org.ujmp.core.graphmatrix
Class DefaultGraphMatrix<N,E>

java.lang.Object
  extended by java.lang.Number
      extended by org.ujmp.core.matrix.AbstractMatrix
          extended by org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix<A>
              extended by org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix<A>
                  extended by org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix2D<E>
                      extended by org.ujmp.core.graphmatrix.AbstractGraphMatrix<N,E>
                          extended by org.ujmp.core.graphmatrix.DefaultGraphMatrix<N,E>
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Matrix>, HasAnnotation, BooleanCalculations, CanPerformCalculations, BasicDoubleCalculations, DoubleCalculations, BasicEntrywiseDoubleCalculations, CreatorDoubleCalculations, EntrywiseDoubleCalculations, HyperbolicDoubleCalculations, MiscEntrywiseDoubleCalculations, RoundingDoubleCalculations, TrigonometricDoubleCalculations, DecompositionDoubleCalculations, DiscretizeCalculations, GeneralDoubleCalculations, MiscGeneralDoubleCalculations, MissingValueDoubleCalculations, StatisticalDoubleCalculations, GenericMatrix<E>, GenericMatrix2D<E>, SparseGenericMatrix<E>, SparseGenericMatrix2D<E>, GenericGraph<N,E>, GraphMatrix<N,E>, BasicMatrixProperties, Clearable, Conversions, CoordinateFunctions, CoreObject, DistanceMeasures, GettersAndSetters, HasGUIObject, HasLabel, IntCalculations, ExportMatrixInterface, Matrix, Matrix2D, SparseMatrix, SparseMatrix2D, ObjectCalculations, StringCalculations

public class DefaultGraphMatrix<N,E>
extends AbstractGraphMatrix<N,E>

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.ujmp.core.Matrix
Matrix.StorageType
 
Field Summary
 
Fields inherited from class org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix
factory
 
Fields inherited from interface org.ujmp.core.Matrix
ALL, chol, COLUMN, divideMatrix, divideScalar, eig, factory, inv, LINK, lu, minusMatrix, minusScalar, mtimes, NEW, NONE, ORIG, plusMatrix, plusScalar, qr, ROW, solve, svd, timesMatrix, timesScalar, transpose, X, Y, Z
 
Fields inherited from interface org.ujmp.core.matrix.SparseMatrix
factory
 
Constructor Summary
DefaultGraphMatrix()
           
DefaultGraphMatrix(List<N> nodes)
           
 
Method Summary
 void addChild(N node, N child)
           
 void addDirectedEdge(long node1, long node2)
           
 void addEdge(long nodeIndex1, long nodeIndex2)
           
 void addEdge(N node1, N node2)
           
 void addNode(N o)
           
 void addUndirectedEdge(long node1, long node2)
           
 Iterable<long[]> availableCoordinates()
          Returns an Iterator that only goes over the coordinates in the Matrix that are stored.
 void clear()
           
 int getChildCount(long nodeIndex)
           
 List<Long> getChildIndices(long index)
           
 int getEdgeCount()
           
 Collection<E> getEdgeList()
           
 E getEdgeValue(long node1, long node2)
           
 N getNode(long index)
           
 int getNodeCount()
           
 List<N> getNodeList()
           
 int getParentCount(long nodeIndex)
           
 List<Long> getParentIndices(long index)
           
 ValueType getValueType()
           
 void insertNode(N node, long index)
           
 boolean isDirected()
           
 void removeDirectedEdge(long nodeIndex1, long nodeIndex2)
           
 void removeEdge(long node1, long node2)
           
 void removeEdge(N node1, N node2)
           
 void removeNode(long node)
           
 void removeNode(N o)
           
 void setDirected(boolean directed)
           
 void setDirectedEdge(E value, long node1, long node2)
           
 void setEdge(E edgeObject, long nodeIndex1, long nodeIndex2)
           
 void setEdge(E edgeObject, N node1, N node2)
           
 void setNode(N node, long index)
           
 void setObject(Object o, int row, int column)
           
 void setObject(Object o, long row, long column)
           
