sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,186 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPARSEUTIL_H
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- #define EIGEN_SPARSEUTIL_H
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-
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- namespace Eigen {
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-
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- #ifdef NDEBUG
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- #define EIGEN_DBG_SPARSE(X)
17
- #else
18
- #define EIGEN_DBG_SPARSE(X) X
19
- #endif
20
-
21
- #define EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(Derived, Op) \
22
- template<typename OtherDerived> \
23
- EIGEN_STRONG_INLINE Derived& operator Op(const Eigen::SparseMatrixBase<OtherDerived>& other) \
24
- { \
25
- return Base::operator Op(other.derived()); \
26
- } \
27
- EIGEN_STRONG_INLINE Derived& operator Op(const Derived& other) \
28
- { \
29
- return Base::operator Op(other); \
30
- }
31
-
32
- #define EIGEN_SPARSE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(Derived, Op) \
33
- template<typename Other> \
34
- EIGEN_STRONG_INLINE Derived& operator Op(const Other& scalar) \
35
- { \
36
- return Base::operator Op(scalar); \
37
- }
38
-
39
- #define EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATORS(Derived) \
40
- EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(Derived, =)
41
-
42
-
43
- #define EIGEN_SPARSE_PUBLIC_INTERFACE(Derived) \
44
- EIGEN_GENERIC_PUBLIC_INTERFACE(Derived)
45
-
46
-
47
- const int CoherentAccessPattern = 0x1;
48
- const int InnerRandomAccessPattern = 0x2 | CoherentAccessPattern;
49
- const int OuterRandomAccessPattern = 0x4 | CoherentAccessPattern;
50
- const int RandomAccessPattern = 0x8 | OuterRandomAccessPattern | InnerRandomAccessPattern;
51
-
52
- template<typename _Scalar, int _Flags = 0, typename _StorageIndex = int> class SparseMatrix;
53
- template<typename _Scalar, int _Flags = 0, typename _StorageIndex = int> class DynamicSparseMatrix;
54
- template<typename _Scalar, int _Flags = 0, typename _StorageIndex = int> class SparseVector;
55
- template<typename _Scalar, int _Flags = 0, typename _StorageIndex = int> class MappedSparseMatrix;
56
-
57
- template<typename MatrixType, unsigned int UpLo> class SparseSelfAdjointView;
58
- template<typename Lhs, typename Rhs> class SparseDiagonalProduct;
59
- template<typename MatrixType> class SparseView;
60
-
61
- template<typename Lhs, typename Rhs> class SparseSparseProduct;
62
- template<typename Lhs, typename Rhs> class SparseTimeDenseProduct;
63
- template<typename Lhs, typename Rhs> class DenseTimeSparseProduct;
64
- template<typename Lhs, typename Rhs, bool Transpose> class SparseDenseOuterProduct;
65
-
66
- template<typename Lhs, typename Rhs> struct SparseSparseProductReturnType;
67
- template<typename Lhs, typename Rhs,
68
- int InnerSize = EIGEN_SIZE_MIN_PREFER_FIXED(internal::traits<Lhs>::ColsAtCompileTime,internal::traits<Rhs>::RowsAtCompileTime)> struct DenseSparseProductReturnType;
69
-
70
- template<typename Lhs, typename Rhs,
71
- int InnerSize = EIGEN_SIZE_MIN_PREFER_FIXED(internal::traits<Lhs>::ColsAtCompileTime,internal::traits<Rhs>::RowsAtCompileTime)> struct SparseDenseProductReturnType;
72
- template<typename MatrixType,int UpLo> class SparseSymmetricPermutationProduct;
73
