/usr/share/cain/gui/TableTimeSeriesAllReactions.py is in cain 1.9-7.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 | """Display all-reaction trajectories in a table."""
# If we are running the unit tests.
if __name__ == '__main__':
import sys
sys.path.insert(1, '..')
import wx
import numpy
from state.TrajectoryCalculator import TrajectoryCalculator
from TableBase import TableBase
class TableEnd(TableBase):
def __init__(self, parent, identifiers, listOfArrays):
TableBase.__init__(self, parent)
self.resize(len(listOfArrays), len(identifiers))
self.setColumnLabels(identifiers)
for row in range(len(listOfArrays)):
# Row number.
self.SetRowLabelValue(row, str(row + 1))
col = 0
# Data.
for x in listOfArrays[row]:
self.SetCellValue(row, col, '%g' % x)
col += 1
class TableAll(TableBase):
def __init__(self, parent, identifiers, listOfTimes, listOfArrays):
TableBase.__init__(self, parent)
numberOfRows = sum([len(x) for x in listOfTimes])
self.resize(numberOfRows, 2 + len(identifiers))
self.setColumnLabels(['Trajectory', 'Time'] + identifiers)
row = 0
# For each trajectory.
for n in range(len(listOfArrays)):
times = listOfTimes[n]
array = listOfArrays[n]
for frame in range(len(times)):
self.SetRowLabelValue(row, str(row + 1))
col = 0
# Trajectory.
self.SetCellValue(row, col, str(n + 1))
col += 1
# Time.
self.SetCellValue(row, col, '%g' % times[frame])
col += 1
# Data.
for x in array[frame]:
self.SetCellValue(row, col, '%g' % x)
col += 1
row += 1
class TablePanel(wx.Panel):
def __init__(self, parent, model, trajectories, target):
wx.Panel.__init__(self, parent)
tc = TrajectoryCalculator(model)
reactionIdentifiers = [r.id for r in model.reactions]
if target == 'PopulationsEnd':
self.grid = TableEnd(self, model.speciesIdentifiers,
[tc.computeFinalPopulations(trajectories, i)
for i in range(len(trajectories.indices))])
elif target == 'ReactionsEnd':
self.grid = TableEnd(self, reactionIdentifiers,
[tc.computeFinalReactionCounts(trajectories, i)
for i in range(len(trajectories.indices))])
elif target == 'PopulationsAll':
listOfTimes = []
listOfPopulations = []
for i in range(len(trajectories.indices)):
# Include the start time, but not the end time.
times, populations, reactionCounts =\
tc.makeFramesAtReactionEvents(trajectories, i, True, False)
listOfTimes.append(times)
listOfPopulations.append(populations)
self.grid = TableAll(self, model.speciesIdentifiers, listOfTimes,
listOfPopulations)
elif target == 'ReactionsAll':
listOfTimes = []
listOfReactionCounts = []
for i in range(len(trajectories.indices)):
# Include the start time, but not the end time.
times, populations, reactionCounts =\
tc.makeFramesAtReactionEvents(trajectories, i, True, False)
listOfTimes.append(times)
listOfReactionCounts.append(reactionCounts)
self.grid = TableAll(self, reactionIdentifiers,
listOfTimes, listOfReactionCounts)
else:
assert False
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.grid, 1, wx.EXPAND)
self.SetSizer(sizer)
self.Fit()
class TableFrame(wx.Frame):
def __init__(self, model, trajectories, target,
title='Trajectories', parent=None):
wx.Frame.__init__(self, parent, title=title, size=(900,600))
display = TablePanel(self, model, trajectories, target)
display.grid.AutoSize()
self.Layout()
#
# Test Code.
#
def main():
from state.Model import Model
from state.Species import Species
from state.SpeciesReference import SpeciesReference
from state.Reaction import Reaction
from state.TimeSeriesAllReactions import TimeSeriesAllReactions
app = wx.PySimpleApp()
# Define a simple model.
model = Model()
model.id = 'model'
model.speciesIdentifiers.append('s1')
model.species['s1'] = Species('C1', 'species 1', '13')
model.speciesIdentifiers.append('s2')
model.species['s2'] = Species('C1', 'species 2', '17')
# s1 -> s2
model.reactions.append(
Reaction('r1', 'reaction 1', [SpeciesReference('s1')],
[SpeciesReference('s2')], True, '1.5'))
# s1 + s2 -> 2 s1
model.reactions.append(
Reaction('r2', 'reaction 2',
[SpeciesReference('s1'), SpeciesReference('s2')],
[SpeciesReference('s1', 2)], True, '2.5'))
# Trajectories.
initialTime = 0.
finalTime = 3.
# One species, two reactions.
t = TimeSeriesAllReactions([0], [0, 1], initialTime, finalTime)
t.appendInitialPopulations([13, 17])
t.appendIndices([0, 1, 0])
t.appendTimes([0, 0.5, 1])
t.appendInitialPopulations([13, 17])
t.appendIndices([0, 1, 1, 0])
t.appendTimes([0, 0.33, 0.67, 1])
TableFrame(model, t, 'PopulationsEnd',
'Populations at the end time.').Show()
TableFrame(model, t, 'ReactionsEnd',
'Reaction counts at the end time.').Show()
TableFrame(model, t, 'PopulationsAll',
'Populations at the start time and reaction events.').Show()
TableFrame(model, t, 'ReactionsAll',
'Reaction counts at the start time and reaction events.').Show()
app.MainLoop()
if __name__ == '__main__':
main()
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