compare-all.h 770 Bytes
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#include <list>
#include <string>
#include <iostream>
#include <iomanip>

#include "dynprog.h"
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#include "bioreader.hpp"
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#include "similarityMatrix.h"
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#include "windows.h"
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SimilarityMatrix compare_all(list <Sequence> sequences,
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                             list <string> sequence_names=list<string>());

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/*Object to compare windows to build a distances matrix between windows
@param windowsStorage: The object which contains windows
@param theCost: The cost to add for the dynamic programming
@param nb_clones: The number of clones to take on board to build the matrix*/
SimilarityMatrix compare_windows(WindowsStorage &windowsStorage, const Cost theCost, int nb_clones);
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// bool compare_all(list <Sequence> sequences, bool min_size=false, std::ostream out=std::cout);