Chaste  Release::2018.1
AbstractWntOdeBasedCellCycleModel.cpp
1 /*
2 
3 Copyright (c) 2005-2018, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
14  * Redistributions of source code must retain the above copyright notice,
15  this list of conditions and the following disclaimer.
16  * Redistributions in binary form must reproduce the above copyright notice,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
35 #include "AbstractWntOdeBasedCellCycleModel.hpp"
36 #include "Exception.hpp"
37 
38 AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
39  : AbstractOdeBasedPhaseBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
40 {
41 }
42 
44 {
45 }
46 
49 {
50  /*
51  * The member variables mDivideTime and mG2PhaseStartTime are
52  * initialized in the AbstractOdeBasedPhaseBasedCellCycleModel
53  * constructor.
54  *
55  * The member variables mCurrentCellCyclePhase, mG1Duration,
56  * mMinimumGapDuration, mStemCellG1Duration, mTransitCellG1Duration,
57  * mSDuration, mG2Duration and mMDuration are initialized in the
58  * AbstractPhaseBasedCellCycleModel constructor.
59  *
60  * The member variables mBirthTime, mReadyToDivide and mDimension
61  * are initialized in the AbstractCellCycleModel constructor.
62  */
63 }
64 
66 {
67  assert(mpCell != nullptr);
68  double level = 0;
69 
70  switch (mDimension)
71  {
72  case 1:
73  {
74  const unsigned DIM = 1;
76  break;
77  }
78  case 2:
79  {
80  const unsigned DIM = 2;
82  break;
83  }
84  case 3:
85  {
86  const unsigned DIM = 3;
88  break;
89  }
90  default:
92  }
93 
94  return level;
95 }
96 
98 {
100 
101  assert(mpOdeSystem != nullptr);
102 
103  // This model needs the protein concentrations and phase resetting to G0/G1.
104  // Keep the Wnt pathway in the same state but reset the cell cycle part
105  // Cell cycle is proteins 0 to 4 (first 5 ODEs)
106  std::vector<double> init_conds = mpOdeSystem->GetInitialConditions();
107  for (unsigned i=0; i<5; i++)
108  {
109  mpOdeSystem->rGetStateVariables()[i] = init_conds[i];
110  }
111 }
112 
114 {
116  if (SimulationTime::Instance()->GetTime() == mLastTime
117  || GetOdeStopTime() == mLastTime)
118  {
119  // Should only be called if we're still running ODEs
121  }
122 }
123 
125 {
126  assert(mpOdeSystem != nullptr);
127  assert(mpCell != nullptr);
129 }
130 
132 {
133  return 16.0;
134 }
135 
137 {
138  return 16.0;
139 }
140 
142 {
143  return false;
144 }
145 
147 {
148  // No new parameters to output, so just call method on direct parent class
150 }
virtual void ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel()=0
double GetWntLevel(double height)
static SimulationTime * Instance()
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
AbstractWntOdeBasedCellCycleModel(const AbstractWntOdeBasedCellCycleModel &rModel)
#define NEVER_REACHED
Definition: Exception.hpp:206
static WntConcentration * Instance()