Uses of Class
ProGAL.math.Matrix

Packages that use Matrix

ProGAL.geom3d.superposition
ProGAL.geom3d.surface
ProGAL.geomNd	This package contains classes that are all related to Euclidean geometric concepts of dimension larger than three.
ProGAL.math	This package contains math-classes that are not necessarily related to geometrical concepts.
ProGAL.proteins.belta
ProGAL.proteins.beltaStructure.loop
ProGAL.proteins.beltaStructure.sheet
ProGAL.proteins.chainTree

Uses of Matrix in ProGAL.geom3d.superposition

Constructors in ProGAL.geom3d.superposition with parameters of type Matrix

Transform(Matrix rotation, Vector translation)

Transform(Matrix rotation, Vector preTranslation, Vector postTranslation)

Uses of Matrix in ProGAL.geom3d.surface

Methods in ProGAL.geom3d.surface that return Matrix

Matrix

ParametricParaboloid.getRotation()

Methods in ProGAL.geom3d.surface with parameters of type Matrix

void	ParametricParaboloid.setRotation(Matrix rot)

Uses of Matrix in ProGAL.geomNd

Methods in ProGAL.geomNd that return Matrix

Matrix	PointList.getCovariance() Get the covariance of the points.
Matrix	Vector.outerProduct(Vector v)

Uses of Matrix in ProGAL.math

Subclasses of Matrix in ProGAL.math

static class	Matrix.ImmutableMatrix
class	Matrix3x3

Methods in ProGAL.math that return Matrix

Matrix	Matrix.add(Matrix m) Add the components of two matrices.
Matrix	Matrix.addThis(Matrix m) Add the components of two matrices.
Matrix	Matrix.ImmutableMatrix.addThis(Matrix m)
Matrix	Matrix.clone() Returns a clone of this matrix.
static Matrix	Matrix.create4x4ColumnMatrix(Vector v1, Vector v2, Vector v3, Vector v4)
static Matrix	Matrix.createIdentityMatrix(int n)
static Matrix	Matrix.createRandomMatrix(int n)
static Matrix	Matrix.createRotationMatrix(double angle, Vector v)
Matrix	Matrix.expand() extends to the smallest power of 2 square matrix by adding appropriate zero rows and columns
Matrix	Matrix.extend() extends to the smallest square matrix by adding appropriate zero rows or columns
Matrix	Matrix.EigenvalueDecomposition.getD() Return the block diagonal eigenvalue matrix.
Matrix	LUDecomposition.getL() Return lower triangular factor
Matrix	SingularValueDecomposition.getS() Return the diagonal matrix of singular values
Matrix	Matrix.getSubmatrix(int i1, int i2, int j1, int j2)
Matrix	Matrix.getTranspose() Get the transpose of this matrix
Matrix	SingularValueDecomposition.getU() Return the left singular vectors
Matrix	LUDecomposition.getU() Return upper triangular factor
Matrix	SingularValueDecomposition.getV() Return the right singular vectors.
Matrix	Matrix.EigenvalueDecomposition.getV() Return the eigenvector matrix (immutable).
Matrix	Matrix.invert() Return the inverse of this matrix.
Matrix	Matrix3x3.invertThis() Invert this matrix (overwrites this and returns it).
Matrix	Matrix.invertThis() Invert this matrix (overwrites this and returns it).
Matrix	Matrix.ImmutableMatrix.invertThis()
Matrix	Matrix.minor(int r, int c) Return the minor, i.e.
Matrix	Matrix.multiply_Strassen(Matrix B)
Matrix	Matrix.multiply(double scalar) Multiply the components of this matrix by a scalar.
Matrix	Matrix.multiply(Matrix m) Multiply this matrix to another matrix and return the result.
Matrix	Matrix.multiplyThis(double scalar) Multiply the components of this matrix by a scalar.
Matrix	Matrix.ImmutableMatrix.multiplyThis(double s)
Matrix	Matrix.multiplyThis(Matrix m) Multiply this matrix to another matrix.
Matrix	Matrix.ImmutableMatrix.multiplyThis(Matrix m)
Matrix	Matrix.orthonormalizeThis() Run Gram-Schmidt orthonormalization procedure.
Matrix	Matrix.reduce() Reduce this matrix to row canonical form (reduced row echelon form).
Matrix	Matrix.reduceThis() Reduce this matrix to row canonical form (reduced row echelon form).
Matrix	LUDecomposition.solve(Matrix B) Solve A*X = B
Matrix	Matrix.subtract(Matrix m) Subtract the components of two matrices.
Matrix	Matrix.subtractThis(Matrix m) Subtract the components of two matrices.
Matrix	Matrix.transpose() Get the transpose of this matrix

Methods in ProGAL.math with parameters of type Matrix

Matrix	Matrix.add(Matrix m) Add the components of two matrices.
Matrix	Matrix.addThis(Matrix m) Add the components of two matrices.
Matrix	Matrix.ImmutableMatrix.addThis(Matrix m)
boolean	Matrix.equals(Matrix m)
Matrix	Matrix.multiply_Strassen(Matrix B)
Matrix	Matrix.multiply(Matrix m) Multiply this matrix to another matrix and return the result.
Matrix	Matrix.multiplyThis(Matrix m) Multiply this matrix to another matrix.
Matrix	Matrix.ImmutableMatrix.multiplyThis(Matrix m)
void	Matrix.setSubmatrix(int i1, int j1, Matrix M)
Matrix	LUDecomposition.solve(Matrix B) Solve A*X = B
Matrix	Matrix.subtract(Matrix m) Subtract the components of two matrices.
Matrix	Matrix.subtractThis(Matrix m) Subtract the components of two matrices.

Constructors in ProGAL.math with parameters of type Matrix

LUDecomposition(Matrix A)
LU Decomposition

SingularValueDecomposition(Matrix Arg)
Construct the singular value decomposition

Uses of Matrix in ProGAL.proteins.belta

Fields in ProGAL.proteins.belta declared as Matrix

Matrix

BetaTopology.pairingMatrix The pairing matrix that indicates which strands are paired.

Uses of Matrix in ProGAL.proteins.beltaStructure.loop

Methods in ProGAL.proteins.beltaStructure.loop with parameters of type Matrix

void	LoopStructure.setFirstTransform(Matrix m)

Uses of Matrix in ProGAL.proteins.beltaStructure.sheet

Methods in ProGAL.proteins.beltaStructure.sheet that return Matrix

Matrix

SurfaceSheetStructure.getLoopTransform(SecondaryStructure.SSSegment seg) TODO

Uses of Matrix in ProGAL.proteins.chainTree

Methods in ProGAL.proteins.chainTree with parameters of type Matrix

void	ChainTree.setFirstTransformation(Matrix m) Change the orientation and translation of the entire chain.