Clirr Results
The following document contains the results of Clirr.
- Current Version: 1.3.2
- Comparison Version: 1.3.0
Summary
| Severity | Number |
|---|---|
| Error | 71 |
| Warning | 0 |
(The results have been filtered to omit less severe results)
Details
| Severity | Message | Class | Method / Field |
|---|---|---|---|
| Class maltcms.datastructures.array.Sparse removed | maltcms.datastructures.array.Sparse | ||
| Method 'public ucar.ma2.Array getMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.AScanLineCache | public ucar.ma2.Array getMassSpectra(java.awt.Point) | |
| Class maltcms.datastructures.caches.CachedScanLineList removed | maltcms.datastructures.caches.CachedScanLineList | ||
| Method 'public ucar.ma2.Array getMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.IScanLine | public ucar.ma2.Array getMassSpectra(int, int) | |
| Method 'public ucar.ma2.Array getMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.IScanLine | public ucar.ma2.Array getMassSpectra(java.awt.Point) | |
| Method 'public ucar.ma2.Array getMassSpectrum(int, int)' has been added to an interface | maltcms.datastructures.caches.IScanLine | public ucar.ma2.Array getMassSpectrum(int, int) | |
| Method 'public ucar.ma2.Array getMassSpectrum(java.awt.Point)' has been added to an interface | maltcms.datastructures.caches.IScanLine | public ucar.ma2.Array getMassSpectrum(java.awt.Point) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.IScanLine | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.IScanLine | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectrum(int, int)' has been added to an interface | maltcms.datastructures.caches.IScanLine | public cross.datastructures.tuple.Tuple2D getSparseMassSpectrum(int, int) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectrum(java.awt.Point)' has been added to an interface | maltcms.datastructures.caches.IScanLine | public cross.datastructures.tuple.Tuple2D getSparseMassSpectrum(java.awt.Point) | |
| In method 'protected ScanLineCache(cross.datastructures.fragments.IFileFragment, int, int)' the number of arguments has changed | maltcms.datastructures.caches.ScanLineCache | protected ScanLineCache(cross.datastructures.fragments.IFileFragment, int, int) | |
| In method 'protected ScanLineCache(cross.datastructures.fragments.IFileFragment)' the number of arguments has changed | maltcms.datastructures.caches.ScanLineCache | protected ScanLineCache(cross.datastructures.fragments.IFileFragment) | |
| Method 'public ucar.ma2.Array getMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.ScanLineCache | public ucar.ma2.Array getMassSpectra(int, int) | |
| Method 'public ucar.ma2.Array getMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.ScanLineCache | public ucar.ma2.Array getMassSpectra(java.awt.Point) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.ScanLineCache | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.ScanLineCache | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point) | |
| Method 'public maltcms.datastructures.caches.IScanLine getCachedListScanLineCache(cross.datastructures.fragments.IFileFragment)' has been removed | maltcms.datastructures.caches.ScanLineCacheFactory | public maltcms.datastructures.caches.IScanLine getCachedListScanLineCache(cross.datastructures.fragments.IFileFragment) | |
| Method 'public maltcms.datastructures.caches.IScanLine getDefaultScanLineCache(cross.datastructures.fragments.IFileFragment)' has been removed | maltcms.datastructures.caches.ScanLineCacheFactory | public maltcms.datastructures.caches.IScanLine getDefaultScanLineCache(cross.datastructures.fragments.IFileFragment) | |
| Method 'public maltcms.datastructures.caches.IScanLine getOldScanLineCache(cross.datastructures.fragments.IFileFragment)' has been removed | maltcms.datastructures.caches.ScanLineCacheFactory | public maltcms.datastructures.caches.IScanLine getOldScanLineCache(cross.datastructures.fragments.IFileFragment) | |
| Class maltcms.datastructures.caches.ScanLineCacheOld removed | maltcms.datastructures.caches.ScanLineCacheOld | ||
| In method 'protected SparseScanLineCache(cross.datastructures.fragments.IFileFragment, int, int)' the number of arguments has changed | maltcms.datastructures.caches.SparseScanLineCache | protected SparseScanLineCache(cross.datastructures.fragments.IFileFragment, int, int) | |
