Clirr Results
The following document contains the results of Clirr.
- Current Version: 1.3.2
- Comparison Version: 1.3.0
Summary
| Severity | Number |
|---|---|
| Error | 83 |
| Warning | 0 |
(The results have been filtered to omit less severe results)
Details
| Severity | Message | Class | Method / Field |
|---|---|---|---|
| Class maltcms.commands.fragments2d.peakfinding.PeakSeparator removed | maltcms.commands.fragments2d.peakfinding.PeakSeparator | ||
| Class maltcms.commands.fragments2d.peakfinding.QualityControl removed | maltcms.commands.fragments2d.peakfinding.QualityControl | ||
| Class maltcms.commands.fragments2d.peakfinding.Reliability removed | maltcms.commands.fragments2d.peakfinding.Reliability | ||
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public boolean canEqual(java.lang.Object) | |
| Method 'public maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit getBbh()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit getBbh() | |
| Method 'public java.lang.String getBbhClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getBbhClass() | |
| Method 'public java.lang.String getExportClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getExportClass() | |
| Method 'public maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification getIdentification()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification getIdentification() | |
| Method 'public java.lang.String getIdentificationClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getIdentificationClass() | |
| Method 'public java.lang.String getIntegrationClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getIntegrationClass() | |
| Return type of method 'public maltcms.commands.fragments2d.peakfinding.PeakSeparator getPeakSeparator()' has been changed to maltcms.commands.fragments2d.peakfinding.srg.IPeakSeparator | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public maltcms.commands.fragments2d.peakfinding.PeakSeparator getPeakSeparator() | |
| Method 'public java.lang.String getPickingClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getPickingClass() | |
| Method 'public java.lang.String getScanAcquTime1DVar()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getScanAcquTime1DVar() | |
| Method 'public java.lang.String getSecondColumnTimeVar()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getSecondColumnTimeVar() | |
| Method 'public double getSecondSeedMinDistance()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public double getSecondSeedMinDistance() | |
| Method 'public maltcms.math.functions.IScalarArraySimilarity getSimilaritySecondRun()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public maltcms.math.functions.IScalarArraySimilarity getSimilaritySecondRun() | |
| Method 'public java.lang.String getSrgClass()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public java.lang.String getSrgClass() | |
| Method 'public boolean isDoBBH()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public boolean isDoBBH() | |
| Method 'public boolean isSecondRun()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public boolean isSecondRun() | |
| Method 'public boolean isSeedNotInRegion()' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public boolean isSeedNotInRegion() | |
| Method 'public void setBbh(maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setBbh(maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit) | |
| Method 'public void setBbhClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setBbhClass(java.lang.String) | |
| Method 'public void setDoBBH(boolean)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setDoBBH(boolean) | |
| Method 'public void setExportClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setExportClass(java.lang.String) | |
| Method 'public void setIdentification(maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setIdentification(maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification) | |
| Method 'public void setIdentificationClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setIdentificationClass(java.lang.String) | |
| Method 'public void setIntegrationClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setIntegrationClass(java.lang.String) | |
| Parameter 1 of 'public void setPeakSeparator(maltcms.commands.fragments2d.peakfinding.PeakSeparator)' has changed its type to maltcms.commands.fragments2d.peakfinding.srg.IPeakSeparator | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setPeakSeparator(maltcms.commands.fragments2d.peakfinding.PeakSeparator) | |
| Method 'public void setPickingClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setPickingClass(java.lang.String) | |
| Method 'public void setScanAcquTime1DVar(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setScanAcquTime1DVar(java.lang.String) | |
| Method 'public void setSecondRun(boolean)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setSecondRun(boolean) | |
| Method 'public void setSecondSeedMinDistance(double)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setSecondSeedMinDistance(double) | |
| Method 'public void setSeedNotInRegion(boolean)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setSeedNotInRegion(boolean) | |
| Method 'public void setSimilaritySecondRun(maltcms.math.functions.IScalarArraySimilarity)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setSimilaritySecondRun(maltcms.math.functions.IScalarArraySimilarity) | |
| Method 'public void setSrgClass(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing | public void setSrgClass(java.lang.String) | |
| Class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing$PeakAreaComparator removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing$PeakAreaComparator | ||
| Class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing$PeakComparator removed | maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing$PeakComparator | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools removed | maltcms.commands.fragments2d.peakfinding.bbh.BBHTools | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit removed | maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit removed | maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit removed | maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit removed | maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D removed | maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D | ||
| Class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique removed | maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique | ||
| Method 'public void exportBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List)' has been removed | maltcms.commands.fragments2d.peakfinding.output.IPeakExporter | public void exportBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List) | |
| Method 'public void exportBBHMultipleAlignmentRT(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List)' has been removed | maltcms.commands.fragments2d.peakfinding.output.IPeakExporter | public void exportBBHMultipleAlignmentRT(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List) | |
