sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl
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- sequenzo/__init__.py +39 -7
- sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
- sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-darwin.so +0 -0
- sequenzo/clustering/KMedoids.py +39 -0
- sequenzo/clustering/hierarchical_clustering.py +107 -5
- sequenzo/define_sequence_data.py +10 -1
- sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
- sequenzo/multidomain/cat.py +0 -53
- sequenzo/multidomain/idcd.py +0 -1
- sequenzo/openmp_setup.py +233 -0
- sequenzo/visualization/plot_transition_matrix.py +21 -22
- {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
- sequenzo-0.1.19.dist-info/RECORD +215 -0
- sequenzo/dissimilarity_measures/setup.py +0 -35
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
- sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
- sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
- sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
- sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
- sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
- sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
- sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
- sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
- sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
- sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
- sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
- sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
- sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
- sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
- sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
- sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
- sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
- sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
- sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
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namespace Eigen {
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struct traits<TensorEvalToOp<XprType, MakePointer_> >
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};
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94
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-
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95
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96
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97
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template<typename ArgType, typename Device, template <class> class MakePointer_>
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98
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struct TensorEvaluator<const TensorEvalToOp<ArgType, MakePointer_>, Device>
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99
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{
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100
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typedef TensorEvalToOp<ArgType, MakePointer_> XprType;
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101
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typedef typename ArgType::Scalar Scalar;
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102
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typedef typename TensorEvaluator<ArgType, Device>::Dimensions Dimensions;
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103
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typedef typename XprType::Index Index;
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104
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typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
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105
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typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
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106
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static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
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107
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typedef typename Eigen::internal::traits<XprType>::PointerType TensorPointerType;
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108
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typedef StorageMemory<CoeffReturnType, Device> Storage;
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109
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typedef typename Storage::Type EvaluatorPointerType;
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110
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enum {
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111
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IsAligned = TensorEvaluator<ArgType, Device>::IsAligned,
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112
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PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
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113
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BlockAccess = true,
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114
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PreferBlockAccess = false,
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115
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Layout = TensorEvaluator<ArgType, Device>::Layout,
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116
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CoordAccess = false, // to be implemented
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117
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RawAccess = true
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118
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};
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119
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-
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120
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static const int NumDims = internal::traits<ArgType>::NumDimensions;
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121
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-
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122
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//===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
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123
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typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
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124
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typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
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125
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126
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typedef typename TensorEvaluator<const ArgType, Device>::TensorBlock
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127
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ArgTensorBlock;
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128
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-
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129
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typedef internal::TensorBlockAssignment<
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130
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CoeffReturnType, NumDims, typename ArgTensorBlock::XprType, Index>
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131
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TensorBlockAssignment;
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132
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//===--------------------------------------------------------------------===//
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133
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-
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134
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EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
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135
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: m_impl(op.expression(), device), m_buffer(device.get(op.buffer())), m_expression(op.expression()){}
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136
|
-
|
|
137
|
-
|
|
138
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-
EIGEN_STRONG_INLINE ~TensorEvaluator() {
|
|
139
|
-
}
|
|
140
|
-
|
|
141
|
-
|
|
142
|
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EIGEN_DEVICE_FUNC const Dimensions& dimensions() const { return m_impl.dimensions(); }
|
|
143
|
-
|
|
144
|
-
EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType scalar) {
|
|
145
|
-
EIGEN_UNUSED_VARIABLE(scalar);
|
|
146
|
-
eigen_assert(scalar == NULL);
|
|
147
|
-
return m_impl.evalSubExprsIfNeeded(m_buffer);
|
|
148
|
-
}
|
|
149
|
-
|
|
150
|
-
#ifdef EIGEN_USE_THREADS
|
|
151
|
-
template <typename EvalSubExprsCallback>
|
|
152
|
-
EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
|
|
153
|
-
EvaluatorPointerType scalar, EvalSubExprsCallback done) {
|
|
154
|
-
EIGEN_UNUSED_VARIABLE(scalar);
|
|
155
|
-
eigen_assert(scalar == NULL);
|
|
156
|
-
m_impl.evalSubExprsIfNeededAsync(m_buffer, std::move(done));
|
|
157
|
-
}
|
|
158
|
-
#endif
|
|
159
|
-
|
|
160
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalScalar(Index i) {
|
|
161
|
-
m_buffer[i] = m_impl.coeff(i);
|
|
162
|
-
}
|
|
163
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalPacket(Index i) {
|
|
164
|
-
internal::pstoret<CoeffReturnType, PacketReturnType, Aligned>(m_buffer + i, m_impl.template packet<TensorEvaluator<ArgType, Device>::IsAligned ? Aligned : Unaligned>(i));
|
|
165
|
-
}
|
|
166
|
-
|
|
167
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
|
|
168
|
-
internal::TensorBlockResourceRequirements getResourceRequirements() const {
|
|
169
|
-
return m_impl.getResourceRequirements();
|
|
170
|
-
}
|
|
171
|
-
|
|
172
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalBlock(
|
|
173
|
-
TensorBlockDesc& desc, TensorBlockScratch& scratch) {
|
|
174
|
-
// Add `m_buffer` as destination buffer to the block descriptor.
