AbstractMatrix (baseCode 1.1.11 API)

java.lang.Object
- ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,V>

All Implemented Interfaces:

Serializable, Matrix2D<R,C,V>

Direct Known Subclasses:

CompressedBitMatrix, DoubleMatrix, IntegerMatrix, ObjectMatrixImpl, StringMatrix
```
public abstract class AbstractMatrix<R,C,V>
extends Object
implements Matrix2D<R,C,V>, Serializable
```
Author:

pavlidis

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

protected static int MAX_ROWS_TO_PRINT

Fields
Modifier and Type	Field and Description
`protected static int`	`MAX_ROWS_TO_PRINT`

Constructor Summary

Constructors
Constructor and Description

AbstractMatrix()

Constructors
Constructor and Description
`AbstractMatrix()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addColumnName(C s)` Add a column name when we don't care what the index will be.
`void`	`addRowName(R s)` Add a row name when we don't care what the index will be.
`double[][]`	`asDoubles()` Attempt to coerce the entries into doubles.
`void`	`assign(V value)` Set all values in the matrix to the given value.
`protected void`	`checkColRange(int startCol, int endCol)`
`protected void`	`checkRowRange(int startRow, int endRow)`
`boolean`	`containsColumnName(C columnName)`
`boolean`	`containsRowName(R rowName)`
`int`	`getColIndexByName(C columnKey)` Get the index of a column by name.
`C`	`getColName(int i)` Gte the column name for an index.
`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>`	`getRowNameMapIterator()`
`List<R>`	`getRowNames()`
`boolean`	`hasColNames()` Check if this matrix has a valid set of column names.
`boolean`	`hasMissingValues()` Test for the presence of missing values (null, or in the case of numbers, NaN)
`boolean`	`hasRow(R r)`
`boolean`	`hasRowNames()`
`int`	`numMissing()` Return the number of missing values in the matrix.
`void`	`setColumnName(C s, int i)` Add a column name associated with an index.
`void`	`setColumnNames(List<C> v)`
`void`	`setRowName(R s, int i)` Add a row name associated with a row index.
`void`	`setRowNames(List<R> v)`
`abstract int`	`size()`

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.Matrix2D
columns, getByKeys, getEntry, isMissing, rows, set, setByKeys

