Uses of Class org.biojava.bio.structure.jama.Matrix (BioJava-1.5-beta API)

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## Uses of Class
org.biojava.bio.structure.jama.Matrix

Packages that use Matrix
org.biojava.bio.structure | Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align |
org.biojava.bio.structure.align.helper |
org.biojava.bio.structure.align.pairwise |
org.biojava.bio.structure.jama |

Uses of Matrix in org.biojava.bio.structure

Methods in org.biojava.bio.structure that return Matrix
`Matrix` | `SVDSuperimposer.getRotation()`

Methods in org.biojava.bio.structure with parameters of type Matrix
`static void` | `Calc.plus(Structure s, Matrix matrix)` calculate structure + Matrix coodinates ...
`void` | `SVDSuperimposer.printMatrix(Matrix m)`
`static void` | `Calc.rotate(Atom atom, Matrix m)` rotate an atom around a Matrix object
`static void` | `Calc.rotate(Group group, Matrix m)` rotate a group object
`static void` | `Calc.rotate(Structure structure, Matrix m)` rotate a structure object

Uses of Matrix in org.biojava.bio.structure.align

Methods in org.biojava.bio.structure.align that return Matrix
`Matrix` | `StructurePairAligner.getDistMat()` return the difference of distance matrix between the two structures

Uses of Matrix in org.biojava.bio.structure.align.helper

Methods in org.biojava.bio.structure.align.helper that return Matrix
`static Matrix` | `AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2)` matrix of all distances between two sets of 3d coords"

Uses of Matrix in org.biojava.bio.structure.align.pairwise

Methods in org.biojava.bio.structure.align.pairwise that return Matrix
`Matrix` | `FragmentPair.getRot()`
`Matrix` | `AlternativeAlignment.getRotationMatrix()` returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1

Methods in org.biojava.bio.structure.align.pairwise with parameters of type Matrix
`static Alignable` | `AligNPE.align_NPE(Matrix sim, StrucAligParameters params)` Align w/o penalizing endpags.
`static boolean` | `FragmentJoiner.reduceFragments(List fragments, FragmentPair f, Matrix rmsmat)` In helices often many similar fragments can be found.
`void` | `FragmentPair.setRot(Matrix rot)`

Uses of Matrix in org.biojava.bio.structure.jama

Methods in org.biojava.bio.structure.jama that return Matrix
`Matrix` | `Matrix.arrayLeftDivide(Matrix B)` Element-by-element left division, C = A.\B
`Matrix` | `Matrix.arrayLeftDivideEquals(Matrix B)` Element-by-element left division in place, A = A.\B
`Matrix` | `Matrix.arrayRightDivide(Matrix B)` Element-by-element right division, C = A./B
`Matrix` | `Matrix.arrayRightDivideEquals(Matrix B)` Element-by-element right division in place, A = A./B
`Matrix` | `Matrix.arrayTimes(Matrix B)` Element-by-element multiplication, C = A.*B
`Matrix` | `Matrix.arrayTimesEquals(Matrix B)` Element-by-element multiplication in place, A = A.*B
`static Matrix` | `Matrix.constructWithCopy(double[][] A)` Construct a matrix from a copy of a 2-D array.
`Matrix` | `Matrix.copy()` Make a deep copy of a matrix
`Matrix` | `EigenvalueDecomposition.getD()` Return the block diagonal eigenvalue matrix
`Matrix` | `QRDecomposition.getH()` Return the Householder vectors
`Matrix` | `CholeskyDecomposition.getL()` Return triangular factor.
`Matrix` | `LUDecomposition.getL()` Return lower triangular factor
`Matrix` | `Matrix.getMatrix(int[] r, int[] c)` Get a submatrix.
`Matrix` | `Matrix.getMatrix(int[] r, int j0, int j1)` Get a submatrix.
`Matrix` | `Matrix.getMatrix(int i0, int i1, int[] c)` Get a submatrix.
`Matrix` | `Matrix.getMatrix(int i0, int i1, int j0, int j1)` Get a submatrix.
`Matrix` | `QRDecomposition.getQ()` Generate and return the (economy-sized) orthogonal factor
`Matrix` | `QRDecomposition.getR()` Return the upper triangular factor
`Matrix` | `SingularValueDecomposition.getS()` Return the diagonal matrix of singular values
`Matrix` | `SingularValueDecomposition.getU()` Return the left singular vectors
`Matrix` | `LUDecomposition.getU()` Return upper triangular factor
`Matrix` | `SingularValueDecomposition.getV()` Return the right singular vectors
`Matrix` | `EigenvalueDecomposition.getV()` Return the eigenvector matrix
`static Matrix` | `Matrix.identity(int m, int n)` Generate identity matrix
`Matrix` | `Matrix.inverse()` Matrix inverse or pseudoinverse
`Matrix` | `Matrix.minus(Matrix B)` C = A - B
`Matrix` | `Matrix.minusEquals(Matrix B)` A = A - B
`Matrix` | `Matrix.plus(Matrix B)` C = A + B
`Matrix` | `Matrix.plusEquals(Matrix B)` A = A + B
`static Matrix` | `Matrix.random(int m, int n)` Generate matrix with random elements
`static Matrix` | `Matrix.read(BufferedReader input)` Read a matrix from a stream.
`Matrix` | `CholeskyDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` | `LUDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` | `Matrix.solve(Matrix B)` Solve A*X = B
`Matrix` | `QRDecomposition.solve(Matrix B)` Least squares solution of A*X = B
`Matrix` | `Matrix.solveTranspose(Matrix B)` Solve X*A = B, which is also A'*X' = B'
`Matrix` | `Matrix.times(double s)` Multiply a matrix by a scalar, C = s*A
`Matrix` | `Matrix.times(Matrix B)` Linear algebraic matrix multiplication, A * B
`Matrix` | `Matrix.timesEquals(double s)` Multiply a matrix by a scalar in place, A = s*A
`Matrix` | `Matrix.transpose()` Matrix transpose.
`Matrix` | `Matrix.uminus()` Unary minus

