Package org.ujmp.core.graphmatrix
Class AbstractGraphMatrix<N,E>
- java.lang.Object
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- java.lang.Number
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- org.ujmp.core.AbstractMatrix
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- org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix<A>
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- org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix<A>
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- org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix2D<E>
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- org.ujmp.core.graphmatrix.AbstractGraphMatrix<N,E>
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Matrix>
,HasMetaData
,BaseMatrix
,BooleanCalculations
,CanPerformCalculations
,DenseMatrix
,DenseMatrix2D
,DenseMatrixMultiD
,BasicDoubleCalculations
,DoubleCalculations
,BasicEntrywiseDoubleCalculations
,CreatorDoubleCalculations
,EntrywiseDoubleCalculations
,HyperbolicDoubleCalculations
,MiscEntrywiseDoubleCalculations
,RoundingDoubleCalculations
,TrigonometricDoubleCalculations
,DecompositionDoubleCalculations
,DiscretizeCalculations
,GeneralDoubleCalculations
,MiscGeneralDoubleCalculations
,MissingValueDoubleCalculations
,StatisticalDoubleCalculations
,BaseGenericMatrix<E>
,DenseGenericMatrix<E>
,DenseGenericMatrix2D<E>
,DenseGenericMatrixMultiD<E>
,GenericMatrix<E>
,GenericMatrix2D<E>
,GenericMatrixMultiD<E>
,SparseGenericMatrix<E>
,SparseGenericMatrix2D<E>
,SparseGenericMatrixMultiD<E>
,GraphMatrix<N,E>
,BaseMatrixProperties
,Clearable
,Conversions
,CoordinateFunctions
,CoreObject
,DistanceMeasures
,ExtendedMatrixProperties
,GettersAndSetters
,HasDescription
,HasGUIObject
,HasId
,HasLabel
,IntCalculations
,Matrix
,Matrix2D
,MatrixMultiD
,ObjectCalculations
,SparseMatrix
,SparseMatrix2D
,SparseMatrixMultiD
,StringCalculations
- Direct Known Subclasses:
DefaultGraphMatrix
public abstract class AbstractGraphMatrix<N,E> extends AbstractSparseGenericMatrix2D<E> implements GraphMatrix<N,E>
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description private static long
serialVersionUID
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Fields inherited from class org.ujmp.core.AbstractMatrix
guiObject, size
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Fields inherited from interface org.ujmp.core.BaseMatrix
ALL, COLUMN, LINK, NEW, NONE, ORIG, ROW, X, Y, Z
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Fields inherited from interface org.ujmp.core.DenseMatrix
Factory
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Fields inherited from interface org.ujmp.core.DenseMatrix2D
Factory
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Fields inherited from interface org.ujmp.core.interfaces.HasDescription
DESCRIPTION
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Fields inherited from interface org.ujmp.core.annotation.HasMetaData
DIMENSIONMETADATA
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Fields inherited from interface org.ujmp.core.Matrix
chol, divideMatrix, divideScalar, eig, Factory, inv, lu, minusMatrix, minusScalar, mtimes, plusMatrix, plusScalar, qr, solve, svd, timesMatrix, timesScalar, transpose
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Fields inherited from interface org.ujmp.core.SparseMatrix
Factory
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Fields inherited from interface org.ujmp.core.SparseMatrix2D
Factory
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Constructor Summary
Constructors Constructor Description AbstractGraphMatrix()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.Iterable<long[]>
availableCoordinates()
Returns an Iterator that only goes over the coordinates in the Matrix that are stored.boolean
containsCoordinates(long... coordinates)
Determines if the given Coordinates are part of the Matrix.int
getChildCount(N node)
java.util.List<java.lang.Long>
getChildIndices(N node)
java.util.List<N>
getChildren(long index)
java.util.List<N>
getChildren(N node)
int
getDegree(long nodeIndex)
int
getDegree(N node)
E
getEdge(N node1, N node2)
java.util.List<E>
getEdgesToChildren(N node)
java.util.List<E>
getEdgesToParents(N node)
long
getIndexOfNode(N o)
E
getObject(int row, int column)
E
getObject(long row, long column)
int
getParentCount(N node)
java.util.List<java.lang.Long>
