org.emboss.jemboss.editor
Class Matrix

java.lang.Object
  org.emboss.jemboss.editor.Matrix

public class Matrix

extends java.lang.Object

Reads and hold a sequence scoring matrix

Field Summary

private java.lang.String	cons
private int	i
private int	idimension
private int	jdimension
private int	k
private java.lang.Object[]	keys
private int[][]	matrix
private java.lang.String	matrixFileName
private java.lang.String	matrixString
private java.util.Hashtable	residueMatrixPosition hashtable of the residue positions in the table

Constructor Summary

Matrix(java.io.File matrixFile)

Matrix(java.lang.String matrixJar, java.lang.String matrixFileName)

Method Summary

java.lang.String	getCurrentMatrixName() Get the current scoring matrix name
int	getIDimension() Get number of rows in the scoring table
int	getJDimension() Get number of columns in the scoring table
java.lang.Object[]	getKeyNames() Scoring matrix names available
java.lang.String	getKeyNamesString() Scoring matrix names available
java.lang.Object[]	getKeys() Scoring matrix filenames in jar file
int[][]	getMatrix() Get the scoring matrix as a 2 dimensional integer array
int	getMatrixIndex(java.lang.String s) Get the residue position in the scoring table
java.lang.String	getMatrixTable() Get the scoring matrix as text
private org.apache.regexp.RE	getRegularExpression() Get regular expression for values in the scoring table
java.util.Hashtable	getResidueMatrixPosition() Get the hashtable of the residue positions in the scoring table
private void	matrixLineCount(java.lang.String line, org.apache.regexp.RE regexp) Count as a matrix row and number of columns
private void	matrixLineParse(java.lang.String line, org.apache.regexp.RE regexp) Parse a line from a scoring matrix file.
private int[][]	matrixRead(java.io.File matrixFile) Read and parse a scoring matrix file
private int[][]	matrixReadString(java.lang.String matrixString) Read and parse a scoring matrix

Methods inherited from class java.lang.Object

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

Field Detail

matrix

private int[][] matrix

idimension

private int idimension

jdimension

private int jdimension

i

private int i

k

private int k

residueMatrixPosition

private java.util.Hashtable residueMatrixPosition

hashtable of the residue positions in the table

keys

private java.lang.Object[] keys

cons

private java.lang.String cons

matrixString

private java.lang.String matrixString

matrixFileName

private java.lang.String matrixFileName

Constructor Detail

Matrix

public Matrix(java.io.File matrixFile)

Parameters:

matrixFile - matrix file

Matrix

public Matrix(java.lang.String matrixJar,
              java.lang.String matrixFileName)

Parameters:

matrixJar - jar file containing scoring matrix

matrixFileName - matrix file

Method Detail

getMatrix

public int[][] getMatrix()

Get the scoring matrix as a 2 dimensional integer array

Returns:

2 dimentional scoring matrix

getMatrixTable

public java.lang.String getMatrixTable()

Get the scoring matrix as text

Returns:

scoring matrix

getCurrentMatrixName

public java.lang.String getCurrentMatrixName()

Get the current scoring matrix name

Returns:

name of matrix

getKeys

public java.lang.Object[] getKeys()

Scoring matrix filenames in jar file

getKeyNames

public java.lang.Object[] getKeyNames()

Scoring matrix names available

getKeyNamesString

public java.lang.String getKeyNamesString()

Scoring matrix names available

getResidueMatrixPosition

public java.util.Hashtable getResidueMatrixPosition()

Get the hashtable of the residue positions in the scoring table

Returns:

hashtable of the residue positions

getMatrixIndex

public int getMatrixIndex(java.lang.String s)

Get the residue position in the scoring table

Parameters:

s - residue

Returns:

position in scoring table

getIDimension

public int getIDimension()

Get number of rows in the scoring table

Returns:

number of rows in the scoring table

getJDimension

public int getJDimension()

Get number of columns in the scoring table

Returns:

number of columns in the scoring table

getRegularExpression

private org.apache.regexp.RE getRegularExpression()

Get regular expression for values in the scoring table

Returns:

RE

matrixLineCount

private void matrixLineCount(java.lang.String line,
                             org.apache.regexp.RE regexp)

Count as a matrix row and number of columns

Parameters:

line - line from matrix file

regexp - regular expression for columns

matrixLineParse

private void matrixLineParse(java.lang.String line,
                             org.apache.regexp.RE regexp)

Parse a line from a scoring matrix file. Add to the matrix array the values in the table.

Parameters:

line - line from matrix file

regexp - regular expression for values

matrixRead

private int[][] matrixRead(java.io.File matrixFile)

Read and parse a scoring matrix file

Parameters:

matrixFile - matrix file

Returns:

matrix 2-d integer array

matrixReadString

private int[][] matrixReadString(java.lang.String matrixString)

Read and parse a scoring matrix

Parameters:

matrixString - matrix as text

Returns:

matrix 2-d integer array