Methods in org.biojava.bio.structure.jama with parameters of type Matrix
`Matrix` | `Matrix.arrayLeftDivide(Matrix B)` Element-by-element left division, C = A.\B
`Matrix` | `Matrix.arrayLeftDivideEquals(Matrix B)` Element-by-element left division in place, A = A.\B
`Matrix` | `Matrix.arrayRightDivide(Matrix B)` Element-by-element right division, C = A./B
`Matrix` | `Matrix.arrayRightDivideEquals(Matrix B)` Element-by-element right division in place, A = A./B
`Matrix` | `Matrix.arrayTimes(Matrix B)` Element-by-element multiplication, C = A.*B
`Matrix` | `Matrix.arrayTimesEquals(Matrix B)` Element-by-element multiplication in place, A = A.*B
`Matrix` | `Matrix.minus(Matrix B)` C = A - B
`Matrix` | `Matrix.minusEquals(Matrix B)` A = A - B
`Matrix` | `Matrix.plus(Matrix B)` C = A + B
`Matrix` | `Matrix.plusEquals(Matrix B)` A = A + B
`void` | `Matrix.setMatrix(int[] r, int[] c, Matrix X)` Set a submatrix.
`void` | `Matrix.setMatrix(int[] r, int j0, int j1, Matrix X)` Set a submatrix.
`void` | `Matrix.setMatrix(int i0, int i1, int[] c, Matrix X)` Set a submatrix.
`void` | `Matrix.setMatrix(int i0, int i1, int j0, int j1, Matrix X)` Set a submatrix.
`Matrix` | `CholeskyDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` | `LUDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` | `Matrix.solve(Matrix B)` Solve A*X = B
`Matrix` | `QRDecomposition.solve(Matrix B)` Least squares solution of A*X = B
`Matrix` | `Matrix.solveTranspose(Matrix B)` Solve X*A = B, which is also A'*X' = B'
`Matrix` | `Matrix.times(Matrix B)` Linear algebraic matrix multiplication, A * B

Constructors in org.biojava.bio.structure.jama with parameters of type Matrix
`CholeskyDecomposition(Matrix Arg)` Cholesky algorithm for symmetric and positive definite matrix.
`EigenvalueDecomposition(Matrix Arg)` Check for symmetry, then construct the eigenvalue decomposition provides a way to access D and V.
`LUDecomposition(Matrix A)` LU Decomposition provides a data structure to access L, U and piv.
`QRDecomposition(Matrix A)` QR Decomposition, computed by Householder reflections.
`SingularValueDecomposition(Matrix Arg)` Construct the singular value decomposition.

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