ccpn.AnalysisMetabolomics package

Module Documentation here

Submodules

ccpn.AnalysisMetabolomics.AnalysisMetabolomics module

class ccpn.AnalysisMetabolomics.AnalysisMetabolomics.Metabolomics(applicationName, applicationVersion, commandLineArguments)[source]

Bases: ccpn.framework.Framework.Framework

Root class for Metabolomics application

setupMenus()[source]
showDecompositionModule()[source]
showPipeline(position='bottom', relativeTo=None)[source]

ccpn.AnalysisMetabolomics.Decomposition module

class ccpn.AnalysisMetabolomics.Decomposition.Decomposition(application, presenter=None)[source]

Bases: object

buildSourceData()[source]
center()[source]
centering

- None, mutable -

decompose()[source]
getSourceData()[source]
loadings

- None, immutable -

method

- None, mutable -

normalization

- None, mutable -

normalize()[source]
presenter

- None, mutable -

refreshSourceDataOptions(*args)[source]
registerNotifiers()[source]
saveLoadingsToSpectra(prefix='test_pca', descale=True, components=None)[source]
scale()[source]
scaling

- None, mutable -

scores

- None, immutable -

setAvailablePlotData()[source]
sources

- None, mutable -

ccpn.AnalysisMetabolomics.GuiPipeLine module

Module Documentation here

class ccpn.AnalysisMetabolomics.GuiPipeLine.AlignSpectra(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.AlignToReference(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
setPositions(positions)[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]
updateRegion()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.Bin(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.Centre(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeBaselinePoints(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
lineMoved(box, linePoint)[source]
setLinePosition(linePoint, pointBox)[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.ExcludeSignalFreeRegions(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.NormaliseSpectra(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.PolyBaseline(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
lineMoved(line)[source]
setPositions(positions)[source]
setValueInValueList()[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]
updateLayout(value=None)[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.Scale(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.SegmentalAlign(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
setPositions(positions)[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerBaseline(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
setPositions(positions)[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]
class ccpn.AnalysisMetabolomics.GuiPipeLine.WhittakerSmooth(parent, project, spectra=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
setPositions(positions)[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]

ccpn.AnalysisMetabolomics.IntegralAssignment module

Module Documentation here

class ccpn.AnalysisMetabolomics.IntegralAssignment.Integral(integralId, range, slope, bias, area)[source]

Bases: object

class ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralAssignment(parent=None)[source]

Bases: PyQt4.QtGui.QWidget

assignAndMove()[source]
assignIntegral()[source]
deassignAndMove()[source]
deassignIntegral()[source]
fillSubstanceTable(value)[source]
class ccpn.AnalysisMetabolomics.IntegralAssignment.IntegralTable(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget

integralCallback()[source]
class ccpn.AnalysisMetabolomics.IntegralAssignment.Substance(name, atom, cs)[source]

Bases: object

class ccpn.AnalysisMetabolomics.IntegralAssignment.SubstanceTable(parent=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

setSubstancename(substance, value)[source]
substanceCallback()[source]

ccpn.AnalysisMetabolomics.Integration module

Module Documentation here

class ccpn.AnalysisMetabolomics.Integration.IntegrationTable(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

setupAreaView()[source]
setupSpectralView()[source]
class ccpn.AnalysisMetabolomics.Integration.IntegrationWidget(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

getParams()[source]
setPositions(positions)[source]
tableCallback()[source]
togglePicking()[source]
turnOffPositionPicking()[source]
turnOnPositionPicking()[source]

ccpn.AnalysisMetabolomics.MetabolomicsPipeline module

Module Documentation here

class ccpn.AnalysisMetabolomics.MetabolomicsPipeline.GoArea(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget

currentSpectrumGroup()[source]
renamePipeline()[source]
class ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MetabolomicsModule(parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.Module.CcpnModule, ccpn.ui.gui.widgets.Base.Base

runPipeline()[source]
updatePipeline()[source]
class ccpn.AnalysisMetabolomics.MetabolomicsPipeline.MyThread[source]

Bases: PyQt4.QtCore.QThread

run()[source]
updated
class ccpn.AnalysisMetabolomics.MetabolomicsPipeline.PipelineWidgets(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget

addMethod(selected)[source]
addRow()[source]

This function will add a new Pipelinewidgets obj in the next row below the clicked button.

disableAddButton(items)[source]

If there is empty row with no method selected, will disable all the addButtons in each other row

enableAddButton(items)[source]

If a method is selected, will enable all the addButtons in each other row

moveRowDown()[source]

obj as above objLayout is the main parent layout (VLayout)

moveRowUp()[source]

obj => sender = button, parent1= buttonList, parent2= GroupBox1, parent3=PipelineWidgets obj objLayout is the main parent layout (VLayout)

removeRow()[source]

This function will remove the Pipelinewidgets selected from the main parent layout (VLayout)

updateLayout()[source]

ccpn.AnalysisMetabolomics.PeakAssignment module

Module Documentation here

class ccpn.AnalysisMetabolomics.PeakAssignment.PeakAssignment(parent=None, project=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

assignAndMove()[source]
assignPeak()[source]
callback()[source]
deassignAndMove()[source]
deassignPeak()[source]
class ccpn.AnalysisMetabolomics.PeakAssignment.Substance(substance, atom, cs)[source]

Bases: object

class ccpn.AnalysisMetabolomics.PeakAssignment.SubstanceTable(parent=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

substanceCallback()[source]

ccpn.AnalysisMetabolomics.PickandFit module

Module Documentation here

class ccpn.AnalysisMetabolomics.PickandFit.AutoPick(parent=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

updateLayout()[source]
class ccpn.AnalysisMetabolomics.PickandFit.Fit(parent=None, strip=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

updateLayout()[source]
class ccpn.AnalysisMetabolomics.PickandFit.PickandFit(parent=None, strip=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

class ccpn.AnalysisMetabolomics.PickandFit.PickandFitTable(parent=None, project=None, fitModule=None, **kw)[source]

Bases: PyQt4.QtGui.QWidget, ccpn.ui.gui.widgets.Base.Base

lr1Moved()[source]
lr2Moved()[source]
lr3Moved()[source]
setDashedLineBoundaries()[source]
setRegionLimits()[source]
tableCallback(peak, row: int, col: int)[source]

ccpn.AnalysisMetabolomics.Pipeline module

Module Documentation here

ccpn.AnalysisMetabolomics.Pipeline.alignSpectra(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.alignToReference(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.autoScale(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.bin(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.excludeBaselinePoints(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.excludeRegions(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.excludeSignalFreeRegions(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.meanCentre(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.normalise(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.polyBaseLine(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.scale(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.segmentalAlign(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.whittakerBaseline(self, inputData, **args)[source]
ccpn.AnalysisMetabolomics.Pipeline.whittakerSmooth(self, inputData, **args)[source]