org.strbio.math
Class IMatrix

java.lang.Object
  org.strbio.math.IMatrix

Direct Known Subclasses:

StatsMatrix

public class IMatrix
extends java.lang.Object

a class to encapsulate a 2-D matrix of integers Can do a bunch of math functions, and save/load from a file.

 Version 1.13, 7/7/99 - added equals
 Version 1.12, 3/1/99 - added print()
 Version 1.11, 1/29/99 - changed some PrintfStream to Printf.
 Version 1,1, 5/18/98 - added saveBinary, autodetecting load.
 Version 1.01, 4/28/98 - fixed a couple of saving bugs
 Version 1.0, 3/30/98 - original version
 

Version:

1.13, 7/7/99

Author:

JMC

See Also:

DMatrix, IVector

Field Summary

int[][]

data data contains the actual matrix itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'im.data[0][0] = tmp' as well as 'tmp = im.data[0][0]' without needing 2 different functions.

Constructor Summary

IMatrix()
makes a blank 0x0 matrix; you can assign a int[][] to the data directly, or load data in from a file

IMatrix(IMatrix x)
copies another IMatrix.

IMatrix(int[][] x)
makes a new IMatrix object out of a int[][] array.

IMatrix(int c, int r)
makes an emptry IMatrix object with a specified number of columns and rows.

Method Summary

void	add(IMatrix x) Adds another IMatrix to this one.
static IMatrix	add(IMatrix a, IMatrix b) Adds two IMatrix's and returns a new IMatrix containing the sum.
int	cols() returns the number of columns in the encapsulated array.
boolean	equals(java.lang.Object x) mathematical objects are equal if their contents are.
boolean	isEmpty() Does the matrix contain all zeroes?
void	load(java.io.BufferedReader infile) Load text matrix from an open BufferedReader.
void	load(java.io.DataInputStream infile) Load binary matrix from an open DataInputStream.
void	load(java.lang.String filename) Loads matrix from a file; file type (text/binary) is autodetected.
int	max() What's the maximum value in the matrix?
int	min() What's the minimum value in the matrix?
static IMatrix	multiply(IMatrix a, int b) Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
void	multiply(int x) Multiplies all values in this IMatrix by a specified int.
static IMatrix	multiply(int b, IMatrix a) Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
void	print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
int	rows() returns the number of rows in the encapsulated array.
void	save(Printf outfile) Save to an open Printf.
void	save(java.lang.String filename) Saves to a new text file.
void	saveBinary(java.io.DataOutputStream outfile) Save in binary format to an open DataOutputStream
void	saveBinary(java.lang.String filename) Saves to a new binary file.
void	setValue(int x) Sets every value in the matrix to a specified int.
void	setValueAt(int c, int r, int d) Sets the data at a given column/row.
void	subtract(IMatrix x) Subtracts another IMatrix from this one.
static IMatrix	subtract(IMatrix a, IMatrix b) Subtracts one IMatrix's from another returns a new IMatrix containing the difference.
int	valueAt(int c, int r) Returns the data at a given column/row.

Methods inherited from class java.lang.Object

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

Field Detail

data

public int[][] data

data contains the actual matrix itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'im.data[0][0] = tmp' as well as 'tmp = im.data[0][0]' without needing 2 different functions. In C++ this could all be hidden by operator overloading, but that would be too elegant for some people.

Constructor Detail

IMatrix

public IMatrix(int c,
               int r)

makes an emptry IMatrix object with a specified number of columns and rows. All data should be zeroed out... this is not done explicitly, but relies on Java's default values.

Parameters:

c - columns

r - rows

IMatrix

public IMatrix()

makes a blank 0x0 matrix; you can assign a int[][] to the data directly, or load data in from a file

IMatrix

public IMatrix(int[][] x)

makes a new IMatrix object out of a int[][] array. It copies the data rather than creating a reference to it, so if you manipulate data in your original array after calling this constructor, it will NOT affect the new object. If you want to do the latter, try im = new IMatrix(), then im.data = my_array.

