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## Uses of Class
pipe.dataLayer.PNMatrix

Packages that use PNMatrix
pipe.dataLayer |
pipe.dataLayer.calculations |
pipe.modules.invariantAnalysis |

Uses of PNMatrix in pipe.dataLayer

Fields in pipe.dataLayer declared as PNMatrix
`private PNMatrix` | `DataLayer.markupHistoryMatrix` Markup Storage Array
`private PNMatrix` | `DataLayer.fowardsIncidenceMatrix` Foward Incidence Matrix
`private PNMatrix` | `DataLayer.backwardsIncidenceMatrix` Backward Incidence Matrix
`private PNMatrix` | `DataLayer.incidenceMatrix` Incidence Matrix

Methods in pipe.dataLayer that return PNMatrix
`PNMatrix` | `PNMatrix.appendVector(PNMatrix X)` Append a column matrix (vector) to the right of another matrix.
`static PNMatrix` | `PNMatrix.constructWithCopy(int[][] A)` Construct a matrix from a copy of a 2-D array.
`PNMatrix` | `PNMatrix.copy()` Make a deep copy of a matrix
`PNMatrix` | `PNMatrix.eliminateCol(int toDelete)` Eliminate a column from the matrix, column index is toDelete
`PNMatrix` | `PNMatrix.nonZeroIndices()` Form a matrix with columns the row indices of non-zero elements.
`PNMatrix` | `PNMatrix.getMatrix(int i0, int i1, int j0, int j1)` Get a submatrix.
`PNMatrix` | `PNMatrix.getMatrix(int[] r, int[] c)` Get a submatrix.
`PNMatrix` | `PNMatrix.getMatrix(int i0, int i1, int[] c)` Get a submatrix.
`PNMatrix` | `PNMatrix.getMatrix(int[] r, int j0, int j1)` Get a submatrix.
`PNMatrix` | `PNMatrix.transpose()` Matrix transpose.
`PNMatrix` | `PNMatrix.uminus()` Unary minus
`PNMatrix` | `PNMatrix.plus(PNMatrix B)` C = A + B
`PNMatrix` | `PNMatrix.plusEquals(PNMatrix B)` A = A + B
`PNMatrix` | `PNMatrix.minus(PNMatrix B)` C = A - B
`PNMatrix` | `PNMatrix.minusEquals(PNMatrix B)` A = A - B
`PNMatrix` | `PNMatrix.timesEquals(int s)` Multiply a matrix by an int in place, A = s*A
`PNMatrix` | `PNMatrix.divideEquals(int s)` Divide a matrix by an int in place, A = s*A
`static PNMatrix` | `PNMatrix.identity(int m, int n)` Generate identity matrix]

Methods in pipe.dataLayer with parameters of type PNMatrix
`PNMatrix` | `PNMatrix.appendVector(PNMatrix X)` Append a column matrix (vector) to the right of another matrix.
`void` | `PNMatrix.setMatrix(int i0, int i1, int j0, int j1, PNMatrix X)` Set a submatrix.
`void` | `PNMatrix.setMatrix(int[] r, int[] c, PNMatrix X)` Set a submatrix.
`void` | `PNMatrix.setMatrix(int[] r, int j0, int j1, PNMatrix X)` Set a submatrix.
`void` | `PNMatrix.setMatrix(int i0, int i1, int[] c, PNMatrix X)` Set a submatrix.
`PNMatrix` | `PNMatrix.plus(PNMatrix B)` C = A + B
`PNMatrix` | `PNMatrix.plusEquals(PNMatrix B)` A = A + B
`PNMatrix` | `PNMatrix.minus(PNMatrix B)` C = A - B
`PNMatrix` | `PNMatrix.minusEquals(PNMatrix B)` A = A - B
`int` | `PNMatrix.vectorTimes(PNMatrix B)` Multiply a row matrix by a column matrix, A = s*A
`private void` | `PNMatrix.checkMatrixDimensions(PNMatrix B)` Throws IllegalArgumentException if dimensions of A and B differ.

Uses of PNMatrix in pipe.dataLayer.calculations

Fields in pipe.dataLayer.calculations declared as PNMatrix
`PNMatrix` | `myTree.CPlus`
`PNMatrix` | `myTree.CMinus`

Constructors in pipe.dataLayer.calculations with parameters of type PNMatrix
`myTree(int[] tree_root, PNMatrix plus, PNMatrix minus)`
`myTree(int[] tree_root, PNMatrix plus, PNMatrix minus, StateList statespace, DataLayer pnmldata)`

Uses of PNMatrix in pipe.modules.invariantAnalysis

Fields in pipe.modules.invariantAnalysis declared as PNMatrix
`private PNMatrix` | `InvariantAnalysis.IncidenceMatrix`
`private PNMatrix` | `InvariantAnalysis.PInvariants`
`private PNMatrix` | `InvariantAnalysis.TInvariants`

Methods in pipe.modules.invariantAnalysis that return PNMatrix
`PNMatrix` | `InvariantAnalysis.findVectors(PNMatrix C)` Transform a matrix to obtain the minimal generating set of vectors.

Methods in pipe.modules.invariantAnalysis with parameters of type PNMatrix
`PNMatrix` | `InvariantAnalysis.findVectors(PNMatrix C)` Transform a matrix to obtain the minimal generating set of vectors.

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