-
74
- namespace internal {
75
-
76
- template<typename T,int Rows,int Cols,int Flags> struct sparse_eval;
77
-
78
- template<typename T> struct eval<T,Sparse>
79
- : sparse_eval<T, traits<T>::RowsAtCompileTime,traits<T>::ColsAtCompileTime,traits<T>::Flags>
80
- {};
81
-
82
- template<typename T,int Cols,int Flags> struct sparse_eval<T,1,Cols,Flags> {
83
- typedef typename traits<T>::Scalar _Scalar;
84
- typedef typename traits<T>::StorageIndex _StorageIndex;
85
- public:
86
- typedef SparseVector<_Scalar, RowMajor, _StorageIndex> type;
87
- };
88
-
89
- template<typename T,int Rows,int Flags> struct sparse_eval<T,Rows,1,Flags> {
90
- typedef typename traits<T>::Scalar _Scalar;
91
- typedef typename traits<T>::StorageIndex _StorageIndex;
92
- public:
93
- typedef SparseVector<_Scalar, ColMajor, _StorageIndex> type;
94
- };
95
-
96
- // TODO this seems almost identical to plain_matrix_type<T, Sparse>
97
- template<typename T,int Rows,int Cols,int Flags> struct sparse_eval {
98
- typedef typename traits<T>::Scalar _Scalar;
99
- typedef typename traits<T>::StorageIndex _StorageIndex;
100
- enum { _Options = ((Flags&RowMajorBit)==RowMajorBit) ? RowMajor : ColMajor };
101
- public:
102
- typedef SparseMatrix<_Scalar, _Options, _StorageIndex> type;
103
- };
104
-
105
- template<typename T,int Flags> struct sparse_eval<T,1,1,Flags> {
106
- typedef typename traits<T>::Scalar _Scalar;
107
- public:
108
- typedef Matrix<_Scalar, 1, 1> type;
109
- };
110
-
111
- template<typename T> struct plain_matrix_type<T,Sparse>
112
- {
113
- typedef typename traits<T>::Scalar _Scalar;
114
- typedef typename traits<T>::StorageIndex _StorageIndex;
115
- enum { _Options = ((evaluator<T>::Flags&RowMajorBit)==RowMajorBit) ? RowMajor : ColMajor };
116
- public:
117
- typedef SparseMatrix<_Scalar, _Options, _StorageIndex> type;
118
- };
119
-
120
- template<typename T>
121
- struct plain_object_eval<T,Sparse>
122
- : sparse_eval<T, traits<T>::RowsAtCompileTime,traits<T>::ColsAtCompileTime, evaluator<T>::Flags>
123
- {};
124
-
125
- template<typename Decomposition, typename RhsType>
126
- struct solve_traits<Decomposition,RhsType,Sparse>
127
- {
128
- typedef typename sparse_eval<RhsType, RhsType::RowsAtCompileTime, RhsType::ColsAtCompileTime,traits<RhsType>::Flags>::type PlainObject;
129
- };
130
-
131
- template<typename Derived>
132
- struct generic_xpr_base<Derived, MatrixXpr, Sparse>
133
- {
134
- typedef SparseMatrixBase<Derived> type;
135
- };
136
-
137
- struct SparseTriangularShape { static std::string debugName() { return "SparseTriangularShape"; } };
138
- struct SparseSelfAdjointShape { static std::string debugName() { return "SparseSelfAdjointShape"; } };
139
-
140
- template<> struct glue_shapes<SparseShape,SelfAdjointShape> { typedef SparseSelfAdjointShape type; };
141
- template<> struct glue_shapes<SparseShape,TriangularShape > { typedef SparseTriangularShape type; };
142
-
143
- // return type of SparseCompressedBase::lower_bound;
144
- struct LowerBoundIndex {
145
- LowerBoundIndex() : value(-1), found(false) {}
146
- LowerBoundIndex(Index val, bool ok) : value(val), found(ok) {}
147
- Index value;
148
- bool found;
149
- };
150
-
151
- } // end namespace internal
152
-
153
- /** \ingroup SparseCore_Module
154
- *
155
- * \class Triplet
156
- *
157
- * \brief A small structure to hold a non zero as a triplet (i,j,value).