| Method 'public void exportDetailedBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List, java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.output.IPeakExporter | public void exportDetailedBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List, java.lang.String) | |
| Method 'public void exportPeakOccurrenceMap(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.output.IPeakExporter | public void exportPeakOccurrenceMap(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.lang.String) | |
| In method 'public void exportPeaksToMSP(java.lang.String, java.util.List, maltcms.datastructures.caches.IScanLine)' the number of arguments has changed | maltcms.commands.fragments2d.peakfinding.output.IPeakExporter | public void exportPeaksToMSP(java.lang.String, java.util.List, maltcms.datastructures.caches.IScanLine) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public boolean canEqual(java.lang.Object) | |
| Method 'public void exportBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List)' has been removed | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public void exportBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List) | |
| Method 'public void exportBBHMultipleAlignmentRT(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List)' has been removed | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public void exportBBHMultipleAlignmentRT(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List) | |
| Method 'public void exportDetailedBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List, java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public void exportDetailedBBHInformation(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.util.List, java.lang.String) | |
| Method 'public void exportPeakOccurrenceMap(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public void exportPeakOccurrenceMap(java.util.List, java.util.List, maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit, java.util.List, java.lang.String) | |
| In method 'public void exportPeaksToMSP(java.lang.String, java.util.List, maltcms.datastructures.caches.IScanLine)' the number of arguments has changed | maltcms.commands.fragments2d.peakfinding.output.PeakExporter | public void exportPeaksToMSP(java.lang.String, java.util.List, maltcms.datastructures.caches.IScanLine) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.output.PeakIdentification | public boolean canEqual(java.lang.Object) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.output.PeakIntegration | public boolean canEqual(java.lang.Object) | |
| Class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization removed | maltcms.commands.fragments2d.peakfinding.output.PeakNormalization | ||
| Parameter 1 of 'public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking | public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment) | |
| Parameter 1 of 'public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking | public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking | public boolean canEqual(java.lang.Object) | |
| Parameter 1 of 'public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking | public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment) | |
| Parameter 1 of 'public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking | public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking | public boolean canEqual(java.lang.Object) | |
| Parameter 1 of 'public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking | public java.util.List findPeaks(cross.datastructures.fragments.IFileFragment) | |
| Parameter 1 of 'public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking | public java.util.List findPeaksNear(cross.datastructures.fragments.IFileFragment, java.awt.Point, int, int) | |
| Parameter 3 of 'public java.util.List getAreasFor(java.util.List, cross.datastructures.fragments.IFileFragment, maltcms.datastructures.caches.IScanLine)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing | public java.util.List getAreasFor(java.util.List, cross.datastructures.fragments.IFileFragment, maltcms.datastructures.caches.IScanLine) | |
| Method 'public java.util.List getIntensities()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing | public java.util.List getIntensities() | |
| Method 'public double getMinDist()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing | public double getMinDist() | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public boolean canEqual(java.lang.Object) | |
| Parameter 3 of 'public java.util.List getAreasFor(java.util.List, cross.datastructures.fragments.IFileFragment, maltcms.datastructures.caches.IScanLine)' has changed its type to maltcms.datastructures.ms.IChromatogram2D | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public java.util.List getAreasFor(java.util.List, cross.datastructures.fragments.IFileFragment, maltcms.datastructures.caches.IScanLine) | |
| Method 'public java.util.List getHold()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public java.util.List getHold() | |
| Return type of method 'public java.util.List getIntensities()' has been changed to ucar.ma2.ArrayDouble$D1 | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public java.util.List getIntensities() | |
| Method 'public double getMinDist()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public double getMinDist() | |
| Method 'public java.lang.String getSecondScanIndexVar()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public java.lang.String getSecondScanIndexVar() | |
| Method 'public maltcms.datastructures.caches.IScanLine getSlc()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public maltcms.datastructures.caches.IScanLine getSlc() | |
| Method 'public java.lang.String getUsedMassValuesVar()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public java.lang.String getUsedMassValuesVar() | |
| Method 'public boolean isFilterMS()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public boolean isFilterMS() | |
| Method 'public boolean isUseAlternativFiltering()' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public boolean isUseAlternativFiltering() | |
| Method 'public void setHold(java.util.List)' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public void setHold(java.util.List) | |
| Method 'public void setSecondScanIndexVar(java.lang.String)' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public void setSecondScanIndexVar(java.lang.String) | |
| Method 'public void setSlc(maltcms.datastructures.caches.IScanLine)' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public void setSlc(maltcms.datastructures.caches.IScanLine) | |
| Method 'public void setUseAlternativFiltering(boolean)' has been removed | maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing | public void setUseAlternativFiltering(boolean) |