20080225c.py

"""Given a rate matrix, get the expected number of transitions per unit time.
"""

import numpy as np

from SnippetUtil import HandlingError
import MatrixUtil
import RateMatrix
import Form
import FormOut

#FIXME numpy may not be necessary

def get_form():
    """
    @return: the body of a form
    """
    # define the default rate matrix
    dictionary_rate_matrix = RateMatrix.get_sample_codon_rate_matrix()
    labels = list(sorted(set(a for a, b in dictionary_rate_matrix)))
    R = MatrixUtil.dict_to_row_major(dictionary_rate_matrix, labels, labels)
    R = np.array(R)
    form_objects = [
            Form.Matrix('matrix', 'rate matrix',
                R, MatrixUtil.assert_rate_matrix)]
    return form_objects

def get_form_out():
    return FormOut.Report()

def get_response_content(fs):
    # read the matrix from the form data
    R = fs.matrix
    # get the expected rate
    states = range(len(R))
    try:
        rate_matrix_object = RateMatrix.RateMatrix(R.tolist(), states)
        expected_rate = rate_matrix_object.get_expected_rate()
    except RateMatrix.RateMatrixError as e:
        raise HandlingError('error calculating the expected rate: ' + str(e))
    # return the response
    return str(expected_rate) + '\n'