.setCurrentSample(sample, 3)
self.qApp.view.sampleDockWidget.cursor().setShape(Qt.ArrowCursor)