getParentIndices(N node)
java.util.List<N>
getParents(long index)
java.util.List<N>
getParents(N node)
long[]
getSize()
long
getValueCount()
boolean
isConnected(long node1, long node2)
boolean
isConnected(N node1, N node2)
void
setObject(E value, int row, int column)
void
setObject(E value, long row, long column)
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Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix2D
getDimensionCount, getObject, setObject
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Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix
isSparse
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Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix
getAsObject, setAsObject
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Methods inherited from class org.ujmp.core.AbstractMatrix
abs, addMissing, allCoordinates, allValues, and, and, append, appendHorizontally, appendVertically, atimes, bigDecimalValue, bigIntegerValue, booleanValue, bootstrap, bootstrap, ceil, center, charValue, chebyshevDistanceTo, chol, clone, compareTo, containsBigDecimal, containsBigInteger, containsBoolean, containsByte, containsChar, containsDate, containsDouble, containsFloat, containsInt, containsLong, containsMissingValues, containsNull, containsObject, containsShort, containsString, convert, convertEncoding, corrcoef, cos, cosh, cosineSimilarity, cosineSimilarityTo, countMissing, cov, cumprod, cumsum, dateValue, delete, delete, delete, deleteColumns, deleteColumns, deleteColumnsWithMissingValues, deleteRows, deleteRows, deleteRowsWithMissingValues, det, diag, diff, discretize, discretize, discretizeToBoolean, discretizeToColumns, divide, divide, divide, divide, doubleValue, eig, eigSymm, eq, eq, equals, equalsAnnotation, equalsContent, euklideanDistance, euklideanDistanceTo, exp, exportTo, extractAnnotation, eye, fadeIn, fadeOut, fill, fireValueChanged, fireValueChanged, fireValueChanged, flipdim, floatValue, floor, ge, ge, getAbsoluteValueMean, getAbsoluteValueSum, getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsByteArray, getAsChar, getAsDate, getAsDouble, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsShort, getAsString, getColumnCount, getColumnForLabel, getColumnLabel, getColumnList, getCoordinatesOfMaximum, getCoordinatesOfMinimum, getCoreObjectId, getDescription, getDimensionLabel, getDimensionMetaData, getEuklideanValue, getFactory, getGUIObject, getId, getLabel, getLabelObject, getMaxValue, getMeanValue, getMetaData, getMetaData, getMetaDataDimensionMatrix, getMetaDataDouble, getMetaDataMatrix, getMetaDataString, getMinValue, getPositionForLabel, getPreferredObject, getRMS, getRowCount, getRowForLabel, getRowLabel, getRowList, getSize, getStdValue, getValueSum, getValueType, getZCount, ginv, grayScale, gt, gt, importFrom, impute, includeAnnotation, indexOfMax, indexOfMin, intValue, inv, invSPD, invSymm, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isReadOnly, isResizable, isRowVector, isScalar, isSingular, isSPD, isSquare, isSymmetric, isTransient, le, le, log, log10, log2, logistic, longValue, lowerCase, lt, lt, lu, manhattenDistance, manhattenDistanceTo, max, mean, min, minkowskiDistance, minkowskiDistanceTo, minus, minus, minus, minus, mtimes, mtimes, mutualInf, nans, ne, ne, nonZeroCoordinates, norm1, norm2, normalize, normF, normInf, not, ones, or, or, pairedTTest, pdet, pinv, pinv, plus, plus, plus, plus, power, power, princomp, prod, qr, rand, randn, rank, removePunctuation, removeWords, replace, replaceMissingBy, replaceRegex, replaceRegex, reshape, round, save, save, select, select, select, selectColumns, selectColumns, selectedCoordinates, selectedCoordinates, selectRows, selectRows, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsByteArray, setAsChar, setAsDate, setAsDouble, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsShort, setAsString, setColumnLabel, setContent, setDescription, setDimensionLabel, setDimensionMetaData, setId, setLabel, setMetaData, setMetaData, setMetaDataDimensionMatrix, setRowLabel, setSize, share, share, showGUI, shuffle, sign, sin, sinh, solve, solveSPD, solveSymm, sortrows, sqrt, squeeze, standardize, std, stem, stringValue, subMatrix, sum, svd, svd, swap, tan, tanh, tanh, tfIdf, times, times, times, times, toBigDecimalArray, toBigDecimalMatrix, toBigIntegerArray, toBigIntegerMatrix, toBooleanArray, toBooleanMatrix, toByteArray, toByteMatrix, toCharArray, toCharMatrix, toColumnVector, toDateArray, toDoubleArray, toDoubleMatrix, toFloatArray, toFloatMatrix, toHtml, toIntArray, toIntMatrix, toListMatrix, toLongArray, toLongMatrix, toMapMatrix, toObjectArray, toObjectMatrix, toRowVector, toSetMatrix, toShortArray, toShortMatrix, toString, toStringArray, toStringMatrix, trace, translate, transpose, transpose, transpose, tril, triu, unique, uniqueValueCount, upperCase, var, xor, xor, zeros
