CombinatorialNetworksSloppyMinimizableDirector.cpp Source File

00001 #include "CombinatorialNetworksSloppyMinimizableDirector.h"
00002 
00003 CCombinatorialNetworksSloppyMinimizableDirector::CCombinatorialNetworksSloppyMinimizableDirector(void)
00004 {
00005         double maxSimTime = 720.0;
00006         int intTime = (int) maxSimTime + 2;
00007         double stepSize = 0.001;
00008         double frequency = 0.1;
00009         double moveTol = 1.0e-06;
00010         int cnt = 0;
00011         int nChemicals;
00012 
00013         m_dGammaSquared = 1.0e-07;
00014 
00015         // D016, IPTG-, aTc-
00016         m_vpRxnNetworks.push_back(new CCombinatorialNetwork());
00017         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00018         nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals();
00019         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00020         m_vpRunnables.push_back(new CRunnable());
00021         m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]);
00022         m_vpRunnables[cnt]->SetRunnableName("D016_IPTGm_aTcm");
00023         // create an observer for the runnable
00024         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00025         m_vpGnuPlotters[cnt]->AddChemicalNumberToList(0);
00026         m_vpGnuPlotters[cnt]->SetTitle("D016 IPTG -, aTc -");
00027         m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]);
00028         cnt++;
00029 
00030         // D016, IPTG+, aTc-
00031         m_vpRxnNetworks.push_back(new CCombinatorialNetwork());
00032         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00033         nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals();
00034         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00035         m_vpRunnables.push_back(new CRunnable());
00036         m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]);
00037         m_vpRunnables[cnt]->SetRunnableName("D016_IPTGp_aTcm");
00038         // create an observer for the runnable
00039         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00040         m_vpGnuPlotters[cnt]->AddChemicalNumberToList(0);
00041         m_vpGnuPlotters[cnt]->SetTitle("D016 IPTG +, aTc -");
00042         m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]);
00043         cnt++;
00044 
00045         // D016, IPTG-, aTc+
00046         m_vpRxnNetworks.push_back(new CCombinatorialNetwork());
00047         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00048         nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals();
00049         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00050         m_vpRunnables.push_back(new CRunnable());
00051         m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]);
00052         m_vpRunnables[cnt]->SetRunnableName("D016_IPTGm_aTcp");
00053         // create an observer for the runnable
00054         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00055         m_vpGnuPlotters[cnt]->AddChemicalNumberToList(0);
00056         m_vpGnuPlotters[cnt]->SetTitle("D016 IPTG -, aTc +");
00057         m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]);
00058         cnt++;
00059 
00060         // D016, IPTG+, aTc+
00061         m_vpRxnNetworks.push_back(new CCombinatorialNetwork());
00062         m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00063         nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals();
00064         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00065         m_vpRunnables.push_back(new CRunnable());
00066         m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]);
00067         m_vpRunnables[cnt]->SetRunnableName("D016_IPTGp_aTcp");
00068         // create an observer for the runnable
00069         m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
00070         m_vpGnuPlotters[cnt]->AddChemicalNumberToList(0);
00071         m_vpGnuPlotters[cnt]->SetTitle("D016 IPTG -, aTc +");
00072         m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]);
00073         cnt++;
00074 
00075         // parse data files
00076         this->ParseDataFile("combinatorial.dat");
00077 
00078         // XXX debug
00079         /*
00080         for(int i = 0; i < m_vpRelationList.size(); i++)
00081         {
00082                 cout << m_vpRelationList[i]->GetR1() << "\t" << m_vpRelationList[i]->GetQ1() << "\t" << m_vpRelationList[i]->Gett1() << "\t";
00083                 cout << m_vpRelationList[i]->GetR2() << "\t" << m_vpRelationList[i]->GetQ2() << "\t" << m_vpRelationList[i]->Gett2() << "\t";
00084                 cout << m_vpRelationList[i]->GetType() << endl;
00085         }
00086         */
00087         // define runs
00088         DefineRuns();
00089 }
00090 
00091 CCombinatorialNetworksSloppyMinimizableDirector::~CCombinatorialNetworksSloppyMinimizableDirector(void)
00092 {
00093 }
00094 
00095 int CCombinatorialNetworksSloppyMinimizableDirector::GetNParameters()
00096 {
00097         // all the combinatorial networks share a master set of rate constants
00098         return m_vpRunnables[0]->GetReactionNetwork()->GetNumberOfRateConstants();
00099 }
00100 
00101 void CCombinatorialNetworksSloppyMinimizableDirector::DefineRuns()
00102 {
00103         int i;
00104         // Strain D016
00105         for(i = 0; i < 4; i++)
00106         {
00107                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(44);
00108                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(43);
00109                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(42);
00110                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(41);
00111                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(40);
00112                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(39);
00113                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(38);
00114                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(37);
00115                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(36);
00116                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(35);
00117                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(34);
00118                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(33);
00119                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(30);
00120                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(29);
00121                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(28);
00122                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(27);
00123                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(26);
00124                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(25);
00125                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(22);
00126                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(21);
00127                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(20);
00128                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(19);
00129                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(18);
00130                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(17);
00131                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(16);
00132                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(14);
00133                 m_vpRunnables[i]->GetReactionNetwork()->RemoveReaction(12);
00134         }
00135 
00136         m_vpRunnables[0]->GetReactionNetwork()->ChemicalReset();
00137         m_vpRunnables[1]->GetReactionNetwork()->ChemicalReset();
00138 }