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# Class SeqMat

source code

```object --+
|
dict --+
|
SeqMat
```
Known Subclasses:

A Generic sequence matrix class.

The key is a 2-tuple containing the letter indices of the matrix. Those should be sorted in the tuple (low, high). Because each matrix is dealt with as a half-matrix.

 Instance Methods

 _alphabet_from_matrix(self) Set alphabet letters from the matrix entries (PRIVATE). source code
```new empty dictionary

```
 __init__(self, data=None, alphabet=None, mat_name=`'``'`, build_later=0) Initialize. source code

 _correct_matrix(self) Sort key tuples (PRIVATE). source code

 _full_to_half(self) Convert a full-matrix to a half-matrix (PRIVATE). source code

 _init_zero(self) Initialize the ab_list values to zero (PRIVATE). source code

 make_entropy(self) Calculate and set the entropy attribute. source code

 sum(self) Return sum of the results. source code

 print_full_mat(self, f=None, format=`'``%4d``'`, topformat=`'``%4s``'`, alphabet=None, factor=1, non_sym=None) Print the full matrix to the file handle f or stdout. source code

 print_mat(self, f=None, format=`'``%4d``'`, bottomformat=`'``%4s``'`, alphabet=None, factor=1) Print a nice half-matrix. source code

 __str__(self) Print a nice half-matrix. source code

 __sub__(self, other) Return integer subtraction product of the two matrices. source code

 __mul__(self, other) Matrix multiplication. source code

Inherited from `dict`: `__cmp__`, `__contains__`, `__delitem__`, `__eq__`, `__ge__`, `__getattribute__`, `__getitem__`, `__gt__`, `__iter__`, `__le__`, `__len__`, `__lt__`, `__ne__`, `__new__`, `__repr__`, `__setitem__`, `__sizeof__`, `clear`, `copy`, `fromkeys`, `get`, `has_key`, `items`, `iteritems`, `iterkeys`, `itervalues`, `keys`, `pop`, `popitem`, `setdefault`, `update`, `values`, `viewitems`, `viewkeys`, `viewvalues`

Inherited from `object`: `__delattr__`, `__format__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__subclasshook__`

 Class Variables

Inherited from `dict`: `__hash__`

 Properties

Inherited from `object`: `__class__`

 Method Details

### __init__(self, data=None, alphabet=None, mat_name=`'``'`, build_later=0)(Constructor)

source code

Initialize.

User may supply:

• data: matrix itself
• mat_name: its name. See below.
• alphabet: an instance of Bio.Alphabet, or a subclass. If not supplied, constructor builds its own from that matrix.
• build_later: skip the matrix size assertion. User will build the matrix after creating the instance. Constructor builds a half matrix filled with zeroes.
Returns:
```new empty dictionary

```
Overrides: object.__init__

### print_mat(self, f=None, format=`'``%4d``'`, bottomformat=`'``%4s``'`, alphabet=None, factor=1)

source code

Print a nice half-matrix.

f=sys.stdout to see on the screen.

User may pass own alphabet, which should contain all letters in the alphabet of the matrix, but may be in a different order. This order will be the order of the letters on the axes.

### __str__(self)(Informal representation operator)

source code
Print a nice half-matrix.
Overrides: object.__str__

### __mul__(self, other)

source code

Matrix multiplication.

Returns a matrix for which each entry is the multiplication product of the two matrices passed.

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