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Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.ujmp.core.BaseMatrix
getFactory
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Methods inherited from interface org.ujmp.core.interfaces.BaseMatrixProperties
allValues, equals, equalsAnnotation, equalsContent, getColumnCount, getColumnList, getDimensionCount, getRowCount, getRowList, getSize, getValueType, getZCount, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isReadOnly, isResizable, isRowVector, isScalar, isSingular, isSparse, isSquare, isSymmetric, isTransient, setSize, toString
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.basic.BasicDoubleCalculations
atimes, divide, divide, divide, divide, minus, minus, minus, minus, mtimes, mtimes, plus, plus, plus, plus, times, times, times, times
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.basic.BasicEntrywiseDoubleCalculations
abs, exp, log, log10, log2, logistic, power, power, sign, sqrt
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Methods inherited from interface org.ujmp.core.booleanmatrix.calculation.BooleanCalculations
and, and, eq, eq, ge, ge, gt, gt, le, le, lt, lt, ne, ne, not, or, or, xor, xor
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Methods inherited from interface org.ujmp.core.interfaces.Conversions
toBigDecimalMatrix, toBigIntegerMatrix, toBooleanMatrix, toByteMatrix, toCharMatrix, toDoubleMatrix, toFloatMatrix, toIntMatrix, toListMatrix, toLongMatrix, toMapMatrix, toObjectMatrix, toSetMatrix, toShortMatrix, toStringMatrix
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Methods inherited from interface org.ujmp.core.interfaces.CoordinateFunctions
allCoordinates, getCoordinatesOfMaximum, getCoordinatesOfMinimum, nonZeroCoordinates, selectedCoordinates, selectedCoordinates
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Methods inherited from interface org.ujmp.core.interfaces.CoreObject
getCoreObjectId
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.creators.CreatorDoubleCalculations
eye, nans, ones, rand, randn, zeros
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.decomposition.DecompositionDoubleCalculations
chol, eig, eigSymm, ginv, inv, invSPD, invSymm, lu, pinv, pinv, princomp, qr, solve, solveSPD, solveSymm, svd, svd
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.discretize.DiscretizeCalculations
discretize, discretize, discretizeToBoolean, discretizeToColumns
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Methods inherited from interface org.ujmp.core.interfaces.DistanceMeasures
chebyshevDistanceTo, cosineSimilarity, cosineSimilarityTo, euklideanDistance, euklideanDistanceTo, manhattenDistance, manhattenDistanceTo, minkowskiDistance, minkowskiDistanceTo
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Methods inherited from interface org.ujmp.core.interfaces.ExtendedMatrixProperties
bigDecimalValue, bigIntegerValue, booleanValue, byteValue, charValue, containsBigDecimal, containsBigInteger, containsBoolean, containsByte, containsChar, containsDate, containsDouble, containsFloat, containsInt, containsLong, containsMissingValues, containsNull, containsObject, containsShort, containsString, dateValue, det, doubleValue, floatValue, getAbsoluteValueMean, getAbsoluteValueSum, getEuklideanValue, getMaxValue, getMeanValue, getMinValue, getRMS, getStdValue, getValueSum, intValue, isSPD, longValue, norm1, norm2, normF, normInf, pdet, rank, setContent, shortValue, stringValue, trace
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Methods inherited from interface org.ujmp.core.interfaces.GettersAndSetters
getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsByteArray, getAsChar, getAsDate, getAsDouble, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsObject, getAsShort, getAsString, getPreferredObject, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsByteArray, setAsChar, setAsDate, setAsDouble, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsObject, setAsShort, setAsString, toBigDecimalArray, toBigIntegerArray, toBooleanArray, toByteArray, toCharArray, toDateArray, toDoubleArray, toFloatArray, toIntArray, toLongArray, toObjectArray, toShortArray, toStringArray
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Methods inherited from interface org.ujmp.core.graphmatrix.GraphMatrix
addNode, getChildCount, getChildIndices, getEdge, getEdgeCount, getNode, getNodeCount, getNodeList, getParentCount, getParentIndices, isDirected, removeEdge, removeEdge, removeNode, removeNode, setDirected, setEdge, setEdge, setNode
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Methods inherited from interface org.ujmp.core.interfaces.HasDescription
getDescription, setDescription
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Methods inherited from interface org.ujmp.core.interfaces.HasGUIObject
getGUIObject, showGUI
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Methods inherited from interface org.ujmp.core.interfaces.HasLabel
getLabel, getLabelObject, setLabel
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Methods inherited from interface org.ujmp.core.annotation.HasMetaData
getColumnForLabel, getColumnLabel, getDimensionLabel, getDimensionMetaData, getMetaData, getMetaData, getMetaDataDimensionMatrix, getMetaDataDouble, getMetaDataMatrix, getMetaDataString, getPositionForLabel, getRowForLabel, getRowLabel, setColumnLabel, setDimensionLabel, setDimensionMetaData, setMetaData, setMetaData, setMetaDataDimensionMatrix, setRowLabel
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.hyperbolic.HyperbolicDoubleCalculations
cosh, sinh, tanh, tanh
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Methods inherited from interface org.ujmp.core.Matrix
clone, exportTo, fireValueChanged, fireValueChanged, fireValueChanged, importFrom, save, save, share, share, toHtml
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.misc.MiscEntrywiseDoubleCalculations
grayScale
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.misc.MiscGeneralDoubleCalculations
append, appendHorizontally, appendVertically, center, fadeIn, fadeOut, normalize, replaceMissingBy, standardize
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.missingvalues.MissingValueDoubleCalculations
addMissing, countMissing, deleteColumnsWithMissingValues, deleteRowsWithMissingValues, impute
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Methods inherited from interface org.ujmp.core.objectmatrix.calculation.ObjectCalculations
bootstrap, bootstrap, convert, delete, delete, delete, deleteColumns, deleteColumns, deleteRows, deleteRows, diag, extractAnnotation, fill, flipdim, includeAnnotation, replace, reshape, select, select, select, selectColumns, selectColumns, selectRows, selectRows, shuffle, sortrows, squeeze, subMatrix, swap, toColumnVector, toRowVector, transpose, transpose, transpose, tril, triu, unique, uniqueValueCount
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.rounding.RoundingDoubleCalculations
ceil, floor, round
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.statistical.StatisticalDoubleCalculations
corrcoef, cov, cumprod, cumsum, diff, indexOfMax, indexOfMin, max, mean, min, mutualInf, pairedTTest, prod, std, sum, var
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Methods inherited from interface org.ujmp.core.stringmatrix.calculation.StringCalculations
convertEncoding, lowerCase, removePunctuation, removeWords, replaceRegex, replaceRegex, stem, tfIdf, translate, upperCase
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Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.trigonometric.TrigonometricDoubleCalculations
cos, sin, tan
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Field Detail
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serialVersionUID
private static final long serialVersionUID
- See Also:
- Constant Field Values
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Method Detail
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containsCoordinates
public boolean containsCoordinates(long... coordinates)
Description copied from interface:CoordinateFunctions
Determines if the given Coordinates are part of the Matrix. If the Matrix is dense, true is returned for all Coordinates smaller than the Matrix's size. For sparse Matrices, this function checks if the coordinates are actually stored in the matrix or not.- Specified by:
containsCoordinates
in interfaceCoordinateFunctions
- Parameters:
coordinates
- The coordinates to check- Returns:
- a boolean stating if the coordinates are part of the Matrix
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isConnected
public boolean isConnected(N node1, N node2)
- Specified by:
isConnected
in interfaceGraphMatrix<N,E>
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getParents
public java.util.List<N> getParents(long index)
- Specified by:
getParents
in interfaceGraphMatrix<N,E>
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getParents
public java.util.List<N> getParents(N node)
- Specified by:
getParents
in interfaceGraphMatrix<N,E>
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getChildren
public java.util.List<N> getChildren(long index)
- Specified by:
getChildren
in interfaceGraphMatrix<N,E>
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getParentIndices
public java.util.List<java.lang.Long> getParentIndices(N node)
- Specified by:
getParentIndices
in interfaceGraphMatrix<N,E>
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getDegree
public int getDegree(N node)
- Specified by:
getDegree
in interfaceGraphMatrix<N,E>
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getDegree
public int getDegree(long nodeIndex)
- Specified by:
getDegree
in interfaceGraphMatrix<N,E>
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getChildCount
public int getChildCount(N node)
- Specified by:
getChildCount
in interfaceGraphMatrix<N,E>
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getParentCount
public int getParentCount(N node)
- Specified by:
getParentCount
in interfaceGraphMatrix<N,E>
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getChildIndices
public java.util.List<java.lang.Long> getChildIndices(N node)
- Specified by:
getChildIndices
in interfaceGraphMatrix<N,E>
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getChildren
public java.util.List<N> getChildren(N node)
- Specified by:
getChildren
in interfaceGraphMatrix<N,E>
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availableCoordinates
public java.lang.Iterable<long[]> availableCoordinates()
Description copied from interface:CoordinateFunctions
Returns an Iterator that only goes over the coordinates in the Matrix that are stored. For most Matrices, this is the same as allCoordinates(). For sparse Matrices, it iterates only over the entries in it.- Specified by:
availableCoordinates
in interfaceCoordinateFunctions
- Returns:
- Iterable over the saved entries in a Matrix.
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getSize
public final long[] getSize()
- Specified by:
getSize
in interfaceBaseMatrixProperties
- Overrides:
getSize
in classAbstractMatrix
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getObject
public final E getObject(long row, long column)
- Specified by:
getObject
in interfaceGenericMatrix2D<N>
- Overrides:
getObject
in classAbstractGenericMatrix<E>
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getObject
public final E getObject(int row, int column)
- Specified by:
getObject
in interfaceGenericMatrix2D<N>
- Overrides:
getObject
in classAbstractGenericMatrix<E>
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getValueCount
public final long getValueCount()
- Specified by:
getValueCount
in interfaceBaseMatrixProperties
- Overrides:
getValueCount
in classAbstractMatrix
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setObject
public final void setObject(E value, long row, long column)
- Specified by:
setObject
in interfaceGenericMatrix2D<N>
- Overrides:
setObject
in classAbstractGenericMatrix<E>
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setObject
public final void setObject(E value, int row, int column)
- Specified by:
setObject
in interfaceGenericMatrix2D<N>
- Overrides:
setObject
in classAbstractGenericMatrix<E>
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isConnected
public final boolean isConnected(long node1, long node2)
- Specified by:
isConnected
in interfaceGraphMatrix<N,E>
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getIndexOfNode
public final long getIndexOfNode(N o)
- Specified by:
getIndexOfNode
in interfaceGraphMatrix<N,E>
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