158
- *
159
- * \sa SparseMatrix::setFromTriplets()
160
- */
161
- template<typename Scalar, typename StorageIndex=typename SparseMatrix<Scalar>::StorageIndex >
162
- class Triplet
163
- {
164
- public:
165
- Triplet() : m_row(0), m_col(0), m_value(0) {}
166
-
167
- Triplet(const StorageIndex& i, const StorageIndex& j, const Scalar& v = Scalar(0))
168
- : m_row(i), m_col(j), m_value(v)
169
- {}
170
-
171
- /** \returns the row index of the element */
172
- const StorageIndex& row() const { return m_row; }
173
-
174
- /** \returns the column index of the element */
175
- const StorageIndex& col() const { return m_col; }
176
-
177
- /** \returns the value of the element */
178
- const Scalar& value() const { return m_value; }
179
- protected:
180
- StorageIndex m_row, m_col;
181
- Scalar m_value;
182
- };
183
-
184
- } // end namespace Eigen
185
-
186
- #endif // EIGEN_SPARSEUTIL_H
@@ -1,478 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_SPARSEVECTOR_H
11
- #define EIGEN_SPARSEVECTOR_H
12
-
13
- namespace Eigen {
14
-
15
- /** \ingroup SparseCore_Module
16
- * \class SparseVector
17
- *
18
- * \brief a sparse vector class
19
- *
20
- * \tparam _Scalar the scalar type, i.e. the type of the coefficients
21
- *
22
- * See http://www.netlib.org/linalg/html_templates/node91.html for details on the storage scheme.
23
- *
24
- * This class can be extended with the help of the plugin mechanism described on the page
25
- * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_SPARSEVECTOR_PLUGIN.
26
- */
27
-
28
- namespace internal {
29
- template<typename _Scalar, int _Options, typename _StorageIndex>
30
- struct traits<SparseVector<_Scalar, _Options, _StorageIndex> >
31
- {
32
- typedef _Scalar Scalar;
33
- typedef _StorageIndex StorageIndex;
34
- typedef Sparse StorageKind;
35
- typedef MatrixXpr XprKind;
36
- enum {
37
- IsColVector = (_Options & RowMajorBit) ? 0 : 1,
38
-
39
- RowsAtCompileTime = IsColVector ? Dynamic : 1,
40
- ColsAtCompileTime = IsColVector ? 1 : Dynamic,
41
- MaxRowsAtCompileTime = RowsAtCompileTime,
42
- MaxColsAtCompileTime = ColsAtCompileTime,
43
- Flags = _Options | NestByRefBit | LvalueBit | (IsColVector ? 0 : RowMajorBit) | CompressedAccessBit,
44
- SupportedAccessPatterns = InnerRandomAccessPattern
45
- };
46
- };
47
-
48
- // Sparse-Vector-Assignment kinds:
49
- enum {
50
- SVA_RuntimeSwitch,
51
- SVA_Inner,
52
- SVA_Outer
53
- };
54
-
55
- template< typename Dest, typename Src,
56
- int AssignmentKind = !bool(Src::IsVectorAtCompileTime) ? SVA_RuntimeSwitch
57
- : Src::InnerSizeAtCompileTime==1 ? SVA_Outer
58
- : SVA_Inner>
59
- struct sparse_vector_assign_selector;
60
-
61
- }
62
-
63
- template<typename _Scalar, int _Options, typename _StorageIndex>
64
- class SparseVector
65
- : public SparseCompressedBase<SparseVector<_Scalar, _Options, _StorageIndex> >
66
- {
67
- typedef SparseCompressedBase<SparseVector> Base;
68
- using Base::convert_index;
69
- public:
70
- EIGEN_SPARSE_PUBLIC_INTERFACE(SparseVector)
71
- EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseVector, +=)
72
- EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseVector, -=)
73
-
74
- typedef internal::CompressedStorage<Scalar,StorageIndex> Storage;
75
- enum { IsColVector = internal::traits<SparseVector>::IsColVector };
76
-
77
- enum {
78
- Options = _Options
79
- };
80
-
81
