WeightMatrix (biojava-legacy 1.9.5 API)

All Known Implementing Classes:

SimpleWeightMatrix
```
public interface WeightMatrix
```
A log odds weight matrix.
The weight matrix uses computer-coordinates. Thus, a 10 column weight matrix has columns (0 - 9). I guess that if you try to access columns outside the logical range, the implementation may throw an IndexOutOfBoundsException.

Author:

Matthew Pocock

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`int`	`columns()`	The number of columns modeled by the weight matrix.
`Alphabet`	`getAlphabet()`	The alphabet for the sequences that this weight matrix models.
`Distribution`	`getColumn(int column)`	Retrieve a column as an EmissionState.

- Method Detail
  - getAlphabet
```
Alphabet getAlphabet()
```
    The alphabet for the sequences that this weight matrix models.
    
    Returns:
    
    the Alphabet
  - columns
```
int columns()
```
    The number of columns modeled by the weight matrix.
    
    Returns:
    
    the number of columns
  - getColumn
```
Distribution getColumn(int column)
                throws IndexOutOfBoundsException
```
    Retrieve a column as an EmissionState.
    To find the emission probability for Symbol sym at column col use: wm.getColumn(col).getWeight(sym).
    
    Parameters:
    
    column - the weight matrix column to retrieve
    
    Returns:
    
    the EmissionState that represents the individual column
    
    Throws:
    
    IndexOutOfBoundsException - if column is not between 0 and columns()-1