QuorumSensingRunDirector.cpp Source File

00001 // QuorumSensingRunDirector.cpp: implementation of the CQuorumSensingRunDirector class.
00002 //
00004 
00005 #include "QuorumSensingRunDirector.h"
00006 
00008 // Construction/Destruction
00010 
00011 CQuorumSensingRunDirector::CQuorumSensingRunDirector()
00012 {
00013         int graphnum = -1;
00014 
00015         double maxSimTime = 5760.0;
00016         int intTime = (int) maxSimTime + 2;
00017         double stepSize = 0.001;
00018         double frequency = 1.0;
00019         double moveTol = 1.0e-06;
00020         int nChemicals;
00021 
00022         // no octopine no OOHL - steady state
00023         m_vpRxnNetworks.push_back(new CQuorumSensingNetwork());
00024         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00025         nChemicals = m_vpRxnNetworks[0]->GetNumberOfChemicals();
00026         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00027         m_vpRunnables.push_back(new CRunnable());
00028         m_vpRunnables[0]->SetComponents(m_vpRxnNetworks[0],m_vpRxnMovers[0],m_vpCellObservers[0]);
00029         // create an observer for the runnable
00030         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00031 //      m_vpGnuPlotters[0]->AddChemicalNumberToList(1);
00032         m_vpGnuPlotters[0]->AddChemicalNumberToList(12);
00033         m_vpGnuPlotters[0]->AddChemicalNumberToList(13);
00034         m_vpGnuPlotters[0]->AddChemicalNumberToList(32);
00035         m_vpGnuPlotters[0]->AddChemicalNumberToList(25);
00036         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00037         m_vpGnuPlotters[1]->AddChemicalNumberToList(1);
00038 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(9);
00039 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(11);
00040 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(12);
00041 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(13);
00042 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(14);
00043 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(27);
00044         // attach the observer
00045         m_vpRunnables[0]->Attach(m_vpGnuPlotters[0]);
00046         m_vpRunnables[0]->Attach(m_vpGnuPlotters[1]);
00047 
00048         //  octopine and OOHL 
00049         m_vpRxnNetworks.push_back(new CQuorumSensingNetwork());
00050         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00051         nChemicals = m_vpRxnNetworks[1]->GetNumberOfChemicals();
00052         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00053         m_vpRunnables.push_back(new CRunnable());
00054         m_vpRunnables[1]->SetComponents(m_vpRxnNetworks[1],m_vpRxnMovers[1],m_vpCellObservers[0]);
00055         // create an observer for the runnable
00056         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00057         m_vpGnuPlotters[2]->AddChemicalNumberToList(12);
00058         m_vpGnuPlotters[2]->AddChemicalNumberToList(13);
00059         m_vpGnuPlotters[2]->AddChemicalNumberToList(32);
00060         m_vpGnuPlotters[2]->AddChemicalNumberToList(25);
00061         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00062         m_vpGnuPlotters[3]->AddChemicalNumberToList(1);
00063 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(9);
00064 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(11);
00065 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(12);
00066 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(13);
00067 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(14);
00068 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(20);
00069 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(27);
00070         // attach the observer
00071         m_vpRunnables[1]->Attach(m_vpGnuPlotters[2]);
00072         m_vpRunnables[1]->Attach(m_vpGnuPlotters[3]);
00073 
00074 
00075 /*
00076 //      m_vpGnuPlotters[0]->AddChemicalNumberToList(0);
00077 //      m_vpGnuPlotters[0]->AddChemicalNumberToList(1);
00078         m_vpGnuPlotters[0]->AddChemicalNumberToList(2);
00079         m_vpGnuPlotters[0]->AddChemicalNumberToList(3);
00080         m_vpGnuPlotters[0]->AddChemicalNumberToList(4);
00081 //      m_vpGnuPlotters[0]->AddChemicalNumberToList(5);
00082         m_vpGnuPlotters[0]->AddChemicalNumberToList(6);
00083         m_vpGnuPlotters[0]->AddChemicalNumberToList(7);
00084         // attach the observer
00085         m_vpRunnables[0]->Attach(m_vpGnuPlotters[0]);
00086 
00087         // create an observer for the runnable
00088         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00089         m_vpGnuPlotters[1]->AddChemicalNumberToList(8);
00090         m_vpGnuPlotters[1]->AddChemicalNumberToList(9);
