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92 lines
3.5 KiB
C++
92 lines
3.5 KiB
C++
// $Id: distanceBasedSeqs2TreeFactory.cpp 1941 2007-04-15 14:17:22Z privmane $
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#include "distanceBasedSeqs2TreeFactory.h"
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#include "ssrvDistanceSeqs2Tree.h"
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distanceBasedSeqs2Tree* distanceBasedSeqs2TreeFactory(const distanceBasedMethod_t distanceBasedMethod,
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stochasticProcess& sp, // may change sp (alpha and/or nu)
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const bool useJcDistance,
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const bool optimizeAlpha,
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const bool useSSRV,
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const double epsilonLikelihoodImprovement4iterNJ,
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const double epsilonLikelihoodImprovement4pairwiseDistance,
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const double epsilonLikelihoodImprovement4alphaOptimiz,
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const double epsilonLikelihoodImprovement4BBL,
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const int maxIterationsBBL)
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{
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// 1. Construct the object of the requested distance-based tree-reconstruction method (class distances2Tree)
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NJalg NJa;
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distances2Tree* d2tPtr = &NJa; // for future polymorphism
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// 2. Construct the object of the requested distance estimation method (class distanceMethod) distanceMethod *dmPtr = NULL;
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// And construct the object of the distance-based sequences-to-tree method (class distanceBasedSeqs2Tree)
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// distanceMethod *dmPtr = NULL;
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distanceBasedSeqs2Tree *s2tPtr = NULL;
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switch (distanceBasedMethod) {
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case homogeneousRatesDTME:
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if (useJcDistance) {
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jcDistance jcd;
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s2tPtr = new distanceBasedSeqs2Tree(jcd, *d2tPtr);
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} else {
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likeDist ld(sp,epsilonLikelihoodImprovement4pairwiseDistance);
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s2tPtr = new distanceBasedSeqs2Tree(ld, *d2tPtr);
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}
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break;
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case pairwiseGammaDTME:
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if (optimizeAlpha) {
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pairwiseGammaDistance pgd(sp,epsilonLikelihoodImprovement4pairwiseDistance); // distance method that optimizes alpha for the pair of sequences
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s2tPtr = new distanceBasedSeqs2Tree(pgd, *d2tPtr);
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} else {
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likeDist ld1(sp,epsilonLikelihoodImprovement4pairwiseDistance); // distance method that uses the given alpha with no optimization
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s2tPtr = new distanceBasedSeqs2Tree(ld1, *d2tPtr);
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}
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break;
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case commonAlphaDTME: {
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if (!useSSRV) {
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likeDist ld2(sp,epsilonLikelihoodImprovement4pairwiseDistance);
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s2tPtr = new commonAlphaDistanceSeqs2Tree(ld2, *d2tPtr, NULL,
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epsilonLikelihoodImprovement4iterNJ,
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epsilonLikelihoodImprovement4alphaOptimiz,
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epsilonLikelihoodImprovement4BBL,
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maxIterationsBBL);
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} else {
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likeDist ld3(sp,epsilonLikelihoodImprovement4pairwiseDistance);
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s2tPtr = new ssrvDistanceSeqs2Tree(ld3, *d2tPtr, NULL,
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epsilonLikelihoodImprovement4iterNJ,
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epsilonLikelihoodImprovement4alphaOptimiz,
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epsilonLikelihoodImprovement4BBL,
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maxIterationsBBL);
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}
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}
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break;
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case rate4siteDTME: {
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givenRatesMLDistance grd(sp,epsilonLikelihoodImprovement4pairwiseDistance);
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s2tPtr = new rate4siteDistanceSeqs2Tree(grd, *d2tPtr, NULL,
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epsilonLikelihoodImprovement4iterNJ,
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epsilonLikelihoodImprovement4alphaOptimiz,
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epsilonLikelihoodImprovement4BBL,
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maxIterationsBBL); }
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break;
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case posteriorDTME: {
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posteriorDistance posd(sp,epsilonLikelihoodImprovement4pairwiseDistance);
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s2tPtr = new posteriorDistanceSeqs2Tree(posd, *d2tPtr, NULL,
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epsilonLikelihoodImprovement4iterNJ,
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epsilonLikelihoodImprovement4alphaOptimiz,
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epsilonLikelihoodImprovement4BBL,
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maxIterationsBBL);}
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break;
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default: errorMsg::reportError("bad distanceBasedMethod - method not in the list of implimented methods");
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}
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return s2tPtr;
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}
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