Commit 29002f00 authored by Carsten Kemena's avatar Carsten Kemena

removed unused header and added comments

parent b1944f4a
......@@ -54,25 +54,52 @@ struct RadsHit
class DBAccess
{
private:
SQLiteDB index_;
AlgorithmPack::Input arrangementDB_;
BSDL::DSM similarityMatrix_;
SQLiteDB index_; // The object used to connect to the sqlite database.
AlgorithmPack::Input arrangementDB_; // The file object containing the domain arrangements
BSDL::DSM similarityMatrix_; // The similarity matrix to be used.
public:
/**
* @brief Construct a new DBAccess object
*
*/
DBAccess()
{}
/**
* @brief Construct a new DBAccess object
*
* @param prefix The prefix of the database path.
* @param matrix The filename of the DSM to be used.
*/
DBAccess(const fs::path &prefix, const fs::path&matrix);
/**
* @brief Opens the database
*
* @param prefix The prefix of the database to open.
*/
void
open(const fs::path &prefix);
/**
* @brief Set the Matrix object to be used for the alignment.
*
* @param matrix The filename of the DSM to be used.
*/
void
setMatrix(const fs::path &matrix);
/**
* @brief Searches in the database for matching sequences.
*
* @param query The query domain arrangement.
* @param matrix The alignment matrix.
* @param all true if all domain types have to occur in the target DA.
* @param scoreThres The minimal score for a target to be reported.
* @param results The results sorted by score
*/
void
search(const BSDL::DomainArrangement<BSDL::Domain> &query, BSDL::AlignmentMatrix<int, BSDL::DSM> &matrix, bool all, int scoreThres,
std::multimap<int, RadsHit, std::greater<int> > &results);
};
......@@ -83,7 +83,7 @@ main(int argc, char *argv[])
// bool filter;
po::options_description filterOpts("Filter options");
filterOpts.add_options()
("databases,d", po::value<string>(&database)->multitoken(), "The database to use")
("databases,d", po::value<string>(&database), "The database to use")
// ("filter,f", po::value<bool>(&filter)->default_value(false)->zero_tokens(), "Remove overlapping domains")
// ("threshold,t", po::value<unsigned int>(&threshold)->default_value(10), "Maximal number of allowed overlap")
;
......
......@@ -22,16 +22,11 @@
// C++
#include <algorithm>
#include <cstdio>
#include <cstdlib>
#include <map>
#include <set>
#include <string>
#include <vector>
#include <fstream>
#include <iostream>
#include <thread>
#include <mutex>
#include <ctime>
#include <chrono>
......@@ -52,7 +47,6 @@
// other
#include "DBAccess.hpp"
#include "Version.hpp"
#include "external/SQLiteDB.hpp"
using namespace std;
using std::chrono::system_clock;
......
......@@ -34,6 +34,7 @@
run ../../build/rads -h
[ $status == 0 ]
rm test1Res.txt testQuerySeq.txt
rm interPro.db interPro.da
}
......@@ -55,5 +56,6 @@
run diff <(grep -v '#' test3Res.txt) <(grep -v '#' results/test3Res.txt)
[ $status == 0 ]
#rm interPro-test.db interPro-test.da
rm interPro-test.db interPro-test.da
rm test3Res.txt test2Res.txt
}
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