Miscellaneous helper functions for ghmm.py.
|
Imported modules
|
|
import ghmmwrapper
import math
from modhmmer import *
import os.path
from random import *
|
|
Functions
|
|
|
|
|
|
arrayd2list
|
arrayd2list ( carray, length )
converts C double array to python list.
|
|
|
arrayint2list
|
arrayint2list ( carray, length )
converts C double array to python list.
|
|
|
classNumber
|
classNumber ( A )
Returns the number of transition classes in the matrix A
|
|
|
extract_in_cos
|
extract_in_cos (
transmat,
cos,
state,
)
Helper function for building HMMs from matrices: Used for
transition matrices with cos transition classes. Extract ingoing transitions for state from the complete list
of transition matrices
Allocates: .in_id vector and .in_a array (of size cos x N)
|
|
|
extract_out
|
extract_out ( lisprobs )
Helper function for building HMMs from matrices: Used for
transition matrices without transition classes. Extract out-/ingoing transitions from the row-vector resp. the
column vector (corresponding to incoming transitions) of the
transition matrix
Allocates: .[out|in]_id and .[out|in]_a vectors
|
|
|
extract_out_cos
|
extract_out_cos (
transmat,
cos,
state,
)
Helper function for building HMMs from matrices: Used for
transition matrices with cos transition classes. Extract outgoing transitions for state from the complete list
of transition matrices
Allocates: .out_id vector and .out_a array (of size cos x N)
|
|
|
list2arrayd
|
list2arrayd ( lisems )
converts python list to C double array
|
|
|
list2arrayint
|
list2arrayint ( lisems )
converts python list to C int array
|
|
|
list2matrixd
|
list2matrixd ( matrix )
Allocation and initialization of a double** based on a
two dimensional Python list (list of lists). The number of elements
in each column can vary.
|
|
|
list2matrixint
|
list2matrixint ( matrix )
Allocation and initialization of an int** based on a
two dimensional Python list (list of lists). The number of elements
in each column can vary.
|
|
|
matrixd2list
|
matrixd2list (
cmatrix,
row,
col,
)
|
|
|
matrixint2list
|
matrixint2list (
cmatrix,
row,
col,
)
|
|
Classes
|
|
|
|