| In method 'protected SparseScanLineCache(cross.datastructures.fragments.IFileFragment)' the number of arguments has changed | maltcms.datastructures.caches.SparseScanLineCache | protected SparseScanLineCache(cross.datastructures.fragments.IFileFragment) | |
| Method 'public ucar.ma2.Array getMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.SparseScanLineCache | public ucar.ma2.Array getMassSpectra(int, int) | |
| Method 'public ucar.ma2.Array getMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.SparseScanLineCache | public ucar.ma2.Array getMassSpectra(java.awt.Point) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int)' has been removed | maltcms.datastructures.caches.SparseScanLineCache | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(int, int) | |
| Method 'public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point)' has been removed | maltcms.datastructures.caches.SparseScanLineCache | public cross.datastructures.tuple.Tuple2D getSparseMassSpectra(java.awt.Point) | |
| Method 'public maltcms.datastructures.caches.IScanLine getScanLineImpl()' has been added to an interface | maltcms.datastructures.ms.IChromatogram2D | public maltcms.datastructures.caches.IScanLine getScanLineImpl() | |
| Method 'public java.awt.geom.Rectangle2D getTimeRange2D()' has been added to an interface | maltcms.datastructures.ms.IChromatogram2D | public java.awt.geom.Rectangle2D getTimeRange2D() | |
| Method 'public double getPrecursorCharge()' has been added to an interface | maltcms.datastructures.ms.IScan | public double getPrecursorCharge() | |
| Method 'public double getPrecursorIntensity()' has been added to an interface | maltcms.datastructures.ms.IScan | public double getPrecursorIntensity() | |
| Method 'public double getPrecursorMz()' has been added to an interface | maltcms.datastructures.ms.IScan | public double getPrecursorMz() | |
| Removed java.io.Externalizable from the set of implemented interfaces | maltcms.datastructures.ms.Scan1D | ||
| Method 'public void readExternal(java.io.ObjectInput)' has been removed | maltcms.datastructures.ms.Scan1D | public void readExternal(java.io.ObjectInput) | |
| Method 'public void writeExternal(java.io.ObjectOutput)' has been removed | maltcms.datastructures.ms.Scan1D | public void writeExternal(java.io.ObjectOutput) | |
| Removed java.io.Externalizable from the set of implemented interfaces | maltcms.datastructures.ms.Scan2D | ||
| Class maltcms.datastructures.peak.Clique removed | maltcms.datastructures.peak.Clique | ||
| Class maltcms.datastructures.peak.FiFoQueue removed | maltcms.datastructures.peak.FiFoQueue | ||
| Class maltcms.datastructures.peak.IBipacePeak removed | maltcms.datastructures.peak.IBipacePeak | ||
| In method 'public void append(cross.datastructures.fragments.IFileFragment, java.util.List, java.util.List, ucar.ma2.Array, java.lang.String, java.lang.String)' the number of arguments has changed | maltcms.datastructures.peak.Peak1D | public void append(cross.datastructures.fragments.IFileFragment, java.util.List, java.util.List, ucar.ma2.Array, java.lang.String, java.lang.String) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.datastructures.peak.Peak1D | public boolean canEqual(java.lang.Object) | |
| Method 'public void setUniqueId(java.util.UUID)' has been removed | maltcms.datastructures.peak.Peak1D | public void setUniqueId(java.util.UUID) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.datastructures.peak.Peak1DGroup | public boolean canEqual(java.lang.Object) | |
| Method 'public java.util.List getNames()' has been removed | maltcms.datastructures.peak.Peak2D | public java.util.List getNames() | |
| Method 'public maltcms.datastructures.peak.Peak2D getReference()' has been removed | maltcms.datastructures.peak.Peak2D | public maltcms.datastructures.peak.Peak2D getReference() | |
| Method 'public int getScanIndex()' has been removed | maltcms.datastructures.peak.Peak2D | public int getScanIndex() | |
| Method 'public double getSim()' has been removed | maltcms.datastructures.peak.Peak2D | public double getSim() | |
| Method 'public void normalizeTo(maltcms.datastructures.peak.Peak2D)' has been removed | maltcms.datastructures.peak.Peak2D | public void normalizeTo(maltcms.datastructures.peak.Peak2D) | |
| Method 'public void setNames(java.util.List)' has been removed | maltcms.datastructures.peak.Peak2D | public void setNames(java.util.List) | |
| Method 'public void setScanIndex(int)' has been removed | maltcms.datastructures.peak.Peak2D | public void setScanIndex(int) | |