- EIGEN_STRONG_INLINE Index rows() const { return IsColVector ? m_size : 1; }
82
- EIGEN_STRONG_INLINE Index cols() const { return IsColVector ? 1 : m_size; }
83
- EIGEN_STRONG_INLINE Index innerSize() const { return m_size; }
84
- EIGEN_STRONG_INLINE Index outerSize() const { return 1; }
85
-
86
- EIGEN_STRONG_INLINE const Scalar* valuePtr() const { return m_data.valuePtr(); }
87
- EIGEN_STRONG_INLINE Scalar* valuePtr() { return m_data.valuePtr(); }
88
-
89
- EIGEN_STRONG_INLINE const StorageIndex* innerIndexPtr() const { return m_data.indexPtr(); }
90
- EIGEN_STRONG_INLINE StorageIndex* innerIndexPtr() { return m_data.indexPtr(); }
91
-
92
- inline const StorageIndex* outerIndexPtr() const { return 0; }
93
- inline StorageIndex* outerIndexPtr() { return 0; }
94
- inline const StorageIndex* innerNonZeroPtr() const { return 0; }
95
- inline StorageIndex* innerNonZeroPtr() { return 0; }
96
-
97
- /** \internal */
98
- inline Storage& data() { return m_data; }
99
- /** \internal */
100
- inline const Storage& data() const { return m_data; }
101
-
102
- inline Scalar coeff(Index row, Index col) const
103
- {
104
- eigen_assert(IsColVector ? (col==0 && row>=0 && row<m_size) : (row==0 && col>=0 && col<m_size));
105
- return coeff(IsColVector ? row : col);
106
- }
107
- inline Scalar coeff(Index i) const
108
- {
109
- eigen_assert(i>=0 && i<m_size);
110
- return m_data.at(StorageIndex(i));
111
- }
112
-
113
- inline Scalar& coeffRef(Index row, Index col)
114
- {
115
- eigen_assert(IsColVector ? (col==0 && row>=0 && row<m_size) : (row==0 && col>=0 && col<m_size));
116
- return coeffRef(IsColVector ? row : col);
117
- }
118
-
119
- /** \returns a reference to the coefficient value at given index \a i
120
- * This operation involes a log(rho*size) binary search. If the coefficient does not
121
- * exist yet, then a sorted insertion into a sequential buffer is performed.
122
- *
123
- * This insertion might be very costly if the number of nonzeros above \a i is large.
124
- */
125
- inline Scalar& coeffRef(Index i)
126
- {
127
- eigen_assert(i>=0 && i<m_size);
128
-
129
- return m_data.atWithInsertion(StorageIndex(i));
130
- }
131
-
132
- public:
133
-
134
- typedef typename Base::InnerIterator InnerIterator;
135
- typedef typename Base::ReverseInnerIterator ReverseInnerIterator;
136
-
137
- inline void setZero() { m_data.clear(); }
138
-
139
- /** \returns the number of non zero coefficients */
140
- inline Index nonZeros() const { return m_data.size(); }
141
-
142
- inline void startVec(Index outer)
143
- {
144
- EIGEN_UNUSED_VARIABLE(outer);
145
- eigen_assert(outer==0);
146
- }
147
-
148
- inline Scalar& insertBackByOuterInner(Index outer, Index inner)
149
- {
150
- EIGEN_UNUSED_VARIABLE(outer);
151
- eigen_assert(outer==0);
152
- return insertBack(inner);
153
- }
154
- inline Scalar& insertBack(Index i)
155
- {
156
- m_data.append(0, i);
157
- return m_data.value(m_data.size()-1);
158
- }
159
-
160
- Scalar& insertBackByOuterInnerUnordered(Index outer, Index inner)
161
- {
162
- EIGEN_UNUSED_VARIABLE(outer);
163
- eigen_assert(outer==0);
164
- return insertBackUnordered(inner);
165
- }
166
- inline Scalar& insertBackUnordered(Index i)
167
- {
168
- m_data.append(0, i);
169
- return m_data.value(m_data.size()-1);
170
- }
171
-
172
- inline Scalar& insert(Index row, Index col)
173
- {
174
- eigen_assert(IsColVector ? (col==0 && row>=0 && row<m_size) : (row==0 && col>=0 && col<m_size));
