def data_analysis(data, out, count, analysis):
DAG = arXiv.arXivDAG(data) #full box is a list with first entry the new boxDAG and second entry a list containg the two extremal points
path_ends = ['0302182', '0012251']
out.write('\n' + 'The start node is %s and the end node is %s' %(path_ends[0], path_ends[1]))
# Do J^2 testing
#start_time = time.clock()
#jsquared_algorithm(DAG, path_ends, out, count)
#jsquared_time = time.clock() - start_time
#print 'J^2 time = %s' % jsquared_time
# Do J^2 testing with birthday
#start_time = time.clock()
#lp.jsquared_with_birthdays(DAG, path_ends, out, count)
#jsquared_with_birthdays_time = time.clock() - start_time
#print 'J^2 with birthdays time = %s' % jsquared_with_birthdays_time
# Do Tim algorithm
#start_time = time.clock()
#lp.tim_algorithm(DAG, path_ends, out, count)
#tim_time = time.clock() - start_time
#print 'Tim time = %s' % tim_time
# Do Tim algorithm with order
start_time = time.clock()
lp.tim_algorithm_with_ordered_search(DAG, path_ends, out, count)
tim_with_order_time = time.clock() - start_time
print 'Tim with order time = %s' % tim_with_order_time
# Do Tim algorithm with order and birthday
start_time = time.clock()
lp.tim_algorithm_with_ordered_search_and_birthdays(DAG, path_ends, out, count)
tim_with_birthdays_time = time.clock() - start_time
print 'Tim with birthdays time = %s' % tim_with_birthdays_time
analysis.write(str(DAG.number_of_edges()) + '\n')
if isinstance(path, list): #if 'path' is a list of lists, carry out the process again to check the composition of THOSE lists
make_list_of_paths(path, pathlist)
return pathlist #Return a list that just contains paths (in list form) of nodes (no lists of lists of lists of...)
if __name__ == "__main__":
out = open(outfile,'w') #output file
count = open(countfile,'a+') #output file
data = open('C:\Users\Jamie\Project\CitNet.DAT', 'r') #input data
analysis = open(analysisfile, 'w') #analysis file
#n_list = [5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100]
#n_list = [50, 75, 100, 125, 150, 175, 200, 225, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500]
#n_list = [5, 10, 15, 20, 25, 30, 35, 40, 45, 50]
#n_list = [10, 10, 10, 20, 30, 30]
DAG = arXiv.arXivDAG(data)
print 'DAG construction complete'
start_time = time.clock()
TR_DAG = TR_from_examining_edges(DAG)
print 'There are %d edges in the original DAG' %DAG.number_of_edges()
print 'There are %d edges in the TR DAG' %TR_DAG.number_of_edges()
total_time = time.clock() - start_time
print 'TR complete in %f' %total_time
'''for N in n_list:
start_time = time.clock()
DAG_and_corners = boxmaker.box_generator_corners(N, 2)
DAG = DAG_and_corners[0]
#out.write('\n' + 'The edges in the original DAG:')
#for edge in DAG.edges():