AbstractMatrix3D (baseCode 1.2-SNAPSHOT API)

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 and 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 and Description

AbstractMatrix3D()

Constructors
Constructor and Description
`AbstractMatrix3D()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addColumnName(C s, int index)` Add a column name associated with an index.
`void`	`addRowName(R s, int index)` Add a row name associated with a row index.
`void`	`addSliceName(S s, int index)` Add a slice name
`abstract int`	`columns()` Get the number of columns the matrix has.
`boolean`	`containsColumnName(Object columnName)` Check if the matrix contains a column name
`boolean`	`containsRowName(Object rowName)` Check if the matrix contains a row name
`boolean`	`containsSliceName(Object sliceName)` Check if the matrix contains a slice name
`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 Detail
  - 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 Detail
  - AbstractMatrix3D
```
public AbstractMatrix3D()
```
- Method Detail
  - 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
  - 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
  - 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>
    
    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>
    
    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>

Class AbstractMatrix3D<R,C,S,V>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

colMap

colNames

rowMap

rowNames

sliceMap

sliceNames

Constructor Detail

AbstractMatrix3D

Method Detail

addColumnName

addRowName

addSliceName

columns

containsColumnName

containsRowName

containsSliceName

getColIndexByName

getColName

getColNameIterator

getColNames

getRowIndexByName

getRowName

getRowNameIterator

getRowNames

getSliceIndexByName

getSliceName

getSliceNameIterator

getSliceNames

hasColNames

hasRow

hasRowNames

hasSliceNames

isMissing

numMissing

rows

setColumnNames

setRowNames

setSliceNames

slices