| Method 'public boolean addNeighOf(java.awt.Point)' has been removed | maltcms.datastructures.peak.PeakArea2D | public boolean addNeighOf(java.awt.Point) | |
| Class maltcms.datastructures.peak.PeakEdge removed | maltcms.datastructures.peak.PeakEdge | ||
| Class maltcms.datastructures.peak.PeakNG removed | maltcms.datastructures.peak.PeakNG | ||
| In method 'public PeakAnnotation()' the number of arguments has changed | maltcms.datastructures.peak.annotations.PeakAnnotation | public PeakAnnotation() | |
| Accessibility of method 'public PeakAnnotation()' has been decreased from public to package | maltcms.datastructures.peak.annotations.PeakAnnotation | public PeakAnnotation() | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.datastructures.peak.annotations.PeakAnnotation | public boolean canEqual(java.lang.Object) | |
| Method 'public void setDatabase(java.lang.String)' has been removed | maltcms.datastructures.peak.annotations.PeakAnnotation | public void setDatabase(java.lang.String) | |
| Method 'public void setMetabolite(maltcms.datastructures.ms.IMetabolite)' has been removed | maltcms.datastructures.peak.annotations.PeakAnnotation | public void setMetabolite(maltcms.datastructures.ms.IMetabolite) | |
| Method 'public void setScore(double)' has been removed | maltcms.datastructures.peak.annotations.PeakAnnotation | public void setScore(double) | |
| In method 'public RetentionIndexPeakAnnotation()' the number of arguments has changed | maltcms.datastructures.peak.annotations.RetentionIndexPeakAnnotation | public RetentionIndexPeakAnnotation() | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.datastructures.peak.annotations.RetentionIndexPeakAnnotation | public boolean canEqual(java.lang.Object) | |
| Method 'public void setRetentionIndex(double)' has been removed | maltcms.datastructures.peak.annotations.RetentionIndexPeakAnnotation | public void setRetentionIndex(double) | |
| Accessibility of method 'public boolean canEqual(java.lang.Object)' has been decreased from public to protected | maltcms.datastructures.peak.normalization.TicAreaNormalizer | public boolean canEqual(java.lang.Object) | |
| Return type of method 'public maltcms.datastructures.array.Sparse createSparseIndexArray(ucar.ma2.ArrayDouble$D1, ucar.ma2.ArrayDouble$D1, int, int, int, double)' has been changed to ucar.ma2.Sparse | maltcms.tools.ArrayTools | public maltcms.datastructures.array.Sparse createSparseIndexArray(ucar.ma2.ArrayDouble$D1, ucar.ma2.ArrayDouble$D1, int, int, int, double) | |
| In method 'public ucar.ma2.Array normalize(ucar.ma2.Array, ucar.ma2.Array, int, org.slf4j.Logger)' the number of arguments has changed | maltcms.tools.ArrayTools2 | public ucar.ma2.Array normalize(ucar.ma2.Array, ucar.ma2.Array, int, org.slf4j.Logger) | |
| Return type of method 'public maltcms.datastructures.array.Sparse createSparse(cross.datastructures.fragments.IVariableFragment, cross.datastructures.fragments.IVariableFragment, int, int, int, double)' has been changed to ucar.ma2.Sparse | maltcms.tools.MaltcmsTools | public maltcms.datastructures.array.Sparse createSparse(cross.datastructures.fragments.IVariableFragment, cross.datastructures.fragments.IVariableFragment, int, int, int, double) | |
| Class maltcms.tools.PublicMemberGetters removed | maltcms.tools.PublicMemberGetters | ||
| Parameter 1 of 'public maltcms.datastructures.array.Sparse mult(maltcms.datastructures.array.Sparse, double)' has changed its type to ucar.ma2.Sparse | maltcms.tools.SparseTools | public maltcms.datastructures.array.Sparse mult(maltcms.datastructures.array.Sparse, double) | |
| Return type of method 'public maltcms.datastructures.array.Sparse mult(maltcms.datastructures.array.Sparse, double)' has been changed to ucar.ma2.Sparse | maltcms.tools.SparseTools | public maltcms.datastructures.array.Sparse mult(maltcms.datastructures.array.Sparse, double) | |
| Return type of method 'public maltcms.datastructures.array.Sparse randomGaussian(int, int, double, double)' has been changed to ucar.ma2.Sparse | maltcms.tools.SparseTools | public maltcms.datastructures.array.Sparse randomGaussian(int, int, double, double) | |
| Return type of method 'public maltcms.datastructures.array.Sparse randomUniform(int, int, double, double)' has been changed to ucar.ma2.Sparse | maltcms.tools.SparseTools | public maltcms.datastructures.array.Sparse randomUniform(int, int, double, double) |