org.ujmp.core.doublematrix.impl
Class DenseFileMatrix

java.lang.Object
  extended by java.lang.Number
      extended by org.ujmp.core.matrix.AbstractMatrix
          extended by org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix<Double>
              extended by org.ujmp.core.doublematrix.stub.AbstractDoubleMatrix
                  extended by org.ujmp.core.doublematrix.stub.AbstractDenseDoubleMatrix
                      extended by org.ujmp.core.doublematrix.impl.DenseFileMatrix
All Implemented Interfaces:
Closeable, Serializable, Cloneable, Comparable<Matrix>, HasAnnotation, BooleanCalculations, CanPerformCalculations, BasicDoubleCalculations, DoubleCalculations, BasicEntrywiseDoubleCalculations, CreatorDoubleCalculations, EntrywiseDoubleCalculations, HyperbolicDoubleCalculations, MiscEntrywiseDoubleCalculations, RoundingDoubleCalculations, TrigonometricDoubleCalculations, DecompositionDoubleCalculations, DiscretizeCalculations, GeneralDoubleCalculations, MiscGeneralDoubleCalculations, MissingValueDoubleCalculations, StatisticalDoubleCalculations, DenseDoubleMatrix, DoubleMatrix, GenericMatrix<Double>, BasicMatrixProperties, Clearable, Conversions, CoordinateFunctions, CoreObject, DistanceMeasures, Erasable, GettersAndSetters, HasGUIObject, HasLabel, IntCalculations, ExportMatrixInterface, Matrix, DenseMatrix, ObjectCalculations, StringCalculations
Direct Known Subclasses:
WaveMatrix

public class DenseFileMatrix
extends AbstractDenseDoubleMatrix
implements Erasable, Closeable

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.ujmp.core.Matrix
Matrix.StorageType
 
Field Summary
static int BOOLEAN
           
static int BYTE
           
static int CHAR
           
static int DOUBLE
           
static int FLOAT
           
static int INT
           
static int INTLITTLEENDIAN
           
static int LONG
           
static int LONGLITTLEENDIAN
           
static int SHORT
           
static int SHORTLITTLEENDIAN
           
static int UNSIGNEDBYTE
           
static int UNSIGNEDSHORT
           
 
Fields inherited from class org.ujmp.core.doublematrix.stub.AbstractDenseDoubleMatrix
factory
 
Fields inherited from interface org.ujmp.core.Matrix
ALL, chol, COLUMN, divideMatrix, divideScalar, eig, inv, LINK, lu, minusMatrix, minusScalar, mtimes, NEW, NONE, ORIG, plusMatrix, plusScalar, qr, ROW, solve, svd, timesMatrix, timesScalar, transpose, X, Y, Z
 
Constructor Summary
DenseFileMatrix(File file)
           
DenseFileMatrix(File file, int dataType, long... size)
           
DenseFileMatrix(File file, long... size)
           
DenseFileMatrix(File file, long offset, int dataType, boolean readOnly, long... size)
           
DenseFileMatrix(int bufferSize, File file, long offset, int dataType, boolean readOnly, long... size)
           
DenseFileMatrix(long... size)
           
DenseFileMatrix(Matrix m)
           
 
Method Summary
 void close()
           
 void erase()
           
protected  void finalize()
           
 int getBitsPerValue()
           
 int getBufferSize()
           
 long getBytesPerValue()
           
 int getDataType()
           
 double getDouble(long... c)
          Returns a double representation of an entry in the matrix.
 File getFile()
           
 long getFileLength()
           
static int getIntLittleEndian(byte[] bytes)
           
 BufferedRandomAccessFile getRandomAccessFile()
           
static int getShortLittleEndian(byte[] bytes)
           
 long[] getSize()
           
 boolean isReadOnly()
           
 void setBufferSize(int bufferSize)
           
 void setDouble(double value, long... c)
          Sets an entry in the matrix to a double value.
 void setSize(long... size)
          Sets the size of the matrix.
 
