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27 lines
1.1 KiB
C++
27 lines
1.1 KiB
C++
// $Id: evaluateCharacterFreq.h 3895 2008-04-21 07:38:32Z itaymay $
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#ifndef __Evaluate_Character_Freq_h
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#define __Evaluate_Character_Freq_h
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#include <iostream>
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using namespace std;
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#include "sequenceContainer.h"
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#include "definitions.h"
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vector<MDOUBLE> sumAlphabetCounts(const sequenceContainer & sc);
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vector<MDOUBLE> evaluateCharacterFreq(const sequenceContainer & sc);
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VVdouble evaluateCharacterFreqOneForEachGene(const vector<sequenceContainer> & scVec);
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vector<MDOUBLE> evaluateCharacterFreqBasedOnManyGenes(const vector<sequenceContainer> & scVec);
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void changeCountsToFreqs(vector<MDOUBLE>& charFreq);
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void makeSureNoZeroFreqs(vector<MDOUBLE> & charFreq);
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//returns the number of each character in each position
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void getCharacterCounts(const sequenceContainer & sc, VVint& counts4pos);
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//returns the number of different character types in each position
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void getCharacterType4pos(const sequenceContainer & sc, Vint& charactersType4pos);
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//returns the distribution of the different character types in each position along the whole alignment
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void getCharacterTypeDistribution(const sequenceContainer & sc, Vint& charactersTypeDist);
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#endif
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