IMatrix

public IMatrix(IMatrix x)

copies another IMatrix. A new copy of the array is made.

Method Detail

equals

public boolean equals(java.lang.Object x)

mathematical objects are equal if their contents are.

Overrides:

equals in class java.lang.Object

cols

public final int cols()

returns the number of columns in the encapsulated array.

rows

public final int rows()

returns the number of rows in the encapsulated array.

valueAt

public final int valueAt(int c,
                         int r)

Returns the data at a given column/row. It's easier to manipulate the data directly, but this method is there if you don't feel like doing that.

Parameters:

c - column

r - row

setValueAt

public final void setValueAt(int c,
                             int r,
                             int d)

Sets the data at a given column/row. It's easier to manipulate the data directly, but this method is there if you don't feel like doing that.

Parameters:

c - column

r - row

d - value to set the data to

setValue

public final void setValue(int x)

Sets every value in the matrix to a specified int.

add

public final void add(IMatrix x)

Adds another IMatrix to this one. If the sizes aren't the same, you will probably get an ArrayOutOfBounds exception.

add

public static final IMatrix add(IMatrix a,
                                IMatrix b)

Adds two IMatrix's and returns a new IMatrix containing the sum. If the sizes aren't the same, you will probably get an ArrayOutOfBounds exception.

subtract

public final void subtract(IMatrix x)

Subtracts another IMatrix from this one. If the sizes aren't the same, you will probably get an ArrayOutOfBounds exception.

subtract

public static final IMatrix subtract(IMatrix a,
                                     IMatrix b)

Subtracts one IMatrix's from another returns a new IMatrix containing the difference. If the sizes aren't the same, you will probably get an ArrayOutOfBounds exception. To do 'c = a - b', use c = subtract(a,b). Too bad operator overloading is so complicated and confusing...

multiply

public final void multiply(int x)

Multiplies all values in this IMatrix by a specified int.

multiply

public static final IMatrix multiply(IMatrix a,
                                     int b)

Multiplies a IMatrix by an int and returns a new IMatrix containing the result.

multiply

public static final IMatrix multiply(int b,
                                     IMatrix a)

Multiplies a IMatrix by an int and returns a new IMatrix containing the result.

isEmpty

public final boolean isEmpty()

Does the matrix contain all zeroes?

max

public final int max()

What's the maximum value in the matrix?

min

public final int min()

What's the minimum value in the matrix?

print

public void print(Printf outfile)
           throws java.io.IOException

prints in ascii to an open Printf, with a nicer format than 'save'.

Throws:

java.io.IOException

See Also:

save(org.strbio.io.Printf)

save

public final void save(Printf outfile)
                throws java.io.IOException

Save to an open Printf.

Throws:

java.io.IOException

saveBinary

public final void saveBinary(java.io.DataOutputStream outfile)
                      throws java.io.IOException

Save in binary format to an open DataOutputStream

Throws:

java.io.IOException

load

public final void load(java.io.BufferedReader infile)
                throws java.io.IOException

Load text matrix from an open BufferedReader.

Throws:

java.io.IOException

See Also:

BufferedReader

load

public final void load(java.io.DataInputStream infile)
                throws java.io.IOException

Load binary matrix from an open DataInputStream.

Throws:

java.io.IOException

save

public final void save(java.lang.String filename)
                throws java.io.IOException

Saves to a new text file. Overwrites any existing file. You can comment the file with lines beginning with a semicolon.

Parameters:

filename - the file name.

Throws:

java.io.IOException

saveBinary

public final void saveBinary(java.lang.String filename)
                      throws java.io.IOException

Saves to a new binary file. Overwrites any existing file.

Parameters:

filename - the file name.

Throws:

java.io.IOException

load

public final void load(java.lang.String filename)
                throws java.io.IOException

Loads matrix from a file; file type (text/binary) is autodetected.

Parameters:

filename - the file name.

Throws:

java.io.IOException