- Field Detail
  - MAX_ROWS_TO_PRINT
```
protected static final int MAX_ROWS_TO_PRINT
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - AbstractMatrix
```
public AbstractMatrix()
```
- Method Detail
  - addColumnName
```
public final void addColumnName(C s)
```
    Add a column name when we don't care what the index will be. The index will be set by the method. This is useful for when we need to set up a matrix before we know how many column or rows there are.
    
    Specified by:
    
    addColumnName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    s -
  - addRowName
```
public final void addRowName(R s)
```
    Add a row name when we don't care what the index will be. The index will be set by the method. This is useful for when we need to set up a matrix before we know how many column or rows there are.
    
    Parameters:
    
    s -
  - asDoubles
```
public double[][] asDoubles()
```
    Description copied from interface: Matrix2D
    
    Attempt to coerce the entries into doubles.
    Numeric entries (Double, BigDecimal, Integer, BigInteger) and Strings that can be parsed as doubles are converted. Booleans are converted to 1 or 0. Dates are converted via Date.getDate(). Null entries are rendered as Double.NaN. For entries that are other types of objects, the HashCode is used.
    
    Specified by:
    
    asDoubles in interface Matrix2D<R,C,V>
    
    Returns:
  - assign
```
public void assign(V value)
```
    Description copied from interface: Matrix2D
    
    Set all values in the matrix to the given value.
    
    Specified by:
    
    assign in interface Matrix2D<R,C,V>
  - containsColumnName
```
public final boolean containsColumnName(C columnName)
```
    Specified by:
    
    containsColumnName in interface Matrix2D<R,C,V>
    
    Returns:
  - containsRowName
```
public final boolean containsRowName(R rowName)
```
    Specified by:
    
    containsRowName in interface Matrix2D<R,C,V>
    
    Returns:
  - getColIndexByName
```
public final int getColIndexByName(C columnKey)
```
    Description copied from interface: Matrix2D
    
    Get the index of a column by name.
    
    Specified by:
    
    getColIndexByName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    columnKey - String
    
    Returns:
    
    int
  - getColName
```
public final C getColName(int i)
```
    Description copied from interface: Matrix2D
    
    Gte the column name for an index.
    
    Specified by:
    
    getColName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    i - int
    
    Returns:
    
    java.lang.String
  - getColNames
```
public final List<C> getColNames()
```
    Specified by:
    
    getColNames in interface Matrix2D<R,C,V>
    
    Returns:
    
    list of column names. Do not modify this list. Use the addColumnName methods.
  - getRowIndexByName
```
public final int getRowIndexByName(R s)
```
    Description copied from interface: Matrix2D
    
    Get the index of a row by name..
    
    Specified by:
    
    getRowIndexByName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    s - String
    
    Returns:
    
    int
  - getRowName
```
public final R getRowName(int i)
```
    Description copied from interface: Matrix2D
    
    Get the row name for an index
    
    Specified by:
    
    getRowName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    i - int
    
    Returns:
    
    java.lang.String
  - getRowNameMapIterator
```
public final Iterator<R> getRowNameMapIterator()
```
    Specified by:
    
    getRowNameMapIterator in interface Matrix2D<R,C,V>
    
    Returns:
    
    java.util.Iterator
  - getRowNames
```
public final List<R> getRowNames()
```
    Specified by:
    
    getRowNames in interface Matrix2D<R,C,V>
    
    Returns:
  - hasColNames
```
public final boolean hasColNames()
```
    Description copied from interface: Matrix2D
    
    Check if this matrix has a valid set of column names.
    
    Specified by:
    
    hasColNames in interface Matrix2D<R,C,V>
    
    Returns:
    
    boolean
  - hasMissingValues
```
public boolean hasMissingValues()
```
    Test for the presence of missing values (null, or in the case of numbers, NaN)
    
    Returns:
  - hasRow
```
public final boolean hasRow(R r)
```
    Specified by:
    
    hasRow in interface Matrix2D<R,C,V>
    
    Parameters:
    
    r - Object
    
    Returns:
    
    boolean
  - hasRowNames
```
public final boolean hasRowNames()
```
    Specified by:
    
    hasRowNames in interface Matrix2D<R,C,V>
    
    Returns:
    
    boolean
  - numMissing
```
public final int numMissing()
```
    Description copied from interface: Matrix2D
    
    Return the number of missing values in the matrix.
    
    Specified by:
    
    numMissing in interface Matrix2D<R,C,V>
    
    Returns:
  - setColumnName
```
public final void setColumnName(C s,
                                int i)
```
    Description copied from interface: Matrix2D
    
    Add a column name associated with an index.
    
    Specified by:
    
    setColumnName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    s - Object a column name
    
    i - int the column index associated with this name
  - setColumnNames
```
public void setColumnNames(List<C> v)
```
    Specified by:
    
    setColumnNames in interface Matrix2D<R,C,V>
  - setRowName
```
public final void setRowName(R s,
                             int i)
```
    Description copied from interface: Matrix2D
    
    Add a row name associated with a row index.
    
    Specified by:
    
    setRowName in interface Matrix2D<R,C,V>
    
    Parameters:
    
    s - Object
    
    i - int
  - setRowNames
```
public final void setRowNames(List<R> v)
```
    Specified by:
    
    setRowNames in interface Matrix2D<R,C,V>
  - size
```
public abstract int size()
```
  - checkColRange
```
protected void checkColRange(int startCol,
                             int endCol)
```
  - checkRowRange
```
protected void checkRowRange(int startRow,
                             int endRow)
```

Class AbstractMatrix<R,C,V>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface ubic.basecode.dataStructure.matrix.Matrix2D

Field Detail

MAX_ROWS_TO_PRINT

Constructor Detail

AbstractMatrix

Method Detail

addColumnName

addRowName

asDoubles

assign

containsColumnName

containsRowName

getColIndexByName

getColName

getColNames

getRowIndexByName

getRowName

getRowNameMapIterator

getRowNames

hasColNames

hasMissingValues

hasRow

hasRowNames

numMissing

setColumnName

setColumnNames

setRowName

setRowNames

size

checkColRange

checkRowRange