org.emboss.jemboss.editor
Class Matrix
java.lang.Object
|
+--org.emboss.jemboss.editor.Matrix
- public class Matrix
- extends java.lang.Object
Constructor Summary |
Matrix(java.io.File matrixFile)
|
Matrix(java.lang.String matrixJar,
java.lang.String matrixFileName)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
keys
private java.lang.Object[] keys
cons
private java.lang.String cons
matrixString
private java.lang.String matrixString
matrixFileName
private java.lang.String matrixFileName
Matrix
public Matrix(java.io.File matrixFile)
Matrix
public Matrix(java.lang.String matrixJar,
java.lang.String matrixFileName)
getMatrix
public int[][] getMatrix()
getMatrixTable
public java.lang.String getMatrixTable()
getCurrentMatrixName
public java.lang.String getCurrentMatrixName()
getKeys
public java.lang.Object[] getKeys()
getKeyNames
public java.lang.Object[] getKeyNames()
getResidueMatrixPosition
public java.util.Hashtable getResidueMatrixPosition()
getMatrixIndex
public int getMatrixIndex(java.lang.String s)
getIDimension
public int getIDimension()
getJDimension
public int getJDimension()
getRegularExpression
private org.apache.regexp.RE getRegularExpression()
matrixLineCount
private void matrixLineCount(java.lang.String line,
org.apache.regexp.RE regexp)
matrixLineParse
private void matrixLineParse(java.lang.String line,
org.apache.regexp.RE regexp)
matrixRead
private int[][] matrixRead(java.io.File matrixFile)
matrixReadString
private int[][] matrixReadString(java.lang.String matrixString)