bpp-phyl
2.2.0
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Listener used internally by the optimizeTreeNNI method. More...
#include <Bpp/Phyl/OptimizationTools.h>
Public Member Functions | |
NNITopologyListener (NNITopologySearch *ts, const ParameterList ¶meters, double tolerance, OutputStream *messenger, OutputStream *profiler, unsigned int verbose, const std::string &optMethod, unsigned int nStep, bool reparametrization) | |
Build a new NNITopologyListener object. More... | |
NNITopologyListener (const NNITopologyListener &tl) | |
NNITopologyListener & | operator= (const NNITopologyListener &tl) |
NNITopologyListener * | clone () const |
virtual | ~NNITopologyListener () |
void | topologyChangeTested (const TopologyChangeEvent &event) |
Notify a topology change event. More... | |
void | topologyChangeSuccessful (const TopologyChangeEvent &event) |
Tell that a topology change is definitive. More... | |
void | setNumericalOptimizationCounter (unsigned int c) |
virtual void | topologyChangePerformed (const TopologyChangeEvent &event) |
Notify a topology change event. More... | |
Private Attributes | |
NNITopologySearch * | topoSearch_ |
ParameterList | parameters_ |
double | tolerance_ |
OutputStream * | messenger_ |
OutputStream * | profiler_ |
unsigned int | verbose_ |
unsigned int | optimizeCounter_ |
unsigned int | optimizeNumerical_ |
std::string | optMethod_ |
unsigned int | nStep_ |
bool | reparametrization_ |
Listener used internally by the optimizeTreeNNI method.
Definition at line 102 of file OptimizationTools.h.
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inline |
Build a new NNITopologyListener object.
This listener listens to a NNITopologySearch object, and optimizes numerical parameters every n topological movements. Optimization is performed using the optimizeNumericalParameters method (see there documentation for more details).
ts | The NNITopologySearch object attached to this listener. |
parameters | The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters. |
tolerance | Tolerance to use during optimizaton. |
messenger | Where to output messages. |
profiler | Where to output optimization steps. |
verbose | Verbose level during optimization. |
optMethod | Optimization method to use. |
nStep | The number of optimization steps to perform. |
reparametrization | Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower. |
Definition at line 136 of file OptimizationTools.h.
Referenced by clone().
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inline |
Definition at line 158 of file OptimizationTools.h.
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inlinevirtual |
Definition at line 190 of file OptimizationTools.h.
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inlinevirtual |
Implements bpp::TopologyListener.
Definition at line 188 of file OptimizationTools.h.
References NNITopologyListener().
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inline |
Definition at line 172 of file OptimizationTools.h.
References messenger_, nStep_, optimizeCounter_, optimizeNumerical_, optMethod_, parameters_, profiler_, reparametrization_, tolerance_, topoSearch_, and verbose_.
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inline |
Definition at line 195 of file OptimizationTools.h.
References optimizeNumerical_.
Referenced by bpp::OptimizationTools::optimizeTreeNNI().
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inlinevirtualinherited |
Notify a topology change event.
This method is to be invoked after one or several NNI are performed. It allows appropriate recomputations.
In most case, this is the same as topologyChangeTested() + topologyChangeSuccessful().
event | The topology change event. |
Definition at line 105 of file TopologySearch.h.
References bpp::TopologyListener::topologyChangeSuccessful(), and bpp::TopologyListener::topologyChangeTested().
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virtual |
Tell that a topology change is definitive.
This method is called after the topologyChangeTested() method.
event | The topology change event. |
Implements bpp::TopologyListener.
Definition at line 536 of file OptimizationTools.cpp.
References bpp::OptimizationTools::optimizeNumericalParameters().
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inlinevirtual |
Notify a topology change event.
event | The topology change event. |
Implements bpp::TopologyListener.
Definition at line 193 of file OptimizationTools.h.
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private |
Definition at line 109 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 115 of file OptimizationTools.h.
Referenced by operator=().
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Definition at line 112 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 113 of file OptimizationTools.h.
Referenced by operator=(), and setNumericalOptimizationCounter().
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private |
Definition at line 114 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 107 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 110 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 116 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 108 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 106 of file OptimizationTools.h.
Referenced by operator=().
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private |
Definition at line 111 of file OptimizationTools.h.
Referenced by operator=().