AbstractCryptStatistics.cpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2009
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 #include "AbstractCryptStatistics.hpp"
00029 
00030 void AbstractCryptStatistics::LabelSPhaseCells()
00031 {
00032     for (AbstractTissue<2>::Iterator cell_iter = mrCrypt.Begin();
00033          cell_iter != mrCrypt.End();
00034          ++cell_iter)
00035     {
00036         if ((*cell_iter).GetCellCycleModel()->GetCurrentCellCyclePhase()== S_PHASE)
00037         {   // This should only be done for healthy or labelled populations, not mutants (at the moment anyway)
00038             assert((*cell_iter).GetMutationState() == HEALTHY || (*cell_iter).GetMutationState() == LABELLED);
00039             (*cell_iter).SetMutationState(LABELLED);
00040         }
00041     }
00042 }
00043 
00044 void AbstractCryptStatistics::LabelAllCellsAsHealthy()
00045 {
00046     for (AbstractTissue<2>::Iterator cell_iter = mrCrypt.Begin();
00047          cell_iter != mrCrypt.End();
00048          ++cell_iter)
00049     {
00050         (*cell_iter).SetMutationState(HEALTHY);
00051     }
00052 }
00053 
00054 std::vector<bool> AbstractCryptStatistics::GetWhetherCryptSectionCellsAreLabelled(std::vector<TissueCell*> cryptSection)
00055 {
00056     std::vector<bool> crypt_section_labelled(cryptSection.size());
00057 
00058     for (unsigned vector_index=0; vector_index<cryptSection.size(); vector_index++)
00059     {
00060         if (cryptSection[vector_index]->GetMutationState() == LABELLED)
00061         {
00062             crypt_section_labelled[vector_index]=true;
00063         }
00064         else
00065         {
00066             crypt_section_labelled[vector_index]=false;
00067         }
00068     }
00069 
00070     return crypt_section_labelled;
00071 }

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