|
|
175
|
-
desc.template AddDestinationBuffer<Layout>(
|
|
176
|
-
/*dst_base=*/m_buffer + desc.offset(),
|
|
177
|
-
/*dst_strides=*/internal::strides<Layout>(m_impl.dimensions()));
|
|
178
|
-
|
|
179
|
-
ArgTensorBlock block =
|
|
180
|
-
m_impl.block(desc, scratch, /*root_of_expr_ast=*/true);
|
|
181
|
-
|
|
182
|
-
// If block was evaluated into a destination buffer, there is no need to do
|
|
183
|
-
// an assignment.
|
|
184
|
-
if (block.kind() != internal::TensorBlockKind::kMaterializedInOutput) {
|
|
185
|
-
TensorBlockAssignment::Run(
|
|
186
|
-
TensorBlockAssignment::target(
|
|
187
|
-
desc.dimensions(), internal::strides<Layout>(m_impl.dimensions()),
|
|
188
|
-
m_buffer, desc.offset()),
|
|
189
|
-
block.expr());
|
|
190
|
-
}
|
|
191
|
-
block.cleanup();
|
|
192
|
-
}
|
|
193
|
-
|
|
194
|
-
EIGEN_STRONG_INLINE void cleanup() {
|
|
195
|
-
m_impl.cleanup();
|
|
196
|
-
}
|
|
197
|
-
|
|
198
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
|
|
199
|
-
{
|
|
200
|
-
return m_buffer[index];
|
|
201
|
-
}
|
|
202
|
-
|
|
203
|
-
template<int LoadMode>
|
|
204
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
|
|
205
|
-
{
|
|
206
|
-
return internal::ploadt<PacketReturnType, LoadMode>(m_buffer + index);
|
|
207
|
-
}
|
|
208
|
-
|
|
209
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
|
|
210
|
-
// We assume that evalPacket or evalScalar is called to perform the
|
|
211
|
-
// assignment and account for the cost of the write here.
|
|
212
|
-
return m_impl.costPerCoeff(vectorized) +
|
|
213
|
-
TensorOpCost(0, sizeof(CoeffReturnType), 0, vectorized, PacketSize);
|
|
214
|
-
}
|
|
215
|
-
|
|
216
|
-
EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_buffer; }
|
|
217
|
-
ArgType expression() const { return m_expression; }
|
|
218
|
-
#ifdef EIGEN_USE_SYCL
|
|
219
|
-
// binding placeholder accessors to a command group handler for SYCL
|
|
220
|
-
EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
|
|
221
|
-
m_impl.bind(cgh);
|
|
222
|
-
m_buffer.bind(cgh);
|
|
223
|
-
}
|
|
224
|
-
#endif
|
|
225
|
-
|
|
226
|
-
|
|
227
|
-
private:
|
|
228
|
-
TensorEvaluator<ArgType, Device> m_impl;
|
|
229
|
-
EvaluatorPointerType m_buffer;
|
|
230
|
-
const ArgType m_expression;
|
|
231
|
-
};
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
} // end namespace Eigen
|
|
235
|
-
|
|
236
|
-
#endif // EIGEN_CXX11_TENSOR_TENSOR_EVAL_TO_H
|