Package ubic.basecode.dataStructure.matrix

Class AbstractMatrix3D<R,C,S,V>

java.lang.Object

ubic.basecode.dataStructure.matrix.AbstractMatrix3D<R,C,S,V>

All Implemented Interfaces:

Matrix3D<R,C,S,V>

Direct Known Subclasses:

DenseObject3DMatrix, DoubleMatrix3D

public abstract class AbstractMatrix3D<R,C,S,V>
extends Object
implements Matrix3D<R,C,S,V>

TODO Document Me

Author:

Raymond

Field Summary

Fields

Modifier and Type	Field	Description
LinkedHashMap<C,Integer>	colMap
List<C>	colNames
LinkedHashMap<R,Integer>	rowMap
List<R>	rowNames
LinkedHashMap<S,Integer>	sliceMap
List<S>	sliceNames

Constructor Summary

Constructors

Constructor	Description
AbstractMatrix3D()

Method Summary

Modifier and Type	Method	Description
final void	addColumnName(C s, int index)	Add a column name associated with an index.
final void	addRowName(R s, int index)	Add a row name associated with a row index.
final void	addSliceName(S s, int index)	Add a slice name
abstract int	columns()	Get the number of columns the matrix has.
final boolean	containsColumnName(Object columnName)	Check if the matrix contains a column name
final boolean	containsRowName(Object rowName)	Check if the matrix contains a row name
final boolean	containsSliceName(Object sliceName)	Check if the matrix contains a slice name
final int	getColIndexByName(Object s)	Get the index of a column by name.
C	getColName(int i)	Get the column name for an index.
Iterator<C>	getColNameIterator()
List<C>	getColNames()
int	getRowIndexByName(R s)	Get the index of a row by name.
R	getRowName(int i)	Get the row name for an index
Iterator<R>	getRowNameIterator()
List<R>	getRowNames()
int	getSliceIndexByName(S s)	Get a slice index
S	getSliceName(int i)	Get a slice name
Iterator<S>	getSliceNameIterator()
List<S>	getSliceNames()
boolean	hasColNames()	Check if this matrix has a valid set of column names.
boolean	hasRow(Object r)
boolean	hasRowNames()
boolean	hasSliceNames()
abstract boolean	isMissing(int slice, int row, int col)	Check if the value at a given index is missing.
abstract int	numMissing()	Return the number of missing values in the matrix.
abstract int	rows()	Get the number of rows the matrix has
void	setColumnNames(List<C> v)
void	setRowNames(List<R> v)
void	setSliceNames(List<S> v)
abstract int	slices()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.basecode.dataStructure.matrix.Matrix3D

getObject

Field Details

colMap

public LinkedHashMap<C,Integer> colMap

colNames

public List<C> colNames

rowMap

public LinkedHashMap<R,Integer> rowMap

rowNames

public List<R> rowNames

sliceMap

public LinkedHashMap<S,Integer> sliceMap

sliceNames

public List<S> sliceNames

Constructor Details

AbstractMatrix3D

public AbstractMatrix3D()

Method Details

addColumnName

public final void addColumnName(C s,
 int index)

Description copied from interface: Matrix3D

Add a column name associated with an index.

Specified by:

addColumnName in interface Matrix3D<R,C,S,V>

Parameters:

s - a column name

index - int the column index associated with this name

addRowName

public final void addRowName(R s,
 int index)

Description copied from interface: Matrix3D

Add a row name associated with a row index.

Specified by:

addRowName in interface Matrix3D<R,C,S,V>

Parameters:

s - row name

index -

addSliceName

public final void addSliceName(S s,
 int index)

Description copied from interface: Matrix3D

Add a slice name

Specified by:

addSliceName in interface Matrix3D<R,C,S,V>

Parameters:

s - name of the slice

index -

columns

public abstract int columns()

Description copied from interface: Matrix3D

Get the number of columns the matrix has.

Specified by:

columns in interface Matrix3D<R,C,S,V>

Returns:

int

containsColumnName

public final boolean containsColumnName(Object columnName)

Description copied from interface: Matrix3D

Check if the matrix contains a column name

Specified by:

containsColumnName in interface Matrix3D<R,C,S,V>

Returns:

true if the matrix contains the column name

containsRowName

public final boolean containsRowName(Object rowName)

Description copied from interface: Matrix3D

Check if the matrix contains a row name

Specified by:

containsRowName in interface Matrix3D<R,C,S,V>

Parameters:

rowName -

Returns:

true if the matrix contains the row name

containsSliceName

public final boolean containsSliceName(Object sliceName)

Description copied from interface: Matrix3D

Check if the matrix contains a slice name

Specified by:

containsSliceName in interface Matrix3D<R,C,S,V>

Returns:

true if the matrix contains the slice name

getColIndexByName

public final int getColIndexByName(Object s)

Description copied from interface: Matrix3D

Get the index of a column by name.