00091 //      m_vpGnuPlotters[1]->AddChemicalNumberToList(10);
00092         m_vpGnuPlotters[1]->AddChemicalNumberToList(11);
00093         m_vpGnuPlotters[1]->AddChemicalNumberToList(12);
00094         m_vpGnuPlotters[1]->AddChemicalNumberToList(13);
00095         m_vpGnuPlotters[1]->AddChemicalNumberToList(14);
00096         m_vpGnuPlotters[1]->AddChemicalNumberToList(15);
00097         // attach the observer
00098         m_vpRunnables[0]->Attach(m_vpGnuPlotters[1]);
00099 
00100         // create an observer for the runnable
00101         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00102         m_vpGnuPlotters[2]->AddChemicalNumberToList(16);
00103 //      m_vpGnuPlotters[2]->AddChemicalNumberToList(17);
00104         m_vpGnuPlotters[2]->AddChemicalNumberToList(18);
00105         m_vpGnuPlotters[2]->AddChemicalNumberToList(19);
00106         m_vpGnuPlotters[2]->AddChemicalNumberToList(20);
00107         m_vpGnuPlotters[2]->AddChemicalNumberToList(21);
00108         m_vpGnuPlotters[2]->AddChemicalNumberToList(22);
00109 //      m_vpGnuPlotters[2]->AddChemicalNumberToList(23);
00110         // attach the observer
00111         m_vpRunnables[0]->Attach(m_vpGnuPlotters[2]);
00112 
00113         // create an observer for the runnable
00114         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00115         m_vpGnuPlotters[3]->AddChemicalNumberToList(24);
00116         m_vpGnuPlotters[3]->AddChemicalNumberToList(25);
00117         m_vpGnuPlotters[3]->AddChemicalNumberToList(26);
00118         m_vpGnuPlotters[3]->AddChemicalNumberToList(27);
00119         m_vpGnuPlotters[3]->AddChemicalNumberToList(28);
00120         m_vpGnuPlotters[3]->AddChemicalNumberToList(29);
00121 //      m_vpGnuPlotters[3]->AddChemicalNumberToList(30);
00122         m_vpGnuPlotters[3]->AddChemicalNumberToList(31);
00123         // attach the observer
00124         m_vpRunnables[0]->Attach(m_vpGnuPlotters[3]);
00125 
00126         // create an observer for the runnable
00127         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00128         m_vpGnuPlotters[4]->AddChemicalNumberToList(32);
00129         m_vpGnuPlotters[4]->AddChemicalNumberToList(33);
00130         m_vpGnuPlotters[4]->AddChemicalNumberToList(34);
00131         m_vpGnuPlotters[4]->AddChemicalNumberToList(35);
00132         m_vpGnuPlotters[4]->AddChemicalNumberToList(36);
00133         m_vpGnuPlotters[4]->AddChemicalNumberToList(37);
00134         m_vpGnuPlotters[4]->AddChemicalNumberToList(38);
00135         // attach the observer
00136         m_vpRunnables[0]->Attach(m_vpGnuPlotters[4]);
00137 */
00138         // define runs
00139         DefineRuns();
00140 
00141 }
00142 
00143 CQuorumSensingRunDirector::~CQuorumSensingRunDirector()
00144 {
00145 
00146 }
00147 
00148 void CQuorumSensingRunDirector::DefineRuns()
00149 {
00150         // set parameters in the runnables to those read from a previous
00151         // optimization pass; assumes all runnables have same number of 
00152         // rate constants
00153         ParameterReader *pReader = new ParameterReader("goodtemp6.par");
00154 //      ParameterReader *pReader = new ParameterReader("optimized.par");
00155         int nRC = m_vpRunnables[0]->GetReactionNetwork()->GetNumberOfRateConstants();
00156         for(int j = 0; j < nRC; j++)
00157         {
00158                 double rate = pReader->ReadParameter();
00159                 for(int i = 0; i < m_vpRunnables.size(); i++)
00160                 {
00161                         m_vpRunnables[i]->GetReactionNetwork()->GetRateConstant(j)->SetRateConstant(rate);
00162                 }
00163         }
00164         delete pReader;
00165 
00166 
00167         // specific to this simulation
00168 
00169 // no octopine no OOHL
00170         m_vpRunnables[0]->GetReactionNetwork()->ChemicalReset();
00171         m_vpGnuPlotters[0]->SetTitle("TraA original OOHL");
00172         m_vpGnuPlotters[1]->SetTitle("TraR forms no octopine no OOHL");
00173 
00174 //octopine and OOHL
00175 //      m_vpRunnables[1]->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1600);
00176         m_vpRunnables[1]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
00177         m_vpRunnables[1]->GetReactionNetwork()->ChemicalReset();
00178         m_vpGnuPlotters[2]->SetTitle("TraA new OOHL");
00179         m_vpGnuPlotters[3]->SetTitle("TraR forms octopine and OOHL");
00180 
00181 /*      m_vpGnuPlotters[1]->SetTitle("no octopine no OOHL 1");
00182         m_vpGnuPlotters[2]->SetTitle("no octopine no OOHL 2");
00183         m_vpGnuPlotters[3]->SetTitle("no octopine no OOHL 3");
00184         m_vpGnuPlotters[4]->SetTitle("no octopine no OOHL 4");
00185 */
00186 }