 
Methods inherited from class org.ujmp.core.graphmatrix.AbstractGraphMatrix
addChild, addDirectedEdge, addParent, addParent, addUndirectedEdge, contains, getChildCount, getChildIndices, getChildren, getChildren, getDegree, getDegree, getEdgeValue, getFactory, getIndexOfNode, getObject, getObject, getParentCount, getParentIndices, getParents, getParents, getSize, getStorageType, getValueCount, isConnected, isConnected, removeDirectedEdge, removeUndirectedEdge, removeUndirectedEdge, setDirectedEdge, setUndirectedEdge, setUndirectedEdge
 
Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractSparseGenericMatrix2D
getObject, setObject
 
Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix
getAsObject, setAsObject
 
Methods inherited from class org.ujmp.core.matrix.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, copy, corrcoef, cos, cosh, countMissing, cov, cumprod, cumsum, dateValue, delete, delete, delete, deleteColumns, deleteColumns, deleteColumnsWithMissingValues, deleteRows, deleteRows, deleteRowsWithMissingValues, det, diff, discretize, discretizeToColumns, divide, divide, divide, divide, doubleValue, eig, eigSymm, eq, eq, equals, equalsAnnotation, equalsContent, euklideanDistanceTo, exp, exportToClipboard, exportToFile, exportToFile, exportToFile, exportToFile, exportToStream, exportToString, exportToWriter, extractAnnotation, eye, fadeIn, fadeOut, fill, flipdim, floatValue, floor, ge, ge, getAbsoluteValueMean, getAbsoluteValueSum, getAnnotation, getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsChar, getAsDate, getAsDouble, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsShort, getAsString, getAxisAnnotation, getAxisAnnotation, getColumnCount, getColumnForLabel, getColumnLabel, getColumnObject, getCoordinatesOfMaximum, getCoordinatesOfMinimum, getCoreObjectId, getDimensionCount, getEuklideanValue, getGUIObject, getLabel, getMatrixAnnotation, getMaxValue, getMeanValue, getMinValue, getPositionForLabel, getPreferredObject, getRMS, getRowCount, getRowForLabel, getRowLabel, getRowObject, getSize, getStdValue, getValueSum, getZCount, ginv, gt, gt, impute, includeAnnotation, indexOfMax, indexOfMin, intValue, inv, invSPD, invSymm, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isReadOnly, isResizable, isRowVector, isScalar, isSingular, isSparse, isSPD, isSquare, isSymmetric, isTransient, le, le, log, log10, log2, longValue, lowerCase, lt, lt, lu, manhattenDistanceTo, max, mean, min, minkowskiDistanceTo, minus, minus, minus, minus, mtimes, mtimes, mtimes, mtimes, mutualInf, ne, ne, nonZeroCoordinates, norm1, norm2, normalize, normF, normInf, not, notifyGUIObject, ones, or, or, pairedTTest, pinv, plus, plus, plus, plus, power, power, princomp, prod, qr, rand, randn, rank, removePunctuation, removeWords, replace, replaceMissingBy, replaceRegex, replaceRegex, reshape, round, select, select, select, selectColumns, selectColumns, selectedCoordinates, selectedCoordinates, selectRows, selectRows, setAnnotation, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsChar, setAsDate, setAsDouble, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsShort, setAsString, setAxisAnnotation, setAxisAnnotation, setColumnLabel, setColumnObject, setLabel, setMatrixAnnotation, setRowLabel, setRowObject, setSize, showGUI, shuffle, sign, sin, sinh, solve, solveSPD, solveSymm, sortrows, sqrt, squeeze, standardize, std, stem, stringValue, subMatrix, sum, svd, swap, tan, tanh, tfIdf, times, times, times, times, toBigDecimalArray, toBigDecimalMatrix, toBigIntegerArray, toBigIntegerMatrix, toBooleanArray, toBooleanMatrix, toByteArray, toByteMatrix, toCharArray, toCharMatrix, toColumnVector, toDateArray, toDateMatrix, toDoubleArray, toDoubleMatrix, toFloatArray, toFloatMatrix, toIntArray, toIntMatrix, toListMatrix, toLongArray, toLongMatrix, toMapMatrix, toObjectArray, toObjectMatrix, toRowVector, toSetMatrix, toShortArray, toShortMatrix, toString, toStringArray, toStringMatrix, trace, transpose, transpose, transpose, tril, triu, unique, uniqueValueCount, upperCase, var, xor, xor, zeros
 
