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68 lines
1.9 KiB
C++
68 lines
1.9 KiB
C++
// $Id: computeUpAlg.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___COMPUTE_UP_ALG
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#define ___COMPUTE_UP_ALG
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#include "definitions.h"
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#include "tree.h"
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#include "suffStatComponent.h"
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#include "sequenceContainer.h"
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#include "computePijComponent.h"
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class computeUpAlg {
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public:
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void fillComputeUp(const tree& et,
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const sequenceContainer& sc,
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const int pos,
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const computePijHom& pi,
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suffStatGlobalHomPos& ssc);
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void fillComputeUp(const tree& et,
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const sequenceContainer & sc,
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const computePijGam& pi,
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suffStatGlobalGam& ssc);
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/*void fillComputeUp(const tree& et, // not to be used at all. problematic in case of a gamma function.
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const sequenceContainer& sc,
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const int pos,
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const stochasticProcess& sp,
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suffStatGlobalHomPos& ssc);*/
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/*void fillComputeUp(const tree& et, // not to be used, accept for debuging (very slow func.)
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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suffStatGlobalGam& ssc);*/
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void fillComputeUpSpecificGlobalRate(const tree& et,
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const sequenceContainer& sc,
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const int pos,
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const stochasticProcess& sp,
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suffStatGlobalHomPos& ssc,
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const MDOUBLE gRate);
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// my attemp to add factors
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void fillComputeUpWithFactors(const tree& et,
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const sequenceContainer& sc,
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const int pos,
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const computePijHom& pi,
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suffStatGlobalHomPos& ssc,
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vector<MDOUBLE>& factors);
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void fillComputeUpWithFactors(const tree& et,
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const sequenceContainer& sc,
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const int pos,
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const stochasticProcess& sp,
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suffStatGlobalHomPos& ssc,
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vector<MDOUBLE>& factors);
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void fillComputeUpSpecificGlobalRateFactors(const tree& et,
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const sequenceContainer& sc,
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const int pos,
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const stochasticProcess& sp,
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suffStatGlobalHomPos& ssc,
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const MDOUBLE gRate,
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vector<MDOUBLE>& factors);
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};
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#endif
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