Specified by:

getColIndexByName in interface Matrix3D<R,C,S,V>

Parameters:

s - name

Returns:

column index

getColName

public C getColName(int i)

Description copied from interface: Matrix3D

Get the column name for an index.

Specified by:

getColName in interface Matrix3D<R,C,S,V>

Parameters:

i - column index

Returns:

column name

getColNameIterator

public Iterator<C> getColNameIterator()

Specified by:

getColNameIterator in interface Matrix3D<R,C,S,V>

getColNames

public List<C> getColNames()

Specified by:

getColNames in interface Matrix3D<R,C,S,V>

Returns:

List of Object

getRowIndexByName

public int getRowIndexByName(R s)

Description copied from interface: Matrix3D

Get the index of a row by name.

Specified by:

getRowIndexByName in interface Matrix3D<R,C,S,V>

Parameters:

s - name

Returns:

row index

getRowName

public R getRowName(int i)

Description copied from interface: Matrix3D

Get the row name for an index

Specified by:

getRowName in interface Matrix3D<R,C,S,V>

Parameters:

i - row index

Returns:

name of the row

getRowNameIterator

public Iterator<R> getRowNameIterator()

Specified by:

getRowNameIterator in interface Matrix3D<R,C,S,V>

Returns:

java.util.Iterator

getRowNames

public List<R> getRowNames()

Specified by:

getRowNames in interface Matrix3D<R,C,S,V>

Returns:

List of Object

getSliceIndexByName

public int getSliceIndexByName(S s)

Description copied from interface: Matrix3D

Get a slice index

Specified by:

getSliceIndexByName in interface Matrix3D<R,C,S,V>

Parameters:

s - name

Returns:

slice index

getSliceName

public S getSliceName(int i)

Description copied from interface: Matrix3D

Get a slice name

Specified by:

getSliceName in interface Matrix3D<R,C,S,V>

Parameters:

i - index

Returns:

slice name

getSliceNameIterator

public Iterator<S> getSliceNameIterator()

Specified by:

getSliceNameIterator in interface Matrix3D<R,C,S,V>

getSliceNames

public List<S> getSliceNames()

Specified by:

getSliceNames in interface Matrix3D<R,C,S,V>

hasColNames

public boolean hasColNames()

Description copied from interface: Matrix3D

Check if this matrix has a valid set of column names.

Specified by:

hasColNames in interface Matrix3D<R,C,S,V>

Returns:

boolean

hasRow

public boolean hasRow(Object r)

Specified by:

hasRow in interface Matrix3D<R,C,S,V>

Parameters:

r - row name

Returns:

whether the row exists

hasRowNames

public boolean hasRowNames()

Specified by:

hasRowNames in interface Matrix3D<R,C,S,V>

Returns:

boolean

hasSliceNames

public boolean hasSliceNames()

Specified by:

hasSliceNames in interface Matrix3D<R,C,S,V>

isMissing

public abstract boolean isMissing(int slice,
 int row,
 int col)

Description copied from interface: Matrix3D

Check if the value at a given index is missing.

Specified by:

isMissing in interface Matrix3D<R,C,S,V>

Parameters:

slice -

row -

col -

Returns:

true if the value is missing, false otherwise.

numMissing

public abstract int numMissing()

Description copied from interface: Matrix3D

Return the number of missing values in the matrix.

Specified by:

numMissing in interface Matrix3D<R,C,S,V>

Returns:

number missing

rows

public abstract int rows()

Description copied from interface: Matrix3D

Get the number of rows the matrix has

Specified by:

rows in interface Matrix3D<R,C,S,V>

Returns:

int

setColumnNames

public void setColumnNames(List<C> v)

Specified by:

setColumnNames in interface Matrix3D<R,C,S,V>

Parameters:

v - List a vector of Strings.

setRowNames

public void setRowNames(List<R> v)

Specified by:

setRowNames in interface Matrix3D<R,C,S,V>

Parameters:

v - List a vector of Strings.

setSliceNames

public void setSliceNames(List<S> v)

Specified by:

setSliceNames in interface Matrix3D<R,C,S,V>

slices

public abstract int slices()

Specified by:

slices in interface Matrix3D<R,C,S,V>