Chaste  Release::2018.1
AbstractSimpleGenerationalCellCycleModel.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 
36 #include "AbstractSimpleGenerationalCellCycleModel.hpp"
37 #include "DifferentiatedCellProliferativeType.hpp"
38 #include "StemCellProliferativeType.hpp"
39 #include "TransitCellProliferativeType.hpp"
40 
43  mGeneration(0),
44  mMaxTransitGenerations(3) // taken from Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
45 {
46 }
47 
49 {
50 }
51 
54  mGeneration(rModel.mGeneration),
55  mMaxTransitGenerations(rModel.mMaxTransitGenerations)
56 {
57  /*
58  * Initialize only those member variables defined in this class.
59  *
60  * The member variables mCurrentCellCyclePhase, mG1Duration,
61  * mMinimumGapDuration, mStemCellG1Duration, mTransitCellG1Duration,
62  * mSDuration, mG2Duration and mMDuration are initialized in the
63  * AbstractPhaseBasedCellCycleModel constructor.
64  *
65  * The member variables mBirthTime, mReadyToDivide and mDimension
66  * are initialized in the AbstractCellCycleModel constructor.
67  *
68  * Note that mG1Duration is (re)set as soon as InitialiseDaughterCell()
69  * is called on the new cell-cycle model.
70  */
71 }
72 
74 {
75  mGeneration++;
77  {
78  /*
79  * This method is usually called within a CellBasedSimulation, after the CellPopulation
80  * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
81  * CellPropertyRegistry::Instance() here when setting the CellProliferativeType, we
82  * would be creating a new CellPropertyRegistry. In this case the cell proliferative
83  * type counts, as returned by AbstractCellPopulation::GetCellProliferativeTypeCount(),
84  * would be incorrect. We must therefore access the CellProliferativeType via the cell's
85  * CellPropertyCollection.
86  */
87  boost::shared_ptr<AbstractCellProperty> p_diff_type =
88  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<DifferentiatedCellProliferativeType>();
89  mpCell->SetCellProliferativeType(p_diff_type);
90  }
91  if (mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
92  {
93  mGeneration = 0;
94  }
96 }
97 
99 {
100  /*
101  * If the parent cell is a stem cell then its generation was reset
102  * to zero when ResetForDivision() was called. The daughter cell's
103  * generation must therefore be incremented here.
104  */
105  if (mGeneration == 0)
106  {
107  mGeneration = 1;
108  }
109  /*
110  * In generation-based cell-cycle models, the daughter cell
111  * is always of type transit or differentiated.
112  */
113  boost::shared_ptr<AbstractCellProperty> p_transit_type =
114  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
115  mpCell->SetCellProliferativeType(p_transit_type);
116 
118  {
119  boost::shared_ptr<AbstractCellProperty> p_diff_type =
120  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<DifferentiatedCellProliferativeType>();
121  mpCell->SetCellProliferativeType(p_diff_type);
122  }
124 }
125 
127 {
128  mGeneration = generation;
129 }
130 
132 {
133  return mGeneration;
134 }
135 
137 {
138  mMaxTransitGenerations = maxTransitGenerations;
139 }
140 
142 {
143  return mMaxTransitGenerations;
144 }
145 
147 {
148  *rParamsFile << "\t\t\t<MaxTransitGenerations>" << mMaxTransitGenerations << "</MaxTransitGenerations>\n";
149 
150  // Call method on direct parent class
152 }
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)