175
-
176
- Index inner = IsColVector ? row : col;
177
- Index outer = IsColVector ? col : row;
178
- EIGEN_ONLY_USED_FOR_DEBUG(outer);
179
- eigen_assert(outer==0);
180
- return insert(inner);
181
- }
182
- Scalar& insert(Index i)
183
- {
184
- eigen_assert(i>=0 && i<m_size);
185
-
186
- Index startId = 0;
187
- Index p = Index(m_data.size()) - 1;
188
- // TODO smart realloc
189
- m_data.resize(p+2,1);
190
-
191
- while ( (p >= startId) && (m_data.index(p) > i) )
192
- {
193
- m_data.index(p+1) = m_data.index(p);
194
- m_data.value(p+1) = m_data.value(p);
195
- --p;
196
- }
197
- m_data.index(p+1) = convert_index(i);
198
- m_data.value(p+1) = 0;
199
- return m_data.value(p+1);
200
- }
201
-
202
- /**
203
- */
204
- inline void reserve(Index reserveSize) { m_data.reserve(reserveSize); }
205
-
206
-
207
- inline void finalize() {}
208
-
209
- /** \copydoc SparseMatrix::prune(const Scalar&,const RealScalar&) */
210
- void prune(const Scalar& reference, const RealScalar& epsilon = NumTraits<RealScalar>::dummy_precision())
211
- {
212
- m_data.prune(reference,epsilon);
213
- }
214
-
215
- /** Resizes the sparse vector to \a rows x \a cols
216
- *
217
- * This method is provided for compatibility with matrices.
218
- * For a column vector, \a cols must be equal to 1.
219
- * For a row vector, \a rows must be equal to 1.
220
- *
221
- * \sa resize(Index)
222
- */
223
- void resize(Index rows, Index cols)
224
- {
225
- eigen_assert((IsColVector ? cols : rows)==1 && "Outer dimension must equal 1");
226
- resize(IsColVector ? rows : cols);
227
- }
228
-
229
- /** Resizes the sparse vector to \a newSize
230
- * This method deletes all entries, thus leaving an empty sparse vector
231
- *
232
- * \sa conservativeResize(), setZero() */
233
- void resize(Index newSize)
234
- {
235
- m_size = newSize;
236
- m_data.clear();
237
- }
238
-
239
- /** Resizes the sparse vector to \a newSize, while leaving old values untouched.
240
- *
241
- * If the size of the vector is decreased, then the storage of the out-of bounds coefficients is kept and reserved.
242
- * Call .data().squeeze() to free extra memory.
243
- *
244
- * \sa reserve(), setZero()
245
- */
246
- void conservativeResize(Index newSize)
247
- {
248
- if (newSize < m_size)
249
- {
250
- Index i = 0;
251
- while (i<m_data.size() && m_data.index(i)<newSize) ++i;
252
- m_data.resize(i);
253
- }
254
- m_size = newSize;
255
- }
256
-
257
- void resizeNonZeros(Index size) { m_data.resize(size); }
258
-
259
- inline SparseVector() : m_size(0) { check_template_parameters(); resize(0); }
260
-
261
- explicit inline SparseVector(Index size) : m_size(0) { check_template_parameters(); resize(size); }
262
-
263
- inline SparseVector(Index rows, Index cols) : m_size(0) { check_template_parameters(); resize(rows,cols); }
264
-
265
- template<typename OtherDerived>
266
- inline SparseVector(const SparseMatrixBase<OtherDerived>& other)
267
- : m_size(0)
268
- {
269
- #ifdef EIGEN_SPARSE_CREATE_TEMPORARY_PLUGIN
270
- EIGEN_SPARSE_CREATE_TEMPORARY_PLUGIN
271
- #endif
272
- check_template_parameters();
273
- *this = other.derived();
274
- }
275
-
276
- inline SparseVector(const SparseVector& other)
277
- : Base(other), m_size(0)
278
- {
279
- check_template_parameters();
280
- *this = other.derived();
281
- }
282
-
283
- /** Swaps the values of \c *this and \a other.
