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java.lang.Object | +--neobio.alignment.OutMatrix
Implements an interface to the OUT matrix of a block. This class is used by the CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an AlignmentBlock.
The OUT matrix defined as OUT[i,j] = I[i] + DIST[i,j] where I is the
 input border array and DIST is the DIST matrix.
The output border of a block is computed from the OUT matrix by taking the maximum value of each column. Note that this class does not compute the OUT matrix, it just stores the necessary information to retrieve a value at any position of the matrix.
It implements the Matrix interface so that the SMAWK algorithm can be used to compute its column maxima.
For more information on how this class is used, please refer to the specification
 of the CrochemoreLandauZivUkelson and its subclasses.
CrochemoreLandauZivUkelson, 
CrochemoreLandauZivUkelsonGlobalAlignment, 
CrochemoreLandauZivUkelsonLocalAlignment, 
AlignmentBlock, 
Smawk| Field Summary | |
| protected  int | dimThe dimension of the OUT matrix. | 
| protected  int[][] | distThe DIST matrix of a block. | 
| protected  int[] | input_borderThe input border of a block. | 
| protected  int | lcThe number of columns of the block. | 
| protected  int | max_lengthThe length of the longest sequence (number of characters) being aligned. | 
| protected  int | max_scoreThe maximum absolute score that the current scoring scheme can return. | 
| Constructor Summary | |
| OutMatrix() | |
| Method Summary | |
|  void | init(int max_length,
         int max_score)Initialised this OUT matrix interface. | 
|  int | numColumns()Returns the number of columns of this OUT matrix. | 
|  int | numRows()Returns the number of rows of this OUT matrix. | 
|  void | setData(int[][] dist,
               int[] input_border,
               int dim,
               int lc)Sets this interface's data to represent an OUT matrix for a block. | 
|  int | valueAt(int row,
               int col)Returns the value at a given position of the matrix. | 
| Methods inherited from class java.lang.Object | 
| clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait | 
| Field Detail | 
protected int max_length
protected int max_score
protected int[][] dist
protected int[] input_border
protected int dim
protected int lc
| Constructor Detail | 
public OutMatrix()
| Method Detail | 
public void init(int max_length,
                 int max_score)
max_length - the length of the longest sequence (number of characters) being
 alignedmax_score - the maximum absolute score that the current scoring scheme can
 return
public void setData(int[][] dist,
                    int[] input_border,
                    int dim,
                    int lc)
dist - the DIST matrixinput_border - the input borderdim - the dimension of the OUT matrixlc - the number of columns of the block
public int valueAt(int row,
                   int col)
DIST[col][row] + input_border[row]. However, special cases
 occur for its upper right and lower left triangular parts.
valueAt in interface Matrixrow - row indexcol - column index
row, column col of this OUT
 matrixpublic int numRows()
numRows in interface Matrixpublic int numColumns()
numColumns in interface Matrix| 
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