Methods inherited from class java.lang.Number
byteValue, shortValue
 
Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.ujmp.core.genericmatrix.GenericMatrix
getObject, setObject
 
Methods inherited from interface org.ujmp.core.Matrix
clone
 
Methods inherited from interface org.ujmp.core.interfaces.CoreObject
getCoreObjectId
 
Methods inherited from interface org.ujmp.core.interfaces.HasGUIObject
getGUIObject, notifyGUIObject, showGUI
 
Methods inherited from interface org.ujmp.core.interfaces.HasLabel
getLabel, setLabel
 
Methods inherited from interface org.ujmp.core.io.ExportMatrixInterface
exportToClipboard, exportToFile, exportToFile, exportToFile, exportToFile, exportToStream, exportToString, exportToWriter
 
Methods inherited from interface org.ujmp.core.interfaces.CoordinateFunctions
allCoordinates, getCoordinatesOfMaximum, getCoordinatesOfMinimum, nonZeroCoordinates, selectedCoordinates, selectedCoordinates
 
Methods inherited from interface org.ujmp.core.interfaces.GettersAndSetters
getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsChar, getAsDate, getAsDouble, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsObject, getAsShort, getAsString, getPreferredObject, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsChar, setAsDate, setAsDouble, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsObject, setAsShort, setAsString, toBigDecimalArray, toBigIntegerArray, toBooleanArray, toByteArray, toCharArray, toDateArray, toDoubleArray, toFloatArray, toIntArray, toLongArray, toObjectArray, toShortArray, toStringArray
 
Methods inherited from interface org.ujmp.core.interfaces.BasicMatrixProperties
allValues, bigDecimalValue, bigIntegerValue, booleanValue, byteValue, charValue, containsBigDecimal, containsBigInteger, containsBoolean, containsByte, containsChar, containsDate, containsDouble, containsFloat, containsInt, containsLong, containsMissingValues, containsNull, containsObject, containsShort, containsString, dateValue, det, doubleValue, equals, equalsAnnotation, equalsContent, floatValue, getAbsoluteValueMean, getAbsoluteValueSum, getColumnCount, getDimensionCount, getEuklideanValue, getMaxValue, getMeanValue, getMinValue, getRMS, getRowCount, getSize, getStdValue, getValueSum, getZCount, intValue, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isReadOnly, isResizable, isRowVector, isScalar, isSingular, isSparse, isSPD, isSquare, isSymmetric, isTransient, longValue, norm1, norm2, normF, normInf, rank, setSize, shortValue, stringValue, toString, trace
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.basic.BasicDoubleCalculations
atimes, divide, divide, divide, divide, minus, minus, minus, minus, mtimes, mtimes, mtimes, mtimes, plus, plus, plus, plus, times, times, times, times
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.basic.BasicEntrywiseDoubleCalculations
abs, exp, log, log10, log2, power, power, sign, sqrt
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.rounding.RoundingDoubleCalculations
ceil, floor, round
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.hyperbolic.HyperbolicDoubleCalculations
cosh, sinh, tanh
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.trigonometric.TrigonometricDoubleCalculations
cos, sin, tan
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.creators.CreatorDoubleCalculations
eye, ones, rand, randn, zeros
 
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
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.decomposition.DecompositionDoubleCalculations
chol, eig, eigSymm, ginv, inv, invSPD, invSymm, lu, pinv, princomp, qr, solve, solveSPD, solveSymm, svd
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.missingvalues.MissingValueDoubleCalculations
addMissing, countMissing, deleteColumnsWithMissingValues, deleteRowsWithMissingValues, impute
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.misc.MiscGeneralDoubleCalculations
append, appendHorizontally, appendVertically, center, fadeIn, fadeOut, normalize, replaceMissingBy, standardize
 
Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.discretize.DiscretizeCalculations
discretizeToColumns
 
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
 
Methods inherited from interface org.ujmp.core.intmatrix.calculation.IntCalculations
discretize
 
Methods inherited from interface org.ujmp.core.stringmatrix.calculation.StringCalculations
lowerCase, removePunctuation, removeWords, replaceRegex, replaceRegex, stem, tfIdf, upperCase
 