284
- * Overloaded for performance: this version performs a \em shallow swap by swapping pointers and attributes only.
285
- * \sa SparseMatrixBase::swap()
286
- */
287
- inline void swap(SparseVector& other)
288
- {
289
- std::swap(m_size, other.m_size);
290
- m_data.swap(other.m_data);
291
- }
292
-
293
- template<int OtherOptions>
294
- inline void swap(SparseMatrix<Scalar,OtherOptions,StorageIndex>& other)
295
- {
296
- eigen_assert(other.outerSize()==1);
297
- std::swap(m_size, other.m_innerSize);
298
- m_data.swap(other.m_data);
299
- }
300
-
301
- inline SparseVector& operator=(const SparseVector& other)
302
- {
303
- if (other.isRValue())
304
- {
305
- swap(other.const_cast_derived());
306
- }
307
- else
308
- {
309
- resize(other.size());
310
- m_data = other.m_data;
311
- }
312
- return *this;
313
- }
314
-
315
- template<typename OtherDerived>
316
- inline SparseVector& operator=(const SparseMatrixBase<OtherDerived>& other)
317
- {
318
- SparseVector tmp(other.size());
319
- internal::sparse_vector_assign_selector<SparseVector,OtherDerived>::run(tmp,other.derived());
320
- this->swap(tmp);
321
- return *this;
322
- }
323
-
324
- #ifndef EIGEN_PARSED_BY_DOXYGEN
325
- template<typename Lhs, typename Rhs>
326
- inline SparseVector& operator=(const SparseSparseProduct<Lhs,Rhs>& product)
327
- {
328
- return Base::operator=(product);
329
- }
330
- #endif
331
-
332
- friend std::ostream & operator << (std::ostream & s, const SparseVector& m)
333
- {
334
- for (Index i=0; i<m.nonZeros(); ++i)
335
- s << "(" << m.m_data.value(i) << "," << m.m_data.index(i) << ") ";
336
- s << std::endl;
337
- return s;
338
- }
339
-
340
- /** Destructor */
341
- inline ~SparseVector() {}
342
-
343
- /** Overloaded for performance */
344
- Scalar sum() const;
345
-
346
- public:
347
-
348
- /** \internal \deprecated use setZero() and reserve() */
349
- EIGEN_DEPRECATED void startFill(Index reserve)
350
- {
351
- setZero();
352
- m_data.reserve(reserve);
353
- }
354
-
355
- /** \internal \deprecated use insertBack(Index,Index) */
356
- EIGEN_DEPRECATED Scalar& fill(Index r, Index c)
357
- {
358
- eigen_assert(r==0 || c==0);
359
- return fill(IsColVector ? r : c);
360
- }
361
-
362
- /** \internal \deprecated use insertBack(Index) */
363
- EIGEN_DEPRECATED Scalar& fill(Index i)
364
- {
365
- m_data.append(0, i);
366
- return m_data.value(m_data.size()-1);
367
- }
368
-
369
- /** \internal \deprecated use insert(Index,Index) */
370
- EIGEN_DEPRECATED Scalar& fillrand(Index r, Index c)
371
- {
372
- eigen_assert(r==0 || c==0);
373
- return fillrand(IsColVector ? r : c);
374
- }
375
-
376
- /** \internal \deprecated use insert(Index) */
377
- EIGEN_DEPRECATED Scalar& fillrand(Index i)
378
- {
379
- return insert(i);
380
- }
381
-
382
- /** \internal \deprecated use finalize() */
383
- EIGEN_DEPRECATED void endFill() {}
384
-
385
- // These two functions were here in the 3.1 release, so let's keep them in case some code rely on them.
