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111 lines
3.0 KiB
C++
111 lines
3.0 KiB
C++
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// $Id: computePijComponent.cpp 9253 2011-01-31 01:37:21Z rubi $
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#include "definitions.h"
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#include "treeIt.h"
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#include "computePijComponent.h"
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#include "logFile.h"
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void computePijHomSpec::fillPij(const MDOUBLE dis, const stochasticProcess& sp, int derivationOrder, bool isReversible)
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{
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if (!(isReversible && sp.isReversible())) // if one is false
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isReversible = false;
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resize(sp.alphabetSize());
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int i,j;
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for (i=0; i<sp.alphabetSize(); i++) {
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switch (derivationOrder) {
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case 0:
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_V[i][i] = sp.Pij_t(i,i,dis);
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break;
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case 1:
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_V[i][i] = sp.dPij_dt(i,i,dis);
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break;
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case 2:
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_V[i][i] = sp.d2Pij_dt2(i,i,dis);
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break;
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default:
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errorMsg::reportError("error in function fillPij - derivationOrder must be 0, 1 or 2");
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}
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for (j=i+1; j<sp.alphabetSize(); j++) {
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switch (derivationOrder) {
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case 0:
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_V[i][j] = sp.Pij_t(i,j,dis);
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if ((_V[i][j] == 0 )&& (dis !=0)){
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_V[i][j] = EPSILON;
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}
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break;
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case 1:
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_V[i][j] = sp.dPij_dt(i,j,dis);
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break;
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case 2:
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_V[i][j] = sp.d2Pij_dt2(i,j,dis);
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break;
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default:
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errorMsg::reportError("error in function fillPij - derivationOrder must be 0, 1 or 2");
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}
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if (sp.freq(j) == 0.0) {
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if (isReversible) {
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errorMsg::reportError("error in function fillPij");
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}
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}
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// else {
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if (isReversible){
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_V[j][i] = _V[i][j]* sp.freq(i)/sp.freq(j);
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}
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else {
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switch (derivationOrder) {
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case 0:
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_V[j][i] = sp.Pij_t(j,i,dis);
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if ((_V[j][i] == 0 )&& (dis !=0))
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_V[j][i] = EPSILON;
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break;
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case 1:
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_V[j][i] = sp.dPij_dt(j,i,dis);
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break;
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case 2:
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_V[j][i] = sp.d2Pij_dt2(j,i,dis);
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break;
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default:
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errorMsg::reportError("error in function fillPij - derivationOrder must be 0, 1 or 2");
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}
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}
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// }
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}
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}
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}
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void computePijHom::fillPij(const tree& et, const stochasticProcess& sp, int derivationOrder, bool isReversible) {
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_V.resize(et.getNodesNum());
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treeIterTopDownConst tIt(et);
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tree::nodeP myNode = tIt.first();
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{// skipping the root, but allocating place for the root pij even if they are not use
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// to maintain that all arrays have the same size.
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_V[myNode->id()].resize(sp.alphabetSize());
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}
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LOGDO(50,et.output(myLog::LogFile(),tree::ANCESTOR));
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LOGDO(50,et.output(myLog::LogFile(),tree::PHYLIP));
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for (; myNode != tIt.end(); myNode = tIt.next()) {
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if (!(myNode->isRoot()))
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_V[myNode->id()].fillPij(myNode->dis2father()*sp.getGlobalRate(),sp,derivationOrder,isReversible);
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// else
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// myLog::LogFile()<<"ROOT IS "<<myNode->name()<<endl;
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}
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}
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void computePijGam::fillPij(const tree& et, const stochasticProcess& sp, int derivationOrder, bool isReversible) {
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_V.resize(sp.categories());
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for (int i=0; i < _V.size(); ++i) {
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tree cp = et;
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cp.multipleAllBranchesByFactor(sp.rates(i)/sp.getGlobalRate());// the global rate is taken care of in the hom pij.
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_V[i].fillPij(cp,sp,derivationOrder,isReversible);
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}
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}
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