Methods inherited from class org.ujmp.core.doublematrix.stub.AbstractDenseDoubleMatrix
contains, getFactory, getStorageType
 
Methods inherited from class org.ujmp.core.doublematrix.stub.AbstractDoubleMatrix
getAsDouble, getObject, getValueType, setAsDouble, 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, availableCoordinates, bigDecimalValue, bigIntegerValue, booleanValue, bootstrap, bootstrap, ceil, center, charValue, chebyshevDistanceTo, chol, clear, 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, 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, getValueCount, getValueSum, getZCount, ginv, gt, gt, impute, includeAnnotation, indexOfMax, indexOfMin, intValue, inv, invSPD, invSymm, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, 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, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsShort, setAsString, setAxisAnnotation, setAxisAnnotation, setColumnLabel, setColumnObject, setLabel, setMatrixAnnotation, setRowLabel, setRowObject, 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
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.Clearable
clear
 
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, availableCoordinates, 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, getValueCount, getValueSum, getValueType, getZCount, intValue, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isResizable, isRowVector, isScalar, isSingular, isSparse, isSPD, isSquare, isSymmetric, isTransient, longValue, norm1, norm2, normF, normInf, rank, 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
 

Field Detail

BYTE

public static final int BYTE
See Also:
Constant Field Values

CHAR

public static final int CHAR
See Also:
Constant Field Values

DOUBLE

public static final int DOUBLE
See Also:
Constant Field Values

FLOAT

public static final int FLOAT
See Also:
Constant Field Values

INT

public static final int INT
See Also:
Constant Field Values

LONG

public static final int LONG
See Also:
Constant Field Values

SHORT

public static final int SHORT
See Also:
Constant Field Values

UNSIGNEDBYTE

public static final int UNSIGNEDBYTE
See Also:
Constant Field Values

UNSIGNEDSHORT

public static final int UNSIGNEDSHORT
See Also:
Constant Field Values

SHORTLITTLEENDIAN

public static final int SHORTLITTLEENDIAN
See Also:
Constant Field Values

INTLITTLEENDIAN

public static final int INTLITTLEENDIAN
See Also:
Constant Field Values

LONGLITTLEENDIAN

public static final int LONGLITTLEENDIAN
See Also:
Constant Field Values

BOOLEAN

public static final int BOOLEAN
See Also:
Constant Field Values
Constructor Detail

DenseFileMatrix

public DenseFileMatrix(File file,
                       long... size)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(File file)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(File file,
                       int dataType,
                       long... size)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(File file,
                       long offset,
                       int dataType,
                       boolean readOnly,
                       long... size)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(int bufferSize,
                       File file,
                       long offset,
                       int dataType,
                       boolean readOnly,
                       long... size)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(long... size)
                throws IOException
Throws:
IOException

DenseFileMatrix

public DenseFileMatrix(Matrix m)
                throws IOException
Throws:
IOException
Method Detail

getBufferSize

public int getBufferSize()

setBufferSize

public void setBufferSize(int bufferSize)

getRandomAccessFile

public BufferedRandomAccessFile getRandomAccessFile()

getFile

public File getFile()

getBytesPerValue

public long getBytesPerValue()

getBitsPerValue

public int getBitsPerValue()

getFileLength

public long getFileLength()

getDataType

public int getDataType()

getDouble

public double getDouble(long... c)
Description copied from interface: DoubleMatrix
Returns a double representation of an entry in the matrix. The stored value will be converted to a double as good as possible.

Specified by:
getDouble in interface DoubleMatrix
Parameters:
c - location of the entry
Returns:
a double representation of the entry

setSize

public void setSize(long... size)
Description copied from interface: BasicMatrixProperties
Sets the size of the matrix. This is an optional method that is not implemented for all matrices. If this method is not implemented, a MatrixException is thrown.

Specified by:
setSize in interface BasicMatrixProperties
Overrides:
setSize in class AbstractMatrix
Parameters:
size - the new size of the matrix

setDouble

public void setDouble(double value,
                      long... c)
Description copied from interface: DoubleMatrix
Sets an entry in the matrix to a double value. If the matrix cannot store double values, the value will be represented as good as possible.

Specified by:
setDouble in interface DoubleMatrix
Parameters:
value - double value
c - location of the entry

finalize

protected void finalize()
                 throws Throwable
Overrides:
finalize in class Object
Throws:
Throwable

getSize

public long[] getSize()
Specified by:
getSize in interface BasicMatrixProperties

isReadOnly

public boolean isReadOnly()
Specified by:
isReadOnly in interface BasicMatrixProperties
Overrides:
isReadOnly in class AbstractMatrix

getShortLittleEndian

public static final int getShortLittleEndian(byte[] bytes)

getIntLittleEndian

public static final int getIntLittleEndian(byte[] bytes)

erase

public void erase()
           throws IOException
Specified by:
erase in interface Erasable
Throws:
IOException

close

public void close()
           throws IOException
Specified by:
close in interface Closeable
Throws:
IOException


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