386
- /** \internal \deprecated use data() */
387
- EIGEN_DEPRECATED Storage& _data() { return m_data; }
388
- /** \internal \deprecated use data() */
389
- EIGEN_DEPRECATED const Storage& _data() const { return m_data; }
390
-
391
- # ifdef EIGEN_SPARSEVECTOR_PLUGIN
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- # include EIGEN_SPARSEVECTOR_PLUGIN
393
- # endif
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-
395
- protected:
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-
397
- static void check_template_parameters()
398
- {
399
- EIGEN_STATIC_ASSERT(NumTraits<StorageIndex>::IsSigned,THE_INDEX_TYPE_MUST_BE_A_SIGNED_TYPE);
400
- EIGEN_STATIC_ASSERT((_Options&(ColMajor|RowMajor))==Options,INVALID_MATRIX_TEMPLATE_PARAMETERS);
401
- }
402
-
403
- Storage m_data;
404
- Index m_size;
405
- };
406
-
407
- namespace internal {
408
-
409
- template<typename _Scalar, int _Options, typename _Index>
410
- struct evaluator<SparseVector<_Scalar,_Options,_Index> >
411
- : evaluator_base<SparseVector<_Scalar,_Options,_Index> >
412
- {
413
- typedef SparseVector<_Scalar,_Options,_Index> SparseVectorType;
414
- typedef evaluator_base<SparseVectorType> Base;
415
- typedef typename SparseVectorType::InnerIterator InnerIterator;
416
- typedef typename SparseVectorType::ReverseInnerIterator ReverseInnerIterator;
417
-
418
- enum {
419
- CoeffReadCost = NumTraits<_Scalar>::ReadCost,
420
- Flags = SparseVectorType::Flags
421
- };
422
-
423
- evaluator() : Base() {}
424
-
425
- explicit evaluator(const SparseVectorType &mat) : m_matrix(&mat)
426
- {
427
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
428
- }
429
-
430
- inline Index nonZerosEstimate() const {
431
- return m_matrix->nonZeros();
432
- }
433
-
434
- operator SparseVectorType&() { return m_matrix->const_cast_derived(); }
435
- operator const SparseVectorType&() const { return *m_matrix; }
436
-
437
- const SparseVectorType *m_matrix;
438
- };
439
-
440
- template< typename Dest, typename Src>
441
- struct sparse_vector_assign_selector<Dest,Src,SVA_Inner> {
442
- static void run(Dest& dst, const Src& src) {
443
- eigen_internal_assert(src.innerSize()==src.size());
444
- typedef internal::evaluator<Src> SrcEvaluatorType;
445
- SrcEvaluatorType srcEval(src);
446
- for(typename SrcEvaluatorType::InnerIterator it(srcEval, 0); it; ++it)
447
- dst.insert(it.index()) = it.value();
448
- }
449
- };
450
-
451
- template< typename Dest, typename Src>
452
- struct sparse_vector_assign_selector<Dest,Src,SVA_Outer> {
453
- static void run(Dest& dst, const Src& src) {
454
- eigen_internal_assert(src.outerSize()==src.size());
455
- typedef internal::evaluator<Src> SrcEvaluatorType;
456
- SrcEvaluatorType srcEval(src);
457
- for(Index i=0; i<src.size(); ++i)
458
- {
459
- typename SrcEvaluatorType::InnerIterator it(srcEval, i);
460
- if(it)
461
- dst.insert(i) = it.value();
462
- }
463
- }
464
- };
465
-
466
- template< typename Dest, typename Src>
467
- struct sparse_vector_assign_selector<Dest,Src,SVA_RuntimeSwitch> {
468
- static void run(Dest& dst, const Src& src) {
469
- if(src.outerSize()==1) sparse_vector_assign_selector<Dest,Src,SVA_Inner>::run(dst, src);
470
- else sparse_vector_assign_selector<Dest,Src,SVA_Outer>::run(dst, src);
471
- }
472
- };
473
-
474
- }
475
-
476
- } // end namespace Eigen
477
-
478
- #endif // EIGEN_SPARSEVECTOR_H