//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage is free software: you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation, either version 3 of the License, or
//(at your option) any later version.
//Bandage is distributed in the hope that it will be useful,
//but WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//GNU General Public License for more details.
//You should have received a copy of the GNU General Public License
//along with Bandage. If not, see .
#ifndef BLASTQUERIES_H
#define BLASTQUERIES_H
#include
#include "blastquery.h"
#include
#include "../program/globals.h"
#include
//This class manages all BLAST queries. It holds BlastQuery
//objects itself, and it creates/modifies/deletes the temp
//files which hold the queries for use in BLAST.
//There are two separate temp files, one for nucleotide
//queries (for blastn) and one for protein queries (for
//tblasn).
class BlastQueries
{
public:
BlastQueries();
~BlastQueries();
std::vector m_queries;
BlastQuery * getQueryFromName(QString queryName);
void createTempQueryFiles();
void addQuery(BlastQuery * newQuery);
QString renameQuery(BlastQuery * newQuery, QString newName);
void clearAllQueries();
void clearSomeQueries(std::vector queriesToRemove);
void searchOccurred();
void clearSearchResults();
int getQueryCount();
int getQueryCountWithAtLeastOnePath();
int getQueryPathCount();
int getQueryCount(SequenceType sequenceType);
bool isQueryPresent(BlastQuery * query);
void findQueryPaths();
std::vector m_presetColours;
private:
QSharedPointer m_tempNuclFile;
QSharedPointer m_tempProtFile;
void deleteTempFiles();
void updateTempFiles();
bool tempNuclFileExists();
bool tempProtFileExists();
void writeTempFile(QSharedPointer file, SequenceType sequenceType);
QString getUniqueName(QString name);
};
#endif // BLASTQUERIES_H