Methods inherited from interface org.ujmp.core.objectmatrix.calculation.ObjectCalculations
bootstrap, bootstrap, convert, copy, delete, delete, delete, deleteColumns, deleteColumns, deleteRows, deleteRows, 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
 
Methods inherited from interface org.ujmp.core.interfaces.DistanceMeasures
chebyshevDistanceTo, euklideanDistanceTo, manhattenDistanceTo, minkowskiDistanceTo
 
Methods inherited from interface java.lang.Comparable
compareTo
 
Methods inherited from interface org.ujmp.core.annotation.HasAnnotation
getAnnotation, getAxisAnnotation, getAxisAnnotation, getColumnForLabel, getColumnLabel, getColumnObject, getMatrixAnnotation, getPositionForLabel, getRowForLabel, getRowLabel, getRowObject, setAnnotation, setAxisAnnotation, setAxisAnnotation, setColumnLabel, setColumnObject, setMatrixAnnotation, setRowLabel, setRowObject
 
Methods inherited from interface org.ujmp.core.interfaces.Conversions
toBigDecimalMatrix, toBigIntegerMatrix, toBooleanMatrix, toByteMatrix, toCharMatrix, toDateMatrix, toDoubleMatrix, toFloatMatrix, toIntMatrix, toListMatrix, toLongMatrix, toMapMatrix, toObjectMatrix, toSetMatrix, toShortMatrix, toStringMatrix
 

Constructor Detail

DefaultGraphMatrix

public DefaultGraphMatrix()

DefaultGraphMatrix

public DefaultGraphMatrix(List<N> nodes)
Method Detail

getEdgeList

public Collection<E> getEdgeList()

availableCoordinates

public 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 interface CoordinateFunctions
Overrides:
availableCoordinates in class AbstractGraphMatrix<N,E>
Returns:
Iterable over the saved entries in a Matrix.

getNodeList

public List<N> getNodeList()

setDirectedEdge

public void setDirectedEdge(E value,
                            long node1,
                            long node2)

addNode

public void addNode(N o)

removeEdge

public void removeEdge(long node1,
                       long node2)

removeNode

public void removeNode(N o)

getEdgeValue

public E getEdgeValue(long node1,
                      long node2)

getEdgeCount

public int getEdgeCount()

getNodeCount

public int getNodeCount()

addDirectedEdge

public void addDirectedEdge(long node1,
                            long node2)
Specified by:
addDirectedEdge in interface GenericGraph<N,E>
Specified by:
addDirectedEdge in class AbstractGraphMatrix<N,E>

addUndirectedEdge

public void addUndirectedEdge(long node1,
                              long node2)
Specified by:
addUndirectedEdge in interface GenericGraph<N,E>
Specified by:
addUndirectedEdge in class AbstractGraphMatrix<N,E>

clear

public void clear()
Specified by:
clear in interface Clearable
Specified by:
clear in class AbstractGraphMatrix<N,E>

addChild

public void addChild(N node,
                     N child)

getChildCount

public int getChildCount(long nodeIndex)

getNode

public N getNode(long index)

getParentCount

public int getParentCount(long nodeIndex)

getParentIndices

public List<Long> getParentIndices(long index)

getChildIndices

public List<Long> getChildIndices(long index)

insertNode

public void insertNode(N node,
                       long index)

removeDirectedEdge

public void removeDirectedEdge(long nodeIndex1,
                               long nodeIndex2)

removeNode

public void removeNode(long node)

isDirected

public boolean isDirected()

setDirected

public void setDirected(boolean directed)

setNode

public void setNode(N node,
                    long index)

setObject

public void setObject(Object o,
                      long row,
                      long column)
               throws MatrixException
Throws:
MatrixException

setObject

public void setObject(Object o,
                      int row,
                      int column)
               throws MatrixException
Throws:
MatrixException

addEdge

public void addEdge(N node1,
                    N node2)

addEdge

public void addEdge(long nodeIndex1,
                    long nodeIndex2)

removeEdge

public void removeEdge(N node1,
                       N node2)

setEdge

public void setEdge(E edgeObject,
                    long nodeIndex1,
                    long nodeIndex2)

setEdge

public void setEdge(E edgeObject,
                    N node1,
                    N node2)

getValueType

public ValueType getValueType()
Specified by:
getValueType in interface BasicMatrixProperties
Overrides:
getValueType in class AbstractMatrix


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