def identify(self):
idx=self.acTree.selectedIndexes()[0]
if not idx.isValid():
print "Error, index is not valid"
return
p = idx.parent()
if p.data().toString() in ("fragments/adducts:","isotopic cluster:"):
p = idx.parent().parent().parent()
sample=self.currentSample[1 if self.acTree is self.view.treeView_2 else 2]#self.model.sample(p.data().toString(), fullNameEntry=False)
if sample is None:
print "Error, sample not found %s"%sample.shortName()
return
#data=None
if len(idx.data().toString().split('/')) > 2:
data=idx.data().toString().split('/')[:-1]
else:
data=idx.data().toString().split('/')
peak=sample.peakAt(*map(float, data))
if peak is None:
self.view.showErrorMessage("Error", "Unable to find the corresponding peak...")
spl=MSSampleList()
s=MSSample("None")
s.rawPeaks=MSPeakList([peak], sample=s)
spl.addSample(s)
dial=MSIdentificationDialog(parent=self.view)
dial.setAttribute(Qt.WA_DeleteOnClose)
controller=MSIdentificationController(spl, dial, False, showDirectResult=True)
def merge(filenames):
sampleList = MSSampleList(kind='MRM')
n = [s.split('-')[-1].split('.')[0][1:] for s in filenames]
print n
for f in filenames:
s = MSSample(os.path.normcase(f), kind='MRM')
s.loadMZXMLData()
sampleList.append(s)
mergedSampleName = "-".join(n) + ".mzXML"
createMergedXml(mergedSampleName, sampleList)
def merge(filenames):
sampleList = MSSampleList(kind='MRM')
n = [s.split('-')[-1].split('.')[0][1:] for s in filenames]
print n
for f in filenames:
s = MSSample(os.path.normcase(f), kind='MRM')
s.loadMZXMLData()
sampleList.append(s)
mergedSampleName = "-".join(n)+".mzXML"
createMergedXml(mergedSampleName, sampleList)
def getElementsToPlot(self,
flags="chroma",
prec=None,
rt=None,
index=None):
"""
think about giving only index;should be lot simpler
flags:
@chroma: TIC in FACT for both MRM and highRes
@peak: peak return Eic objects...
@spectra: return spectra objects
"""
if flags == "chroma":
return [spl.chroma[0] for spl in self.model if spl.checked]
elif flags == 'peak':
return MSSampleList([spl for spl in self.model
if spl.checked]).peakGroup(prec, rt)
elif flags == 'spectra':
if index is not None:
l = []
for spl in self.model:
try:
#if qApp.instance().lowMemory:
# l.append(spl.loadSpectrum(index))
#else:
l.append(spl.spectra[index])
except IndexError:
pass
return l
def identify(self):
idx = self.acTree.selectedIndexes()[0]
if not idx.isValid():
print "Error, index is not valid"
return
p = idx.parent()
if p.data().toString() in ("fragments/adducts:", "isotopic cluster:"):
p = idx.parent().parent().parent()
sample = self.currentSample[
1 if self.acTree is self.view.treeView_2 else
2] #self.model.sample(p.data().toString(), fullNameEntry=False)
if sample is None:
print "Error, sample not found %s" % sample.shortName()
return
#data=None
if len(idx.data().toString().split('/')) > 2:
data = idx.data().toString().split('/')[:-1]
else:
data = idx.data().toString().split('/')
peak = sample.peakAt(*map(float, data))
if peak is None:
self.view.showErrorMessage(
"Error", "Unable to find the corresponding peak...")
spl = MSSampleList()
s = MSSample("None")
s.rawPeaks = MSPeakList([peak], sample=s)
spl.addSample(s)
dial = MSIdentificationDialog(parent=self.view)
dial.setAttribute(Qt.WA_DeleteOnClose)
controller = MSIdentificationController(spl,
dial,
False,
showDirectResult=True)
def buildGui(self):
STEP = 4
#if self.showSplash:
self.splash.showMessage((u'Loading core objects...'),
Qt.AlignCenter | Qt.AlignBottom, Qt.black)
from core.MetObjects import MSSampleList
self.model = MSSampleList()
from pluginmanager.MetPluginFactory import MSPluginManager
self.pluginManager = MSPluginManager(self)
plugs = self.pluginManager.getAvailablePlugins()
self.splash.showMessage((u'Loading task manager...'),
Qt.AlignCenter | Qt.AlignBottom, Qt.black)
from controller.MetBaseControl import MSTaskManager
self.taskManager = MSTaskManager()
self.splash.setValue(100. / STEP)
#if self.showSplash:
self.splash.showMessage((u'Loading gui files...'),
Qt.AlignCenter | Qt.AlignBottom, Qt.black)
from gui.MetMainGui import MSMainWindow
self.view = MSMainWindow(plugs)
def closeEvent(e):
self.writeSettings()
e.accept()
self.view.closeEvent = closeEvent
self.view.setWindowIcon(
QIcon(QPixmap(path.normcase("gui/icons/deluge.png"))))
self.view.setWindowTitle(u' '.join(
[self.APPLICATION_NAME_STR, self.VERSION_STR]))
self.splash.setValue(2 * (100. / STEP))
#if self.showSplash:
self.splash.showMessage((u'Loading controllers...'),
Qt.AlignCenter | Qt.AlignBottom, Qt.black)
from controller.MetDockWidgetControl import MSDockController
from controller.MetMenuBarControl import MSMenuController
from controller.MetMdiControl import MSMdiAreaController
self.menuControl = MSMenuController(self.model, self.view)
self.dockControl = MSDockController(self.model, self.view)
self.mdiControl = MSMdiAreaController(self.model, self.view)
self.splash.setValue(3 * (100. / STEP))
#if self.showSplash:
#self.splash.showMessage((u'Loading plugins...'), Qt.AlignCenter|Qt.AlignBottom, Qt.black)
#the following allow to delete threads and controllers
#it is very important ;)
#self.connect(self, SIGNAL('deleteLastController()'), self.taskManager.deleteController)
self.splash.setValue(4 * (100. / STEP))
self.splash.showMessage((u'Loading last parameters...'),
Qt.AlignCenter | Qt.AlignBottom, Qt.black)
if self.settings.value("fullScreen", True).toBool():
self.view.showMaximized()
else:
self.view.resize(
self.settings.value("size", QSize(600, 600)).toSize())
self.view.move(
self.settings.value("pos", QPoint(200, 200)).toPoint())
self.view.show()
self.splash.finish(self.view)
